Multiple sequence alignment - TraesCS5B01G167800

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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 TraesCS5B01G167800 chr5B 100.000 2429 0 0 1 2429 310050158 310052586 0 4486
1 TraesCS5B01G167800 chr1D 93.962 2418 140 5 1 2414 370318154 370315739 0 3651
2 TraesCS5B01G167800 chr1D 88.386 2428 258 22 1 2414 136959446 136957029 0 2900
3 TraesCS5B01G167800 chr1D 88.206 2425 270 10 1 2414 9832966 9835385 0 2880
4 TraesCS5B01G167800 chr5D 92.497 2279 161 6 144 2414 445706985 445704709 0 3253
5 TraesCS5B01G167800 chr7D 87.836 2417 279 14 1 2407 22677619 22680030 0 2820
6 TraesCS5B01G167800 chr7D 84.072 2436 353 32 1 2414 277561595 277559173 0 2316
7 TraesCS5B01G167800 chr7A 90.971 2060 176 4 364 2414 289137995 289135937 0 2765
8 TraesCS5B01G167800 chr3A 86.897 2427 293 22 1 2414 539362903 539360489 0 2697
9 TraesCS5B01G167800 chr2D 84.082 2425 364 19 1 2414 81842753 81840340 0 2320


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 TraesCS5B01G167800 chr5B 310050158 310052586 2428 False 4486 4486 100.000 1 2429 1 chr5B.!!$F1 2428
1 TraesCS5B01G167800 chr1D 370315739 370318154 2415 True 3651 3651 93.962 1 2414 1 chr1D.!!$R2 2413
2 TraesCS5B01G167800 chr1D 136957029 136959446 2417 True 2900 2900 88.386 1 2414 1 chr1D.!!$R1 2413
3 TraesCS5B01G167800 chr1D 9832966 9835385 2419 False 2880 2880 88.206 1 2414 1 chr1D.!!$F1 2413
4 TraesCS5B01G167800 chr5D 445704709 445706985 2276 True 3253 3253 92.497 144 2414 1 chr5D.!!$R1 2270
5 TraesCS5B01G167800 chr7D 22677619 22680030 2411 False 2820 2820 87.836 1 2407 1 chr7D.!!$F1 2406
6 TraesCS5B01G167800 chr7D 277559173 277561595 2422 True 2316 2316 84.072 1 2414 1 chr7D.!!$R1 2413
7 TraesCS5B01G167800 chr7A 289135937 289137995 2058 True 2765 2765 90.971 364 2414 1 chr7A.!!$R1 2050
8 TraesCS5B01G167800 chr3A 539360489 539362903 2414 True 2697 2697 86.897 1 2414 1 chr3A.!!$R1 2413
9 TraesCS5B01G167800 chr2D 81840340 81842753 2413 True 2320 2320 84.082 1 2414 1 chr2D.!!$R1 2413

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
287 290 0.249073 CATGAGGTCCGGTCTAAGCG 60.249 60.0 0.0 0.0 39.06 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1631 0.181114 TGATGGAGAATTGGCCGGAG 59.819 55.0 5.05 0.0 0.0 4.63 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
85 86 0.462759 CGCTCATCCCCAAAGTCTCC 60.463 60.000 0.00 0.00 0.00 3.71
111 114 1.447838 CGACATCCACCAGTTCCGG 60.448 63.158 0.00 0.00 0.00 5.14
261 264 2.660064 GGTGCTGGTCCTCCACGAT 61.660 63.158 0.00 0.00 39.03 3.73
287 290 0.249073 CATGAGGTCCGGTCTAAGCG 60.249 60.000 0.00 0.00 39.06 4.68
291 294 2.577593 GTCCGGTCTAAGCGCCTT 59.422 61.111 2.29 0.00 37.85 4.35
418 421 0.809636 CCGCGTAATGCAGATGGTGA 60.810 55.000 4.92 0.00 46.97 4.02
496 499 1.426251 ATGTGGGGTCTGTCAAGGCA 61.426 55.000 0.00 0.00 0.00 4.75
555 558 2.194056 CTTGCCGCCATCCTGGAT 59.806 61.111 2.57 2.57 40.96 3.41
579 582 1.941668 GCTAAGGCTGCGGGACATATC 60.942 57.143 0.00 0.00 35.22 1.63
713 716 2.122768 CCTCCTCCTATGCTTCCAACT 58.877 52.381 0.00 0.00 0.00 3.16
726 729 3.690460 CTTCCAACTAATGTCTGGCCTT 58.310 45.455 3.32 0.00 0.00 4.35
1026 1029 0.803117 TCTACAGCCTTCACGAGACG 59.197 55.000 0.00 0.00 0.00 4.18
1042 1045 0.460811 GACGCTGCACCATGAGATCA 60.461 55.000 0.00 0.00 0.00 2.92
1051 1054 2.674852 CACCATGAGATCACCAAAGTCG 59.325 50.000 0.00 0.00 0.00 4.18
1318 1323 1.068333 CCCAGTTTTGGCAGTCGATTG 60.068 52.381 3.12 3.12 43.58 2.67
1425 1430 4.483243 GATTCCCCCTTCGCGGCA 62.483 66.667 6.13 0.00 0.00 5.69
1432 1437 1.524621 CCCTTCGCGGCATGATTCT 60.525 57.895 6.13 0.00 0.00 2.40
1625 1631 0.035739 TTAGGTGGCGTCTTGAACCC 59.964 55.000 0.00 0.00 32.85 4.11
1642 1648 1.533711 CCTCCGGCCAATTCTCCAT 59.466 57.895 2.24 0.00 0.00 3.41
1659 1665 2.314852 TCCATCAAGTCCCTCTACCAGA 59.685 50.000 0.00 0.00 0.00 3.86
1679 1687 2.109799 ATTGCTCCCTCCATCGCG 59.890 61.111 0.00 0.00 0.00 5.87
1718 1731 1.488705 TTGGTCCATCCGTCTGCCTT 61.489 55.000 0.00 0.00 39.52 4.35
1726 1739 2.859165 TCCGTCTGCCTTTGAAGATT 57.141 45.000 0.00 0.00 0.00 2.40
1782 1795 2.283676 GTCTGGGGTCGAGGTCCA 60.284 66.667 0.00 0.00 0.00 4.02
1858 1871 5.047731 AGACTCGAATCACATCTTCTTCACA 60.048 40.000 0.00 0.00 0.00 3.58
1939 1952 1.280998 CATACCAACTTCCCCGACCTT 59.719 52.381 0.00 0.00 0.00 3.50
1980 1993 1.141053 CCCCCTACTATCTTGCCACAC 59.859 57.143 0.00 0.00 0.00 3.82
2072 2085 4.394712 CTCTTCGGCGGGCCACTT 62.395 66.667 7.21 0.00 35.37 3.16
2104 2117 9.294030 CTATTCAAATTATCTGGTTTCTTGCAC 57.706 33.333 0.00 0.00 0.00 4.57
2170 2183 2.752640 TTCATCGCCGACCTCCGA 60.753 61.111 0.00 0.00 41.76 4.55
2237 2250 1.519719 CCTGACTAGGGCTGCTGTC 59.480 63.158 0.00 4.39 40.63 3.51
2245 2258 4.687215 GGCTGCTGTCAGTCGCCA 62.687 66.667 22.08 4.24 42.29 5.69
2309 2336 3.957288 GCCCTCAGCAGAACCTTTA 57.043 52.632 0.00 0.00 42.97 1.85
2348 2381 2.208132 TGGGTGTGTGTGTTGAACTT 57.792 45.000 0.00 0.00 0.00 2.66
2351 2385 2.490115 GGGTGTGTGTGTTGAACTTTGA 59.510 45.455 0.00 0.00 0.00 2.69
2362 2396 8.126074 GTGTGTTGAACTTTGATTGTATGTGTA 58.874 33.333 0.00 0.00 0.00 2.90
2415 2450 2.606717 CGAAAGCCTTTTTCGGTACC 57.393 50.000 12.72 0.16 45.17 3.34
2416 2451 1.874872 CGAAAGCCTTTTTCGGTACCA 59.125 47.619 13.54 0.00 45.17 3.25
2417 2452 2.486592 CGAAAGCCTTTTTCGGTACCAT 59.513 45.455 13.54 0.00 45.17 3.55
2418 2453 3.425758 CGAAAGCCTTTTTCGGTACCATC 60.426 47.826 13.54 0.00 45.17 3.51
2419 2454 2.871096 AGCCTTTTTCGGTACCATCA 57.129 45.000 13.54 0.00 0.00 3.07
2420 2455 3.149005 AGCCTTTTTCGGTACCATCAA 57.851 42.857 13.54 0.00 0.00 2.57
2421 2456 2.817844 AGCCTTTTTCGGTACCATCAAC 59.182 45.455 13.54 0.00 0.00 3.18
2422 2457 2.817844 GCCTTTTTCGGTACCATCAACT 59.182 45.455 13.54 0.00 0.00 3.16
2423 2458 3.254903 GCCTTTTTCGGTACCATCAACTT 59.745 43.478 13.54 0.00 0.00 2.66
2424 2459 4.794169 CCTTTTTCGGTACCATCAACTTG 58.206 43.478 13.54 0.00 0.00 3.16
2425 2460 4.517453 CCTTTTTCGGTACCATCAACTTGA 59.483 41.667 13.54 0.00 0.00 3.02
2426 2461 5.334879 CCTTTTTCGGTACCATCAACTTGAG 60.335 44.000 13.54 0.00 0.00 3.02
2427 2462 3.328382 TTCGGTACCATCAACTTGAGG 57.672 47.619 13.54 0.00 0.00 3.86
2428 2463 2.531771 TCGGTACCATCAACTTGAGGA 58.468 47.619 13.54 0.00 27.97 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.232941 GGACCCAACGTAGAACTCATCA 59.767 50.000 0.00 0.00 0.00 3.07
43 44 4.160329 AGATGATCCCATAGTTAAGGCGA 58.840 43.478 0.00 0.00 32.09 5.54
111 114 0.096976 CGTTGATCACCGTGATTGGC 59.903 55.000 15.20 3.87 37.20 4.52
178 181 0.621082 TGGGTAATGTGATCGGCCAA 59.379 50.000 2.24 0.00 0.00 4.52
287 290 5.860090 CTTAAGGAAGACCGCCCTAAGGC 62.860 56.522 0.00 0.00 45.05 4.35
291 294 2.537633 TCTTAAGGAAGACCGCCCTA 57.462 50.000 1.85 0.00 36.75 3.53
487 490 1.004745 GGAGAAGGGATTGCCTTGACA 59.995 52.381 14.87 0.00 0.00 3.58
496 499 2.929043 ACAAGAATGGGGAGAAGGGATT 59.071 45.455 0.00 0.00 0.00 3.01
555 558 1.687840 TCCCGCAGCCTTAGCCTTA 60.688 57.895 0.00 0.00 41.25 2.69
681 684 1.981495 AGGAGGAGGAACTTGAGGTTG 59.019 52.381 0.00 0.00 41.55 3.77
713 716 7.012327 CGAAATTGATCTTAAGGCCAGACATTA 59.988 37.037 5.01 0.00 0.00 1.90
948 951 0.757561 TGATAAGGATCGTCCGGGCA 60.758 55.000 6.96 0.00 42.75 5.36
1026 1029 0.393402 TGGTGATCTCATGGTGCAGC 60.393 55.000 9.47 9.47 0.00 5.25
1042 1045 0.674534 AAGCGAGACTCGACTTTGGT 59.325 50.000 28.43 7.14 43.74 3.67
1051 1054 0.101579 GCCCAGTAGAAGCGAGACTC 59.898 60.000 0.00 0.00 0.00 3.36
1227 1232 8.202461 ACTTATTCCGGATGATATCTAACCAA 57.798 34.615 4.15 0.00 0.00 3.67
1296 1301 0.400213 TCGACTGCCAAAACTGGGAT 59.600 50.000 0.00 0.00 0.00 3.85
1425 1430 3.636679 TGGAGAAGAGGTCGAGAATCAT 58.363 45.455 0.00 0.00 33.17 2.45
1432 1437 1.205655 CAGCAATGGAGAAGAGGTCGA 59.794 52.381 0.00 0.00 0.00 4.20
1594 1600 0.546747 CCACCTAACCTGGTCTGGGA 60.547 60.000 18.29 0.00 38.45 4.37
1625 1631 0.181114 TGATGGAGAATTGGCCGGAG 59.819 55.000 5.05 0.00 0.00 4.63
1642 1648 1.431633 TGGTCTGGTAGAGGGACTTGA 59.568 52.381 0.00 0.00 41.55 3.02
1659 1665 1.528824 CGATGGAGGGAGCAATGGT 59.471 57.895 0.00 0.00 0.00 3.55
1726 1739 2.291365 CATTGCCACATGAAGATCCGA 58.709 47.619 0.00 0.00 0.00 4.55
1858 1871 5.009710 CCATTGAAACTGAGCAGATATGCAT 59.990 40.000 15.82 3.79 37.25 3.96
1878 1891 2.843113 ACCTCTCTAAAGCAGCTCCATT 59.157 45.455 0.00 0.00 0.00 3.16
1939 1952 0.959553 AGAGCTGGAGTTCGTCGAAA 59.040 50.000 9.70 0.00 0.00 3.46
1944 1957 1.985116 GGGGAGAGCTGGAGTTCGT 60.985 63.158 0.00 0.00 0.00 3.85
1980 1993 2.813354 GCCCCAATCTCAAGCCATCTAG 60.813 54.545 0.00 0.00 0.00 2.43
2072 2085 8.958119 AAACCAGATAATTTGAATAGAGCGTA 57.042 30.769 0.00 0.00 0.00 4.42
2104 2117 4.899239 CTAAGCGGCCGCCAGAGG 62.899 72.222 44.47 26.02 43.17 3.69
2170 2183 2.833582 AGACGGACGGCCATCGAT 60.834 61.111 8.76 0.00 42.43 3.59
2231 2244 2.340078 GAGTGGCGACTGACAGCA 59.660 61.111 5.94 0.00 29.71 4.41
2309 2336 4.307432 CCAAGTCTCACGACACAAAGTAT 58.693 43.478 0.00 0.00 42.73 2.12
2348 2381 5.065859 CCGCCAAGAATACACATACAATCAA 59.934 40.000 0.00 0.00 0.00 2.57
2351 2385 4.523083 ACCGCCAAGAATACACATACAAT 58.477 39.130 0.00 0.00 0.00 2.71
2362 2396 5.852282 ATATAAAGCAAACCGCCAAGAAT 57.148 34.783 0.00 0.00 44.04 2.40


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

AutoCloner maintained by Alex Coulton.