Multiple sequence alignment - TraesCS7B01G120100

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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 TraesCS7B01G120100 chr7B 100.000 2244 0 0 1 2244 139608362 139610605 0 4145
1 TraesCS7B01G120100 chr7B 96.413 2258 64 4 1 2244 716784607 716786861 0 3705
2 TraesCS7B01G120100 chr7B 96.236 2258 68 4 1 2244 742948738 742946484 0 3683
3 TraesCS7B01G120100 chr7A 96.413 2258 64 4 1 2244 60168767 60166513 0 3705
4 TraesCS7B01G120100 chr7A 96.191 2258 69 4 1 2244 60084936 60087190 0 3677
5 TraesCS7B01G120100 chr5A 96.324 2258 66 4 1 2244 16544554 16546808 0 3694
6 TraesCS7B01G120100 chr5A 95.704 2258 68 5 1 2244 420185702 420187944 0 3605
7 TraesCS7B01G120100 chr1D 95.088 2260 87 7 1 2244 275778927 275781178 0 3537
8 TraesCS7B01G120100 chr6B 94.704 2247 111 7 1 2244 388287038 388284797 0 3483
9 TraesCS7B01G120100 chr6B 95.076 1056 35 6 1203 2244 388038508 388037456 0 1646
10 TraesCS7B01G120100 chr2A 96.549 1478 50 1 1 1478 755480549 755482025 0 2446
11 TraesCS7B01G120100 chr3B 95.644 1056 30 3 1203 2244 759913746 759914799 0 1681
12 TraesCS7B01G120100 chrUn 95.558 1058 29 3 1203 2244 396261129 396262184 0 1677
13 TraesCS7B01G120100 chr7D 95.369 1058 31 3 1203 2244 579000819 578999764 0 1666
14 TraesCS7B01G120100 chr1B 94.223 1056 43 4 1203 2243 491502507 491503559 0 1596


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 TraesCS7B01G120100 chr7B 139608362 139610605 2243 False 4145 4145 100.000 1 2244 1 chr7B.!!$F1 2243
1 TraesCS7B01G120100 chr7B 716784607 716786861 2254 False 3705 3705 96.413 1 2244 1 chr7B.!!$F2 2243
2 TraesCS7B01G120100 chr7B 742946484 742948738 2254 True 3683 3683 96.236 1 2244 1 chr7B.!!$R1 2243
3 TraesCS7B01G120100 chr7A 60166513 60168767 2254 True 3705 3705 96.413 1 2244 1 chr7A.!!$R1 2243
4 TraesCS7B01G120100 chr7A 60084936 60087190 2254 False 3677 3677 96.191 1 2244 1 chr7A.!!$F1 2243
5 TraesCS7B01G120100 chr5A 16544554 16546808 2254 False 3694 3694 96.324 1 2244 1 chr5A.!!$F1 2243
6 TraesCS7B01G120100 chr5A 420185702 420187944 2242 False 3605 3605 95.704 1 2244 1 chr5A.!!$F2 2243
7 TraesCS7B01G120100 chr1D 275778927 275781178 2251 False 3537 3537 95.088 1 2244 1 chr1D.!!$F1 2243
8 TraesCS7B01G120100 chr6B 388284797 388287038 2241 True 3483 3483 94.704 1 2244 1 chr6B.!!$R2 2243
9 TraesCS7B01G120100 chr6B 388037456 388038508 1052 True 1646 1646 95.076 1203 2244 1 chr6B.!!$R1 1041
10 TraesCS7B01G120100 chr2A 755480549 755482025 1476 False 2446 2446 96.549 1 1478 1 chr2A.!!$F1 1477
11 TraesCS7B01G120100 chr3B 759913746 759914799 1053 False 1681 1681 95.644 1203 2244 1 chr3B.!!$F1 1041
12 TraesCS7B01G120100 chrUn 396261129 396262184 1055 False 1677 1677 95.558 1203 2244 1 chrUn.!!$F1 1041
13 TraesCS7B01G120100 chr7D 578999764 579000819 1055 True 1666 1666 95.369 1203 2244 1 chr7D.!!$R1 1041
14 TraesCS7B01G120100 chr1B 491502507 491503559 1052 False 1596 1596 94.223 1203 2243 1 chr1B.!!$F1 1040

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
237 238 1.586154 CCGCCTTCGCTCAATTTGGT 61.586 55.000 0.0 0.0 0.00 3.67 F
678 679 3.527533 CCATGCGTAAACCAAGCTACTA 58.472 45.455 0.0 0.0 32.19 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1056 0.613260 TCCAATACCGACAGCAGCTT 59.387 50.000 0.0 0.0 0.00 3.74 R
1653 1655 1.068333 CACAGGAGGTGGCGAAAAATG 60.068 52.381 0.0 0.0 44.04 2.32 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
53 54 4.139786 CCCACCAATGTGATCTCCATTAG 58.860 47.826 9.80 6.69 45.76 1.73
113 114 4.219944 TCGCGGAATTAGACCAGCTATTAT 59.780 41.667 6.13 0.00 0.00 1.28
115 116 5.479306 GCGGAATTAGACCAGCTATTATCA 58.521 41.667 0.00 0.00 0.00 2.15
237 238 1.586154 CCGCCTTCGCTCAATTTGGT 61.586 55.000 0.00 0.00 0.00 3.67
407 408 5.645067 TGCCACTAGACAGAATTTCTCAATG 59.355 40.000 0.00 0.00 0.00 2.82
473 474 4.398319 TCCTTCTTAGAAAAAGGTGGCTG 58.602 43.478 0.00 0.00 42.28 4.85
485 486 5.669164 AAAGGTGGCTGAACTAACAAAAA 57.331 34.783 0.00 0.00 0.00 1.94
580 581 4.279671 CCTTACTCGCAGATGTAGGAAGAT 59.720 45.833 9.57 0.00 33.89 2.40
678 679 3.527533 CCATGCGTAAACCAAGCTACTA 58.472 45.455 0.00 0.00 32.19 1.82
778 779 5.191827 ACCCCCTACCTATACCTATACCTT 58.808 45.833 0.00 0.00 0.00 3.50
830 831 6.500684 TCCACAGCTCATTTTCTTGAATAC 57.499 37.500 0.00 0.00 0.00 1.89
939 940 6.094048 CCCAAGTACTTCGAATCATCAACAAT 59.906 38.462 4.77 0.00 0.00 2.71
1013 1014 4.523173 TCGACTTGAGATGTTAGAAGGTGT 59.477 41.667 0.00 0.00 0.00 4.16
1028 1029 9.227777 GTTAGAAGGTGTTAAATCAATAGGTGT 57.772 33.333 0.00 0.00 0.00 4.16
1055 1056 2.677836 CTGCTACAATTGCTTTAGCCGA 59.322 45.455 18.65 5.64 37.95 5.54
1078 1079 2.422597 CTGCTGTCGGTATTGGAAACA 58.577 47.619 0.00 0.00 39.83 2.83
1106 1107 4.398319 AGTTCTTTGATTCATTCCGTGGT 58.602 39.130 0.00 0.00 0.00 4.16
1109 1110 1.902938 TTGATTCATTCCGTGGTGCA 58.097 45.000 0.00 0.00 0.00 4.57
1420 1422 6.825721 GTCCATTTATTTCTGTGTCCTCATCT 59.174 38.462 0.00 0.00 0.00 2.90
1423 1425 3.708403 ATTTCTGTGTCCTCATCTGCA 57.292 42.857 0.00 0.00 0.00 4.41
1489 1491 1.135024 CAGGTAGGGCGCGTTACTTTA 60.135 52.381 8.43 0.00 0.00 1.85
1589 1591 3.844211 TGTTCAATGCTAGTCCCTAACCT 59.156 43.478 0.00 0.00 0.00 3.50
1695 1697 8.433421 TGTGTCTTTCTGTTTAAGGTCTTTAG 57.567 34.615 0.00 0.00 0.00 1.85
1706 1712 7.444792 TGTTTAAGGTCTTTAGTTCGGCATTAA 59.555 33.333 0.00 0.00 0.00 1.40
1750 1756 4.009675 GTGAACTACAAAGCATGGGATCA 58.990 43.478 0.00 0.00 0.00 2.92
1815 1821 3.364549 ACTTCAGAGAGGAGAGACATGG 58.635 50.000 0.00 0.00 0.00 3.66
1853 1859 7.308589 GCGTAGAAAAGGCATATGGTATGAAAT 60.309 37.037 4.56 0.00 38.86 2.17
1938 1958 2.481289 GCTAAAGAGCCCACTTCAGT 57.519 50.000 0.00 0.00 43.49 3.41
2044 2064 4.929211 GGCTTTACTTGATTTTGGCGAAAT 59.071 37.500 12.50 12.50 40.61 2.17
2057 2077 3.575965 GGCGAAATAAAGGCCATATGG 57.424 47.619 18.07 18.07 46.13 2.74
2072 2092 4.384208 GCCATATGGTCTACTTTCTGGTGT 60.384 45.833 22.79 0.00 37.57 4.16
2165 2209 5.071653 AGAGTTCTGAAGCTCCTTTCTTTCT 59.928 40.000 12.99 0.00 32.47 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.022428 TGGTGGGGATATAGGCCGATAT 60.022 50.000 17.34 17.34 0.00 1.63
53 54 6.760770 TGTTTCCAAACAAATTTGTCCATCTC 59.239 34.615 23.47 12.11 45.17 2.75
113 114 2.481276 CGACTGACGGATAAGCCAATGA 60.481 50.000 0.00 0.00 38.46 2.57
115 116 1.806623 GCGACTGACGGATAAGCCAAT 60.807 52.381 1.32 0.00 42.83 3.16
237 238 0.321346 TCGCAGCATCAAGGTCTGAA 59.679 50.000 0.00 0.00 37.67 3.02
525 526 8.585018 CCTTTTTGATTAATTCACAGGTAAGGT 58.415 33.333 0.00 0.00 32.84 3.50
639 640 4.736793 GCATGGCACGAAAATCTATCTTTG 59.263 41.667 0.00 0.00 0.00 2.77
678 679 0.178903 TGTGGCTGGGGTAGACTCTT 60.179 55.000 0.00 0.00 34.56 2.85
753 754 4.798472 GGTATAGGTATAGGTAGGGGGTCT 59.202 50.000 0.00 0.00 0.00 3.85
793 794 5.477637 TGAGCTGTGGATTGAAAATCATCAA 59.522 36.000 0.00 0.00 43.03 2.57
830 831 1.788308 CAATTTGCAAGGCTTGTCACG 59.212 47.619 26.71 8.74 0.00 4.35
939 940 6.768861 TCCTTCGTTGTTCTTTCTTGGATTTA 59.231 34.615 0.00 0.00 0.00 1.40
957 958 3.264104 TCTTGTCACGTTTTTCCTTCGT 58.736 40.909 0.00 0.00 38.34 3.85
996 997 9.739276 ATTGATTTAACACCTTCTAACATCTCA 57.261 29.630 0.00 0.00 0.00 3.27
1013 1014 5.116180 CAGCTCCGACACCTATTGATTTAA 58.884 41.667 0.00 0.00 0.00 1.52
1028 1029 0.250234 AGCAATTGTAGCAGCTCCGA 59.750 50.000 7.40 0.00 30.05 4.55
1055 1056 0.613260 TCCAATACCGACAGCAGCTT 59.387 50.000 0.00 0.00 0.00 3.74
1078 1079 7.066284 CACGGAATGAATCAAAGAACTAAGGAT 59.934 37.037 0.00 0.00 0.00 3.24
1106 1107 5.177326 GTTTAGCCAATGATGGATTTTGCA 58.823 37.500 0.00 0.00 44.90 4.08
1109 1110 7.622713 TGATTGTTTAGCCAATGATGGATTTT 58.377 30.769 0.00 0.00 44.90 1.82
1155 1156 2.831685 TAGCTTCGGTGAGAGCAAAA 57.168 45.000 0.00 0.00 0.00 2.44
1190 1191 4.583073 TGAGATCAGAAATGCCATCATTGG 59.417 41.667 0.00 0.00 41.77 3.16
1420 1422 6.515832 CCTATCTAACACAGACATACATGCA 58.484 40.000 0.00 0.00 35.62 3.96
1423 1425 6.780031 AGAGCCTATCTAACACAGACATACAT 59.220 38.462 0.00 0.00 36.10 2.29
1511 1513 7.341769 AGGGCAAGTAAATAATCTAAACATGCA 59.658 33.333 0.00 0.00 36.71 3.96
1562 1564 4.327680 AGGGACTAGCATTGAACAAAGTC 58.672 43.478 7.95 7.95 36.02 3.01
1652 1654 1.202879 ACAGGAGGTGGCGAAAAATGA 60.203 47.619 0.00 0.00 0.00 2.57
1653 1655 1.068333 CACAGGAGGTGGCGAAAAATG 60.068 52.381 0.00 0.00 44.04 2.32
1654 1656 1.247567 CACAGGAGGTGGCGAAAAAT 58.752 50.000 0.00 0.00 44.04 1.82
1750 1756 2.032030 CGCTTTCTTTCGTGGTGTTCAT 60.032 45.455 0.00 0.00 0.00 2.57
1815 1821 5.686834 CCTTTTCTACGCCTAAAACAAGTC 58.313 41.667 0.00 0.00 0.00 3.01
1853 1859 7.338710 CAGTCCCTACCTCTTTTCAATCAATA 58.661 38.462 0.00 0.00 0.00 1.90
1938 1958 2.024176 GGCTTGATCGAGTGCCTTAA 57.976 50.000 11.71 0.00 41.92 1.85
2044 2064 6.409234 CCAGAAAGTAGACCATATGGCCTTTA 60.409 42.308 22.18 6.36 39.32 1.85
2057 2077 2.352519 GGACCGACACCAGAAAGTAGAC 60.353 54.545 0.00 0.00 0.00 2.59
2072 2092 2.093658 GCTATCTTTGTGAAGGGACCGA 60.094 50.000 0.00 0.00 33.56 4.69


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

AutoCloner maintained by Alex Coulton.