Multiple sequence alignment - TraesCS5A01G231900

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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 TraesCS5A01G231900 chr5A 100.000 3140 0 0 1 3140 447366636 447369775 0.000000e+00 5799
1 TraesCS5A01G231900 chr5D 95.961 3144 98 11 1 3140 344695260 344692142 0.000000e+00 5075
2 TraesCS5A01G231900 chr5B 93.480 3175 116 21 1 3140 407124783 407127901 0.000000e+00 4632
3 TraesCS5A01G231900 chr1D 83.394 548 66 9 2483 3010 457876730 457876188 4.710000e-133 484
4 TraesCS5A01G231900 chr1A 81.555 553 65 17 2483 3010 550339480 550338940 3.740000e-114 422
5 TraesCS5A01G231900 chr1B 81.818 242 22 12 2786 3010 627944203 627943967 1.920000e-42 183


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 TraesCS5A01G231900 chr5A 447366636 447369775 3139 False 5799 5799 100.000 1 3140 1 chr5A.!!$F1 3139
1 TraesCS5A01G231900 chr5D 344692142 344695260 3118 True 5075 5075 95.961 1 3140 1 chr5D.!!$R1 3139
2 TraesCS5A01G231900 chr5B 407124783 407127901 3118 False 4632 4632 93.480 1 3140 1 chr5B.!!$F1 3139
3 TraesCS5A01G231900 chr1D 457876188 457876730 542 True 484 484 83.394 2483 3010 1 chr1D.!!$R1 527
4 TraesCS5A01G231900 chr1A 550338940 550339480 540 True 422 422 81.555 2483 3010 1 chr1A.!!$R1 527

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
659 669 0.179468 GGACGGCTTATACTTGCCCA 59.821 55.0 0.0 0.0 45.9 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 2534 0.178981 ACACCTGGTTCTGCAAGCAT 60.179 50.0 0.0 0.0 39.29 3.79 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
190 191 2.423446 GAGGGCTGCATACGGGAG 59.577 66.667 0.50 0.00 38.13 4.30
538 540 9.522804 TTCACAAGTTTAATGTATTGGTTTGAC 57.477 29.630 0.00 0.00 0.00 3.18
659 669 0.179468 GGACGGCTTATACTTGCCCA 59.821 55.000 0.00 0.00 45.90 5.36
668 678 2.876368 ATACTTGCCCAGCACGAGCC 62.876 60.000 0.00 0.00 43.56 4.70
669 679 4.711949 CTTGCCCAGCACGAGCCT 62.712 66.667 0.00 0.00 43.56 4.58
670 680 4.704833 TTGCCCAGCACGAGCCTC 62.705 66.667 0.00 0.00 43.56 4.70
675 685 4.154347 CAGCACGAGCCTCCCCTC 62.154 72.222 0.00 0.00 43.56 4.30
901 911 0.804989 CAAGAACCTGTGGATTCGGC 59.195 55.000 0.00 0.00 0.00 5.54
1620 1633 2.602878 GTGAAATTCTGCGACTACGGA 58.397 47.619 0.00 0.00 40.15 4.69
1689 1702 3.553095 GATCCCCTACATGGCGCCC 62.553 68.421 26.77 6.44 0.00 6.13
1771 1784 0.468648 CATGGCAGAGATGCTCTCCA 59.531 55.000 13.89 13.89 44.42 3.86
1791 1804 2.383527 CGAGGAGTTGTTCAGCGGC 61.384 63.158 0.00 0.00 0.00 6.53
1806 1819 3.116531 GGCGAAAAGACGACGGGG 61.117 66.667 0.00 0.00 35.09 5.73
1971 1987 3.385384 CCCGAGGAGCTGCTGTCA 61.385 66.667 14.48 0.00 0.00 3.58
1982 1998 0.179076 CTGCTGTCATGGCACGGATA 60.179 55.000 0.00 0.00 35.71 2.59
2229 2245 8.958119 ACAGCGAAGGAATAAATAAGAATGTA 57.042 30.769 0.00 0.00 0.00 2.29
2293 2309 4.294416 CTCTACTGGAGTGGATTGTACG 57.706 50.000 0.00 0.00 35.00 3.67
2356 2372 2.216940 CACTTGCATGTGAAAAACGCAG 59.783 45.455 24.41 0.00 42.42 5.18
2487 2531 7.639113 ATTTTTCCTTGACAGTACACAGAAA 57.361 32.000 0.00 0.00 0.00 2.52
2609 2662 3.196469 TCTGTTGCCTCCATCAGTTCTAG 59.804 47.826 0.00 0.00 39.01 2.43
2776 2843 2.645838 AATGAGAACACACCACAGCT 57.354 45.000 0.00 0.00 0.00 4.24
2807 2874 8.981647 CCAAAACATTTATGCCTGATAATAAGC 58.018 33.333 0.00 0.00 0.00 3.09
2810 2877 9.533253 AAACATTTATGCCTGATAATAAGCAAC 57.467 29.630 0.00 0.00 38.99 4.17
2817 2884 4.214332 GCCTGATAATAAGCAACTAGGCAC 59.786 45.833 0.00 0.00 46.53 5.01
2972 3052 2.944349 GTTTGAACAAAGACCGGTGGTA 59.056 45.455 14.63 0.00 35.25 3.25
3022 3102 1.669115 GCTTCTTCGGTGCAGCAGA 60.669 57.895 17.33 9.29 32.17 4.26
3040 3120 3.350031 ATTTGGGAGGAGGCGCAGG 62.350 63.158 10.83 0.00 32.08 4.85
3062 3142 3.741476 CCTGCAGTCTTTGGCGGC 61.741 66.667 13.81 0.00 35.06 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 3.430565 CTCCACCAGCTCGCGCATA 62.431 63.158 8.75 0.00 39.10 3.14
639 641 3.772619 GGCAAGTATAAGCCGTCCA 57.227 52.632 0.00 0.00 41.70 4.02
668 678 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
672 682 3.795924 ATGGGAGGGGAGGGGAGG 61.796 72.222 0.00 0.00 0.00 4.30
673 683 2.122189 GATGGGAGGGGAGGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
674 684 3.791076 GGATGGGAGGGGAGGGGA 61.791 72.222 0.00 0.00 0.00 4.81
675 685 4.928520 GGGATGGGAGGGGAGGGG 62.929 77.778 0.00 0.00 0.00 4.79
676 686 4.122670 TGGGATGGGAGGGGAGGG 62.123 72.222 0.00 0.00 0.00 4.30
677 687 2.774351 GTGGGATGGGAGGGGAGG 60.774 72.222 0.00 0.00 0.00 4.30
901 911 0.602638 TGTGCTTCTGCCAACCGTAG 60.603 55.000 0.00 0.00 38.71 3.51
954 964 2.813908 GTCATGGTCGTCGTGCCC 60.814 66.667 0.00 0.09 32.54 5.36
1108 1118 1.379176 GCCTTCTCCCTTTCTGGCC 60.379 63.158 0.00 0.00 34.81 5.36
1299 1309 2.964310 GCAGGCCTCCTTGAGCAGA 61.964 63.158 0.00 0.00 0.00 4.26
1543 1553 3.686726 GTCTTCATGTCCCTGTGAATGAC 59.313 47.826 0.00 0.00 34.18 3.06
1689 1702 2.974845 CTTCTCCAGCAGCATCTCG 58.025 57.895 0.00 0.00 0.00 4.04
1771 1784 1.373497 CGCTGAACAACTCCTCGCT 60.373 57.895 0.00 0.00 0.00 4.93
1791 1804 2.356553 TGCCCCGTCGTCTTTTCG 60.357 61.111 0.00 0.00 0.00 3.46
1806 1819 0.861837 CGAATATCTTGCCGACCTGC 59.138 55.000 0.00 0.00 0.00 4.85
1982 1998 0.329596 GAGGCCCTTCAAGACATGGT 59.670 55.000 0.00 0.00 0.00 3.55
2229 2245 6.460781 TCCGATCGTAATAAACAAGCCATAT 58.539 36.000 15.09 0.00 0.00 1.78
2233 2249 5.473796 TTTCCGATCGTAATAAACAAGCC 57.526 39.130 15.09 0.00 0.00 4.35
2293 2309 9.262358 ACTTTAATTGAAGTAATCGCCTAGATC 57.738 33.333 13.51 0.00 38.06 2.75
2487 2531 2.041701 ACCTGGTTCTGCAAGCATTTT 58.958 42.857 0.00 0.00 39.29 1.82
2490 2534 0.178981 ACACCTGGTTCTGCAAGCAT 60.179 50.000 0.00 0.00 39.29 3.79
2609 2662 2.359230 GGCTGCAGACACCTGGAC 60.359 66.667 20.43 0.00 40.72 4.02
2776 2843 6.166984 TCAGGCATAAATGTTTTGGTTTGA 57.833 33.333 0.00 0.00 0.00 2.69
2807 2874 4.455533 TGATGTTAGCTTTGTGCCTAGTTG 59.544 41.667 0.00 0.00 44.23 3.16
2810 2877 5.049818 GCTATGATGTTAGCTTTGTGCCTAG 60.050 44.000 0.00 0.00 44.23 3.02
2972 3052 0.958091 TTTGGTGCGCTGTGCTTATT 59.042 45.000 14.92 0.00 46.63 1.40
3022 3102 2.273449 CTGCGCCTCCTCCCAAAT 59.727 61.111 4.18 0.00 0.00 2.32
3040 3120 1.600413 CGCCAAAGACTGCAGGTTTTC 60.600 52.381 19.93 6.29 0.00 2.29
3042 3122 1.455383 CCGCCAAAGACTGCAGGTTT 61.455 55.000 19.93 14.15 0.00 3.27
3062 3142 0.173481 ACAGGGTGATGATGTCGTCG 59.827 55.000 0.00 0.00 34.69 5.12
3110 3190 3.733960 CGGACTGTCGACGAGGCA 61.734 66.667 18.50 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.