Multiple sequence alignment - TraesCS7B01G105200

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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 TraesCS7B01G105200 chr7B 100.000 1880 0 0 1 1880 121319794 121321673 0.000000e+00 3472.0
1 TraesCS7B01G105200 chr7B 98.025 1873 29 7 1 1868 121241551 121243420 0.000000e+00 3247.0
2 TraesCS7B01G105200 chr7B 88.299 1752 125 38 132 1841 121052646 121054359 0.000000e+00 2026.0
3 TraesCS7B01G105200 chr7B 95.285 1018 29 7 875 1880 121166748 121167758 0.000000e+00 1596.0
4 TraesCS7B01G105200 chr7B 95.187 1018 29 8 875 1880 121115422 121116431 0.000000e+00 1591.0
5 TraesCS7B01G105200 chr7B 87.770 1112 97 22 593 1681 121495624 121496719 0.000000e+00 1264.0
6 TraesCS7B01G105200 chr7B 98.227 677 11 1 1 677 121385448 121386123 0.000000e+00 1182.0
7 TraesCS7B01G105200 chr7B 96.190 630 12 3 1229 1848 121386488 121387115 0.000000e+00 1020.0
8 TraesCS7B01G105200 chr7B 100.000 404 0 0 2122 2525 121321915 121322318 0.000000e+00 747.0
9 TraesCS7B01G105200 chr7B 96.782 404 13 0 2122 2525 121243757 121244160 0.000000e+00 675.0
10 TraesCS7B01G105200 chr7B 96.491 399 12 1 2127 2525 121387490 121387886 0.000000e+00 658.0
11 TraesCS7B01G105200 chr7B 92.211 398 17 2 2127 2524 121116472 121116855 3.670000e-153 551.0
12 TraesCS7B01G105200 chr7B 92.211 398 17 2 2127 2524 121167799 121168182 3.670000e-153 551.0
13 TraesCS7B01G105200 chr7B 89.630 405 34 4 2122 2525 121054669 121055066 2.240000e-140 508.0
14 TraesCS7B01G105200 chr7B 80.153 655 91 18 132 770 121113269 121113900 1.060000e-123 453.0
15 TraesCS7B01G105200 chr7B 79.847 655 93 18 132 770 121164625 121165256 2.310000e-120 442.0
16 TraesCS7B01G105200 chr7B 97.156 211 3 3 676 886 121386282 121386489 1.110000e-93 353.0
17 TraesCS7B01G105200 chr7B 76.487 353 66 7 76 428 121494309 121494644 2.580000e-40 176.0
18 TraesCS7B01G105200 chr7A 88.791 1365 75 32 338 1661 161279223 161280550 0.000000e+00 1602.0
19 TraesCS7B01G105200 chr7A 87.251 1153 94 33 563 1681 161650186 161651319 0.000000e+00 1266.0
20 TraesCS7B01G105200 chr7A 77.515 338 60 3 76 413 161648351 161648672 3.320000e-44 189.0
21 TraesCS7B01G105200 chr7D 86.109 1555 128 34 176 1680 160486868 160488384 0.000000e+00 1594.0
22 TraesCS7B01G105200 chr7D 88.029 1111 93 24 593 1679 160533745 160534839 0.000000e+00 1279.0
23 TraesCS7B01G105200 chr7D 89.826 403 36 5 2127 2525 160488644 160489045 1.730000e-141 512.0
24 TraesCS7B01G105200 chr7D 76.504 349 64 5 81 428 160532978 160533309 9.280000e-40 174.0
25 TraesCS7B01G105200 chr7D 89.344 122 4 2 1700 1812 160488371 160488492 7.280000e-31 145.0
26 TraesCS7B01G105200 chr7D 97.297 37 1 0 1812 1848 160488522 160488558 2.100000e-06 63.9


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 TraesCS7B01G105200 chr7B 121319794 121322318 2524 False 2109.500 3472 100.000000 1 2525 2 chr7B.!!$F5 2524
1 TraesCS7B01G105200 chr7B 121241551 121244160 2609 False 1961.000 3247 97.403500 1 2525 2 chr7B.!!$F4 2524
2 TraesCS7B01G105200 chr7B 121052646 121055066 2420 False 1267.000 2026 88.964500 132 2525 2 chr7B.!!$F1 2393
3 TraesCS7B01G105200 chr7B 121113269 121116855 3586 False 865.000 1591 89.183667 132 2524 3 chr7B.!!$F2 2392
4 TraesCS7B01G105200 chr7B 121164625 121168182 3557 False 863.000 1596 89.114333 132 2524 3 chr7B.!!$F3 2392
5 TraesCS7B01G105200 chr7B 121385448 121387886 2438 False 803.250 1182 97.016000 1 2525 4 chr7B.!!$F6 2524
6 TraesCS7B01G105200 chr7B 121494309 121496719 2410 False 720.000 1264 82.128500 76 1681 2 chr7B.!!$F7 1605
7 TraesCS7B01G105200 chr7A 161279223 161280550 1327 False 1602.000 1602 88.791000 338 1661 1 chr7A.!!$F1 1323
8 TraesCS7B01G105200 chr7A 161648351 161651319 2968 False 727.500 1266 82.383000 76 1681 2 chr7A.!!$F2 1605
9 TraesCS7B01G105200 chr7D 160532978 160534839 1861 False 726.500 1279 82.266500 81 1679 2 chr7D.!!$F2 1598
10 TraesCS7B01G105200 chr7D 160486868 160489045 2177 False 578.725 1594 90.644000 176 2525 4 chr7D.!!$F1 2349

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
191 192 0.606401 CATCAGGGTTGCGTTGGTCT 60.606 55.000 0.0 0.0 0.00 3.85 F
569 2515 1.274167 CACCAACCAGTAGCGGTAAGA 59.726 52.381 0.0 0.0 38.76 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 4572 0.109597 GGCGAACATTGCAAGACTGG 60.110 55.0 4.94 0.0 0.00 4.00 R
2478 6194 3.157881 CTGAGTGAGAGGGAACACTACA 58.842 50.0 0.00 0.0 45.54 2.74 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
73 74 1.553706 ATCGTAACGGTCCTGGTCTT 58.446 50.000 0.00 0.0 0.00 3.01
191 192 0.606401 CATCAGGGTTGCGTTGGTCT 60.606 55.000 0.00 0.0 0.00 3.85
283 284 7.325097 GGTAGTGTATGTTTGAAAATTTCACCG 59.675 37.037 8.06 0.0 39.87 4.94
286 287 7.858879 AGTGTATGTTTGAAAATTTCACCGTAC 59.141 33.333 19.60 19.6 39.87 3.67
569 2515 1.274167 CACCAACCAGTAGCGGTAAGA 59.726 52.381 0.00 0.0 38.76 2.10
879 4419 6.540189 TCTTCTTGCTAGCATCCTTGAAATAC 59.460 38.462 20.13 0.0 0.00 1.89
883 4423 7.442364 TCTTGCTAGCATCCTTGAAATACATAC 59.558 37.037 20.13 0.0 0.00 2.39
1016 4572 4.023365 GCTAATCATGGCATCTTCCAAGAC 60.023 45.833 0.00 0.0 39.96 3.01
1681 5251 4.460034 TCTGTGGAGCGTGTAAGTGTAATA 59.540 41.667 0.00 0.0 0.00 0.98
2166 5876 6.767524 AGCGATATGGTTGGTTTTGATTTA 57.232 33.333 0.00 0.0 0.00 1.40
2409 6125 0.676782 GGCATGGGTTCTTACTGCGT 60.677 55.000 0.00 0.0 33.69 5.24
2478 6194 4.576463 GCGATTGGAATTCATCTAGGTTGT 59.424 41.667 7.93 0.0 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.370953 GCTCTTTTTGCCTCCTCCTCATA 60.371 47.826 0.00 0.00 0.00 2.15
191 192 2.038814 TTGGCAAGAGCTCCACGACA 62.039 55.000 10.93 4.39 41.70 4.35
283 284 4.622701 ATCTACCGTAACACTTCCGTAC 57.377 45.455 0.00 0.00 0.00 3.67
286 287 3.314635 AGCTATCTACCGTAACACTTCCG 59.685 47.826 0.00 0.00 0.00 4.30
431 1536 7.120579 TGCGACATTATGAGTCAATAAAAACCT 59.879 33.333 0.00 0.00 35.77 3.50
432 1537 7.247728 TGCGACATTATGAGTCAATAAAAACC 58.752 34.615 0.00 0.00 35.77 3.27
569 2515 1.803366 GCCGCTATAGCCTACCGTGT 61.803 60.000 19.00 0.00 37.91 4.49
879 4419 4.533919 TTTTTGAACTGCATGGGGTATG 57.466 40.909 0.00 0.00 39.88 2.39
985 4537 5.336945 AGATGCCATGATTAGCTAGTAGGA 58.663 41.667 0.00 0.00 0.00 2.94
1016 4572 0.109597 GGCGAACATTGCAAGACTGG 60.110 55.000 4.94 0.00 0.00 4.00
1242 4798 1.342672 GCCCGGAACCCCAGAAGATA 61.343 60.000 0.73 0.00 0.00 1.98
2121 5735 3.825143 AAATATAAGGGTACACGCGGT 57.175 42.857 12.47 8.38 0.00 5.68
2122 5736 4.151157 GCTTAAATATAAGGGTACACGCGG 59.849 45.833 12.47 1.27 39.17 6.46
2123 5737 4.143473 CGCTTAAATATAAGGGTACACGCG 60.143 45.833 3.53 3.53 43.46 6.01
2166 5876 7.876068 TGTCTTCGTTATACCTCTGACATTTTT 59.124 33.333 0.00 0.00 0.00 1.94
2171 5881 5.970317 TTGTCTTCGTTATACCTCTGACA 57.030 39.130 0.00 0.00 0.00 3.58
2270 5983 4.969816 ACTTGTGTCTTTCTGTTGTTTCG 58.030 39.130 0.00 0.00 0.00 3.46
2409 6125 9.751542 GCAATATAGTTTCTACTCTAGCAAAGA 57.248 33.333 0.00 0.00 35.78 2.52
2478 6194 3.157881 CTGAGTGAGAGGGAACACTACA 58.842 50.000 0.00 0.00 45.54 2.74


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

AutoCloner maintained by Alex Coulton.