Multiple sequence alignment - TraesCS5A01G188400

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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 TraesCS5A01G188400 chr5A 100.000 3113 0 0 1 3113 390228914 390232026 0.000000e+00 5749
1 TraesCS5A01G188400 chr5B 93.924 3045 108 31 1 3015 352485386 352482389 0.000000e+00 4527
2 TraesCS5A01G188400 chr5B 91.429 105 7 2 3010 3113 352482337 352482234 3.240000e-30 143
3 TraesCS5A01G188400 chr5D 95.506 2470 72 17 1 2442 307482085 307479627 0.000000e+00 3910
4 TraesCS5A01G188400 chr5D 91.537 579 33 9 2433 2998 307478209 307477634 0.000000e+00 784


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 TraesCS5A01G188400 chr5A 390228914 390232026 3112 False 5749 5749 100.0000 1 3113 1 chr5A.!!$F1 3112
1 TraesCS5A01G188400 chr5B 352482234 352485386 3152 True 2335 4527 92.6765 1 3113 2 chr5B.!!$R1 3112
2 TraesCS5A01G188400 chr5D 307477634 307482085 4451 True 2347 3910 93.5215 1 2998 2 chr5D.!!$R1 2997

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
46 47 0.529992 GTGTCCCATGCTACTACGGC 60.530 60.000 0.0 0.0 0.00 5.68 F
47 48 1.299926 GTCCCATGCTACTACGGCG 60.300 63.158 4.8 4.8 0.00 6.46 F
1972 2001 0.317854 GCAGTTGTTTGCTCGGAACC 60.318 55.000 0.0 0.0 40.89 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1739 0.036732 TCTTGCGTGGAGGAAGCATT 59.963 50.0 0.00 0.0 46.32 3.56 R
2003 2032 2.357569 GGACAGGCAATCTCCAATTCCT 60.358 50.0 0.00 0.0 0.00 3.36 R
3027 4554 0.033601 ATGGTAATGGGAAGCGGCAA 60.034 50.0 1.45 0.0 0.00 4.52 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
40 41 3.421844 AGGAAAAAGTGTCCCATGCTAC 58.578 45.455 0.00 0.00 35.59 3.58
41 42 3.074538 AGGAAAAAGTGTCCCATGCTACT 59.925 43.478 0.00 0.00 35.59 2.57
42 43 4.288626 AGGAAAAAGTGTCCCATGCTACTA 59.711 41.667 0.00 0.00 35.59 1.82
43 44 4.395231 GGAAAAAGTGTCCCATGCTACTAC 59.605 45.833 0.00 0.00 0.00 2.73
44 45 2.961526 AAGTGTCCCATGCTACTACG 57.038 50.000 0.00 0.00 0.00 3.51
46 47 0.529992 GTGTCCCATGCTACTACGGC 60.530 60.000 0.00 0.00 0.00 5.68
47 48 1.299926 GTCCCATGCTACTACGGCG 60.300 63.158 4.80 4.80 0.00 6.46
279 292 4.763793 AGGCAAAGCATCATATACATCCAC 59.236 41.667 0.00 0.00 0.00 4.02
280 293 4.082571 GGCAAAGCATCATATACATCCACC 60.083 45.833 0.00 0.00 0.00 4.61
445 462 2.442188 CCTGCTTCGTTCGTACCGC 61.442 63.158 0.00 0.00 0.00 5.68
527 544 4.379394 CGGTGGTTCGTTGATTTGATTGAT 60.379 41.667 0.00 0.00 0.00 2.57
592 609 4.021894 GCCTCTTCAGTCTACAAGAACTCA 60.022 45.833 0.00 0.00 0.00 3.41
605 622 3.923563 AACTCAGACAGCTCGCCGC 62.924 63.158 0.00 0.00 39.57 6.53
639 656 2.281484 TGGTGCGAGTTCCTTGGC 60.281 61.111 0.00 0.00 0.00 4.52
658 676 1.444836 CGGCGTAATTGAAACCTCCA 58.555 50.000 0.00 0.00 0.00 3.86
841 867 5.221722 TGGATCATGGAGGTATGTAAAGCTC 60.222 44.000 0.00 0.00 42.10 4.09
897 926 9.605955 CGTTTCTTGTGTTGATATTTGTGATTA 57.394 29.630 0.00 0.00 0.00 1.75
960 989 4.223700 TCAAGCCTGATCAGTAGTGATTGT 59.776 41.667 21.11 0.00 43.92 2.71
1000 1029 2.233676 TCGCCTAGCAAGACTTTGATGA 59.766 45.455 0.00 0.00 36.36 2.92
1001 1030 3.118629 TCGCCTAGCAAGACTTTGATGAT 60.119 43.478 0.00 0.00 36.36 2.45
1002 1031 3.002042 CGCCTAGCAAGACTTTGATGATG 59.998 47.826 0.00 0.00 36.36 3.07
1003 1032 4.194640 GCCTAGCAAGACTTTGATGATGA 58.805 43.478 0.00 0.00 36.36 2.92
1295 1324 1.973812 GGCCCTTGGTTGCTCAGAC 60.974 63.158 0.00 0.00 0.00 3.51
1485 1514 2.032030 CCCGTCAACTAAGCAACACAAG 60.032 50.000 0.00 0.00 0.00 3.16
1626 1655 6.560003 AGAGGTATACATGTGAATGGTTCA 57.440 37.500 9.11 0.00 37.33 3.18
1681 1710 6.841119 TCTTCATCACGTATCAATTGTTTGG 58.159 36.000 5.13 0.00 33.44 3.28
1690 1719 7.271223 CACGTATCAATTGTTTGGATCTTCAAC 59.729 37.037 5.13 0.00 33.44 3.18
1710 1739 7.310072 TCAACGTGAAAAGTTTGATGTCTTA 57.690 32.000 0.00 0.00 36.04 2.10
1755 1784 2.158475 TGGAGGGCATTGTTCTTTGTCT 60.158 45.455 0.00 0.00 0.00 3.41
1972 2001 0.317854 GCAGTTGTTTGCTCGGAACC 60.318 55.000 0.00 0.00 40.89 3.62
1977 2006 4.092968 CAGTTGTTTGCTCGGAACCTATAC 59.907 45.833 0.00 0.00 0.00 1.47
2003 2032 6.885918 TGCTATGATCCAAATTCAAACTCTGA 59.114 34.615 0.00 0.00 0.00 3.27
2071 2100 9.549509 GCATTCATACGTTTGTTGAAAGTATAA 57.450 29.630 5.89 0.00 39.76 0.98
2362 2393 8.056407 AGTCCAAGTTAGGAAGAATATTTTGC 57.944 34.615 0.00 0.00 39.92 3.68
2417 2448 4.706962 GGGAACAGCTTGGTTGAGATATTT 59.293 41.667 0.00 0.00 0.00 1.40
2418 2449 5.185828 GGGAACAGCTTGGTTGAGATATTTT 59.814 40.000 0.00 0.00 0.00 1.82
2480 3938 6.883756 TGTGGCATGTAAAATCAGACTAATGA 59.116 34.615 0.00 0.00 0.00 2.57
2487 3945 9.739276 ATGTAAAATCAGACTAATGACTTTCCA 57.261 29.630 0.00 0.00 31.64 3.53
2502 3960 1.437573 TCCATTACGGAGCTGCTCG 59.562 57.895 22.25 18.84 39.64 5.03
2543 4001 2.327568 CATGTAAAAGCTTGGTTGCCG 58.672 47.619 0.00 0.00 0.00 5.69
2581 4048 0.453390 GCTGGTTTGCATAGTCTGGC 59.547 55.000 0.00 0.00 0.00 4.85
2620 4087 0.028902 GTTGTGAGTGCACCCGTTTC 59.971 55.000 14.63 4.50 44.51 2.78
2675 4142 8.655970 TCACATGATACTATCGTTTTTGTCTTG 58.344 33.333 0.00 0.00 0.00 3.02
2694 4161 7.028962 TGTCTTGATAATGTTGTAAATGCAGC 58.971 34.615 0.00 0.00 0.00 5.25
2725 4192 1.323412 AGCTGGCCATAGAGAGTACG 58.677 55.000 5.51 0.00 0.00 3.67
2741 4208 0.819666 TACGGTTGCCATGTTGTGCA 60.820 50.000 0.00 0.00 35.27 4.57
2790 4257 3.696051 GCTAGGAAATCATGTTTGGCTCA 59.304 43.478 0.00 0.00 0.00 4.26
2798 4265 5.549742 ATCATGTTTGGCTCAAAGGAAAA 57.450 34.783 0.00 0.00 33.82 2.29
2814 4283 8.742777 TCAAAGGAAAATTGATGATAACAGGAG 58.257 33.333 0.00 0.00 32.10 3.69
2816 4285 8.655935 AAGGAAAATTGATGATAACAGGAGTT 57.344 30.769 0.00 0.00 41.74 3.01
2865 4334 2.038387 AGAAACCACAGCGTTCAGTT 57.962 45.000 0.00 0.00 0.00 3.16
2867 4336 2.354821 AGAAACCACAGCGTTCAGTTTC 59.645 45.455 11.83 11.83 44.14 2.78
2893 4362 3.378112 TCAGCTCAGGTCAAACACAAAAG 59.622 43.478 0.00 0.00 0.00 2.27
2931 4400 7.176165 TCTCTACAGGATTCGAAACTAGAACAA 59.824 37.037 0.00 0.00 0.00 2.83
2999 4468 0.818938 GCCATGTGATGTGCATCCAA 59.181 50.000 9.39 0.00 37.02 3.53
3022 4549 0.460987 AGGCATTTCTTCGAGAGCGG 60.461 55.000 0.00 0.00 38.28 5.52
3027 4554 2.743636 TTTCTTCGAGAGCGGTTGAT 57.256 45.000 0.00 0.00 38.28 2.57
3031 4558 1.019278 TTCGAGAGCGGTTGATTGCC 61.019 55.000 0.00 0.00 38.28 4.52
3037 4564 2.485122 CGGTTGATTGCCGCTTCC 59.515 61.111 0.00 0.00 42.82 3.46
3038 4565 2.885113 GGTTGATTGCCGCTTCCC 59.115 61.111 0.00 0.00 0.00 3.97
3075 4602 4.502259 CGGCATCCATCTTAGCTCTAGTTT 60.502 45.833 0.00 0.00 0.00 2.66
3085 4612 6.123651 TCTTAGCTCTAGTTTCCTAGACAGG 58.876 44.000 0.00 0.00 43.76 4.00
3086 4613 4.325084 AGCTCTAGTTTCCTAGACAGGT 57.675 45.455 0.00 0.00 43.76 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.010617 TGGGACACTTTTTCCTTTTAGCATC 59.989 40.000 0.00 0.00 33.17 3.91
162 175 2.829592 GGATAAGAGGGGGTGCCG 59.170 66.667 0.00 0.00 0.00 5.69
226 239 2.075489 GTCTCGTGCGTGTCGACTG 61.075 63.158 17.92 10.46 33.71 3.51
297 310 6.206498 GTTGCTTTCGTCCTTGTTTAATTCT 58.794 36.000 0.00 0.00 0.00 2.40
298 311 5.401376 GGTTGCTTTCGTCCTTGTTTAATTC 59.599 40.000 0.00 0.00 0.00 2.17
471 488 2.347731 CGGCTAAGGAAACAAGGAGAC 58.652 52.381 0.00 0.00 0.00 3.36
476 493 1.644786 CGGGCGGCTAAGGAAACAAG 61.645 60.000 9.56 0.00 0.00 3.16
527 544 2.099921 CCGAACCAACACAACCAATCAA 59.900 45.455 0.00 0.00 0.00 2.57
605 622 1.302949 CACATGGTAGGTGGGTGGG 59.697 63.158 0.00 0.00 32.65 4.61
639 656 1.396996 CTGGAGGTTTCAATTACGCCG 59.603 52.381 0.00 0.00 0.00 6.46
897 926 4.643463 TGGTTGCTGCAAATTGATGAAAT 58.357 34.783 17.80 0.00 0.00 2.17
960 989 1.552337 GAGGACATGCTCACTGGAGAA 59.448 52.381 0.00 0.00 44.26 2.87
1000 1029 3.075134 ACCTTTGCTTTCTTCCCTCTCAT 59.925 43.478 0.00 0.00 0.00 2.90
1001 1030 2.443255 ACCTTTGCTTTCTTCCCTCTCA 59.557 45.455 0.00 0.00 0.00 3.27
1002 1031 3.147553 ACCTTTGCTTTCTTCCCTCTC 57.852 47.619 0.00 0.00 0.00 3.20
1003 1032 3.653352 ACTACCTTTGCTTTCTTCCCTCT 59.347 43.478 0.00 0.00 0.00 3.69
1295 1324 1.392589 AGAGTTGTGCACAAACAGGG 58.607 50.000 32.61 0.00 37.63 4.45
1387 1416 1.732917 TTGGCTTCGGCAACACAAG 59.267 52.632 0.00 0.00 42.98 3.16
1485 1514 2.494073 TCCCGGGTAAAAATGTGCAATC 59.506 45.455 22.86 0.00 0.00 2.67
1491 1520 1.353022 TGAGCTCCCGGGTAAAAATGT 59.647 47.619 22.86 0.00 0.00 2.71
1626 1655 6.235664 ACGGAACCTTGTCAAATAATACACT 58.764 36.000 0.00 0.00 0.00 3.55
1681 1710 6.912591 ACATCAAACTTTTCACGTTGAAGATC 59.087 34.615 8.76 0.00 37.70 2.75
1690 1719 6.857964 AGCATTAAGACATCAAACTTTTCACG 59.142 34.615 0.00 0.00 0.00 4.35
1710 1739 0.036732 TCTTGCGTGGAGGAAGCATT 59.963 50.000 0.00 0.00 46.32 3.56
1755 1784 2.832129 ACATAGTTTTCCCTCGAGCTCA 59.168 45.455 15.40 0.00 0.00 4.26
1977 2006 7.066645 TCAGAGTTTGAATTTGGATCATAGCAG 59.933 37.037 0.00 0.00 31.34 4.24
2003 2032 2.357569 GGACAGGCAATCTCCAATTCCT 60.358 50.000 0.00 0.00 0.00 3.36
2071 2100 6.115446 TGAAATTATCTTGACGCAGAGGAAT 58.885 36.000 0.00 0.00 0.00 3.01
2379 2410 3.937706 CTGTTCCCTGAGCAATTACAGAG 59.062 47.826 0.00 0.00 34.87 3.35
2417 2448 0.183492 AGGTTCACAAGCTGGAGCAA 59.817 50.000 0.00 0.00 45.16 3.91
2418 2449 1.839191 AGGTTCACAAGCTGGAGCA 59.161 52.632 0.00 0.00 45.16 4.26
2487 3945 0.179134 GTCACGAGCAGCTCCGTAAT 60.179 55.000 17.16 0.00 37.23 1.89
2502 3960 2.417719 CCACAAAGCCAGACTAGTCAC 58.582 52.381 24.44 13.18 0.00 3.67
2551 4009 2.102084 TGCAAACCAGCTTTTACATGCA 59.898 40.909 0.00 0.00 39.95 3.96
2552 4010 2.753296 TGCAAACCAGCTTTTACATGC 58.247 42.857 0.00 0.00 34.99 4.06
2553 4011 5.713025 ACTATGCAAACCAGCTTTTACATG 58.287 37.500 6.79 0.00 34.99 3.21
2554 4012 5.711976 AGACTATGCAAACCAGCTTTTACAT 59.288 36.000 0.00 2.87 34.99 2.29
2555 4013 5.048782 CAGACTATGCAAACCAGCTTTTACA 60.049 40.000 0.00 0.00 34.99 2.41
2556 4014 5.393962 CAGACTATGCAAACCAGCTTTTAC 58.606 41.667 0.00 0.00 34.99 2.01
2581 4048 4.164822 ACCATGCGTCAATTTCAGAAAG 57.835 40.909 1.28 0.00 0.00 2.62
2620 4087 3.490155 TGCATCAATTTCAAAACACGCAG 59.510 39.130 0.00 0.00 0.00 5.18
2675 4142 6.135290 TGAGGCTGCATTTACAACATTATC 57.865 37.500 0.50 0.00 0.00 1.75
2694 4161 2.271497 CCAGCTTGAGGCCTGAGG 59.729 66.667 12.00 2.13 43.05 3.86
2725 4192 0.388659 TCTTGCACAACATGGCAACC 59.611 50.000 3.34 0.00 44.41 3.77
2741 4208 2.092158 GGGCTTGGGAAATCTAGCTCTT 60.092 50.000 0.00 0.00 31.41 2.85
2790 4257 8.655935 ACTCCTGTTATCATCAATTTTCCTTT 57.344 30.769 0.00 0.00 0.00 3.11
2798 4265 5.128919 GGAGCAACTCCTGTTATCATCAAT 58.871 41.667 6.38 0.00 46.41 2.57
2814 4283 3.645268 AATGGAGCCGGGGAGCAAC 62.645 63.158 2.18 0.00 34.23 4.17
2816 4285 2.917897 AAAATGGAGCCGGGGAGCA 61.918 57.895 2.18 0.00 34.23 4.26
2865 4334 3.141398 GTTTGACCTGAGCTGATGTGAA 58.859 45.455 0.00 0.00 0.00 3.18
2867 4336 2.225019 GTGTTTGACCTGAGCTGATGTG 59.775 50.000 0.00 0.00 0.00 3.21
2931 4400 5.762825 CTATGTAATGCATGGCTCAAGTT 57.237 39.130 0.00 0.00 38.47 2.66
2999 4468 2.676463 GCTCTCGAAGAAATGCCTCAGT 60.676 50.000 0.00 0.00 34.09 3.41
3022 4549 0.532115 AATGGGAAGCGGCAATCAAC 59.468 50.000 1.45 0.00 0.00 3.18
3027 4554 0.033601 ATGGTAATGGGAAGCGGCAA 60.034 50.000 1.45 0.00 0.00 4.52
3031 4558 2.618709 GAGGAAATGGTAATGGGAAGCG 59.381 50.000 0.00 0.00 0.00 4.68
3035 4562 1.133915 GCCGAGGAAATGGTAATGGGA 60.134 52.381 0.00 0.00 0.00 4.37
3037 4564 2.051334 TGCCGAGGAAATGGTAATGG 57.949 50.000 0.00 0.00 0.00 3.16
3038 4565 2.554032 GGATGCCGAGGAAATGGTAATG 59.446 50.000 0.00 0.00 0.00 1.90
3085 4612 0.613777 AGGTCGATTGTGAAGGGGAC 59.386 55.000 0.00 0.00 0.00 4.46
3086 4613 0.613260 CAGGTCGATTGTGAAGGGGA 59.387 55.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.