Multiple sequence alignment - TraesCS4B01G274800

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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 TraesCS4B01G274800 chr4B 100.000 3405 0 0 807 4211 552796836 552800240 0 6288
1 TraesCS4B01G274800 chr4B 97.353 3400 90 0 809 4208 636565979 636569378 0 5781
2 TraesCS4B01G274800 chr4B 100.000 392 0 0 1 392 552796030 552796421 0 725
3 TraesCS4B01G274800 chrUn 96.920 3409 99 3 807 4211 87505498 87502092 0 5709
4 TraesCS4B01G274800 chrUn 96.944 3403 100 1 809 4207 87515322 87511920 0 5705
5 TraesCS4B01G274800 chrUn 97.194 392 11 0 1 392 87505887 87505496 0 664
6 TraesCS4B01G274800 chrUn 96.931 391 11 1 1 390 87515714 87515324 0 654
7 TraesCS4B01G274800 chr3B 97.152 1861 52 1 807 2666 745234 747094 0 3142
8 TraesCS4B01G274800 chr3B 96.774 1860 60 0 807 2666 817687151 817689010 0 3103
9 TraesCS4B01G274800 chr3B 98.441 1539 23 1 2670 4208 817712687 817714224 0 2708
10 TraesCS4B01G274800 chr3B 98.311 1539 25 1 2670 4208 817689532 817691069 0 2697
11 TraesCS4B01G274800 chr3B 97.471 1542 38 1 2670 4211 784349713 784348173 0 2630
12 TraesCS4B01G274800 chr3B 97.449 392 9 1 1 392 817686763 817687153 0 667
13 TraesCS4B01G274800 chr3B 97.172 389 11 0 1 389 784352092 784351704 0 658
14 TraesCS4B01G274800 chr7A 96.935 1860 57 0 807 2666 395514331 395516190 0 3120
15 TraesCS4B01G274800 chr7A 96.939 392 12 0 1 392 395513942 395514333 0 658
16 TraesCS4B01G274800 chr7B 96.828 1860 59 0 807 2666 695575371 695573512 0 3109
17 TraesCS4B01G274800 chr7B 97.471 1542 39 0 2670 4211 695572990 695571449 0 2632
18 TraesCS4B01G274800 chr7B 96.684 392 13 0 1 392 695575760 695575369 0 652
19 TraesCS4B01G274800 chr6A 96.830 1861 58 1 807 2666 307921841 307919981 0 3109
20 TraesCS4B01G274800 chr6A 96.939 392 12 0 1 392 307922230 307921839 0 658
21 TraesCS4B01G274800 chr5A 96.826 1859 59 0 807 2665 213047565 213049423 0 3107
22 TraesCS4B01G274800 chr5A 97.471 1542 39 0 2670 4211 631066806 631065265 0 2632
23 TraesCS4B01G274800 chr5A 97.194 392 11 0 1 392 213047176 213047567 0 664
24 TraesCS4B01G274800 chr6B 97.925 1542 32 0 2670 4211 83869232 83870773 0 2671
25 TraesCS4B01G274800 chr6B 97.416 387 10 0 1 387 83866462 83866848 0 660


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 TraesCS4B01G274800 chr4B 552796030 552800240 4210 False 3506.500000 6288 100.000000 1 4211 2 chr4B.!!$F2 4210
1 TraesCS4B01G274800 chr4B 636565979 636569378 3399 False 5781.000000 5781 97.353000 809 4208 1 chr4B.!!$F1 3399
2 TraesCS4B01G274800 chrUn 87502092 87505887 3795 True 3186.500000 5709 97.057000 1 4211 2 chrUn.!!$R1 4210
3 TraesCS4B01G274800 chrUn 87511920 87515714 3794 True 3179.500000 5705 96.937500 1 4207 2 chrUn.!!$R2 4206
4 TraesCS4B01G274800 chr3B 745234 747094 1860 False 3142.000000 3142 97.152000 807 2666 1 chr3B.!!$F1 1859
5 TraesCS4B01G274800 chr3B 817712687 817714224 1537 False 2708.000000 2708 98.441000 2670 4208 1 chr3B.!!$F2 1538
6 TraesCS4B01G274800 chr3B 817686763 817691069 4306 False 2155.666667 3103 97.511333 1 4208 3 chr3B.!!$F3 4207
7 TraesCS4B01G274800 chr3B 784348173 784352092 3919 True 1644.000000 2630 97.321500 1 4211 2 chr3B.!!$R1 4210
8 TraesCS4B01G274800 chr7A 395513942 395516190 2248 False 1889.000000 3120 96.937000 1 2666 2 chr7A.!!$F1 2665
9 TraesCS4B01G274800 chr7B 695571449 695575760 4311 True 2131.000000 3109 96.994333 1 4211 3 chr7B.!!$R1 4210
10 TraesCS4B01G274800 chr6A 307919981 307922230 2249 True 1883.500000 3109 96.884500 1 2666 2 chr6A.!!$R1 2665
11 TraesCS4B01G274800 chr5A 631065265 631066806 1541 True 2632.000000 2632 97.471000 2670 4211 1 chr5A.!!$R1 1541
12 TraesCS4B01G274800 chr5A 213047176 213049423 2247 False 1885.500000 3107 97.010000 1 2665 2 chr5A.!!$F1 2664
13 TraesCS4B01G274800 chr6B 83866462 83870773 4311 False 1665.500000 2671 97.670500 1 4211 2 chr6B.!!$F1 4210

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
993 1005 0.776810 ACATGGTTGTGGATGGGACA 59.223 50.000 0.00 0.0 37.48 4.02 F
2780 3316 1.149401 GGATTGCCTAGTGCCCCTC 59.851 63.158 1.42 0.0 40.16 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2957 3493 0.456628 GTAGGAGAAGGACTCACCGC 59.543 60.000 0.00 0.0 46.54 5.68 R
4147 4684 3.579302 CAACCTCCCCAGGCCACA 61.579 66.667 5.01 0.0 45.05 4.17 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
116 117 1.429463 GGATCGTGGATAATCACCGC 58.571 55.000 0.00 0.00 34.36 5.68
947 949 0.787084 TCTCCTCCTCACCTCACCTT 59.213 55.000 0.00 0.00 0.00 3.50
993 1005 0.776810 ACATGGTTGTGGATGGGACA 59.223 50.000 0.00 0.00 37.48 4.02
1034 1046 2.365635 CCTCCATGGGACGGGTCT 60.366 66.667 13.02 0.00 0.00 3.85
1161 1173 1.987855 CGCCAAGGTACCCTCCTCA 60.988 63.158 8.74 0.00 36.74 3.86
1164 1176 1.657804 CCAAGGTACCCTCCTCAACT 58.342 55.000 8.74 0.00 36.74 3.16
1192 1204 2.168503 GTCCGTGCGTGTGTCAACA 61.169 57.895 0.00 0.00 0.00 3.33
1296 1308 3.842925 GAACTGGTGCCCGGAAGCA 62.843 63.158 0.73 0.74 41.46 3.91
1443 1455 4.933400 GTGATAGTTTTACCCTTCTTCGCA 59.067 41.667 0.00 0.00 0.00 5.10
1448 1460 4.067192 GTTTTACCCTTCTTCGCACCTAA 58.933 43.478 0.00 0.00 0.00 2.69
1457 1469 1.200716 CTTCGCACCTAACCGTACTCA 59.799 52.381 0.00 0.00 0.00 3.41
1465 1477 5.657474 CACCTAACCGTACTCATGTATGTT 58.343 41.667 0.00 0.00 34.69 2.71
1517 1529 6.484643 GTGTCCTGTGATTAGATGCAATATGT 59.515 38.462 0.00 0.00 0.00 2.29
1522 1534 8.285394 CCTGTGATTAGATGCAATATGTTGTAC 58.715 37.037 4.00 0.00 37.65 2.90
1802 1814 6.659668 TGCAGTTAGTCTGTATCTGTCTTAGT 59.340 38.462 0.00 0.00 45.23 2.24
2359 2373 8.717821 GCCTTAATACAATCTGCGTATCATTAA 58.282 33.333 0.00 0.00 0.00 1.40
2780 3316 1.149401 GGATTGCCTAGTGCCCCTC 59.851 63.158 1.42 0.00 40.16 4.30
2945 3481 2.162921 CTTGTGTGCGGCTTCGACTG 62.163 60.000 0.00 0.00 35.61 3.51
2957 3493 0.318441 TTCGACTGCAACCTCCTCTG 59.682 55.000 0.00 0.00 0.00 3.35
3529 4065 9.935241 ACATAAATATCGAGTTGATAGCTGATT 57.065 29.630 6.26 0.00 42.69 2.57
3890 4426 6.469410 TCGTAACTTTCTTATGTGTGGGATT 58.531 36.000 0.00 0.00 0.00 3.01
4147 4684 2.111878 GCCACGCTGGATGCCTAT 59.888 61.111 8.04 0.00 40.96 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
993 1005 2.579201 CCTCCTGCCATCGTCGTT 59.421 61.111 0.00 0.00 0.00 3.85
1034 1046 0.252881 AGCTCCATCTCCTTGGTGGA 60.253 55.000 0.00 0.00 43.86 4.02
1296 1308 2.234908 CAGAGGCCAAGCTGTACTACTT 59.765 50.000 5.01 0.00 0.00 2.24
1346 1358 5.273208 AGCTACAATCTTCCTGGTCTAAGA 58.727 41.667 0.00 0.00 36.24 2.10
1443 1455 5.927281 AACATACATGAGTACGGTTAGGT 57.073 39.130 0.00 0.00 32.48 3.08
1448 1460 7.350744 TGGTATTAACATACATGAGTACGGT 57.649 36.000 0.00 0.00 37.59 4.83
1517 1529 5.813157 TGAAATCACTGAGTTGAACGTACAA 59.187 36.000 0.00 0.00 0.00 2.41
1522 1534 4.747108 AGACTGAAATCACTGAGTTGAACG 59.253 41.667 0.00 0.00 0.00 3.95
1714 1726 6.974932 AGCATAACAAAGTGATGTAGTGAG 57.025 37.500 0.00 0.00 32.02 3.51
1802 1814 5.344743 AACAGTCTTCTCTTGTGTCTTCA 57.655 39.130 0.00 0.00 0.00 3.02
2359 2373 9.261035 CTAAACTATCTCCATATGGATACCAGT 57.739 37.037 24.73 19.86 44.46 4.00
2585 2599 7.227873 TGTACATTGATCAGGTTGTAAAGGAA 58.772 34.615 13.57 0.00 0.00 3.36
2780 3316 3.157087 ACAAGTTTAGCCCACCATGAAG 58.843 45.455 0.00 0.00 0.00 3.02
2927 3463 2.108157 AGTCGAAGCCGCACACAA 59.892 55.556 0.00 0.00 35.37 3.33
2945 3481 2.743928 CACCGCAGAGGAGGTTGC 60.744 66.667 0.00 0.00 45.81 4.17
2957 3493 0.456628 GTAGGAGAAGGACTCACCGC 59.543 60.000 0.00 0.00 46.54 5.68
4147 4684 3.579302 CAACCTCCCCAGGCCACA 61.579 66.667 5.01 0.00 45.05 4.17


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

AutoCloner maintained by Alex Coulton.