Multiple sequence alignment - TraesCS2A01G245300

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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 TraesCS2A01G245300 chr2A 100.000 2282 0 0 1 2282 352643370 352645651 0.000000e+00 4215
1 TraesCS2A01G245300 chr2A 96.235 2284 84 2 1 2282 352651380 352653663 0.000000e+00 3740
2 TraesCS2A01G245300 chr2A 87.017 1086 87 36 1204 2282 604016769 604017807 0.000000e+00 1175
3 TraesCS2A01G245300 chr2A 88.642 766 63 19 1204 1965 604025249 604025994 0.000000e+00 911
4 TraesCS2A01G245300 chr4A 94.790 2284 90 6 1 2282 85922177 85924433 0.000000e+00 3531
5 TraesCS2A01G245300 chr4A 94.705 2285 91 7 1 2282 85954390 85956647 0.000000e+00 3522
6 TraesCS2A01G245300 chr4A 88.907 604 53 12 1688 2282 409180732 409181330 0.000000e+00 732
7 TraesCS2A01G245300 chr4A 87.914 604 60 11 1688 2282 374723994 374724593 0.000000e+00 699
8 TraesCS2A01G245300 chr4A 79.624 692 94 34 1617 2282 494563815 494563145 9.610000e-124 453
9 TraesCS2A01G245300 chr4A 79.424 695 93 35 1617 2282 732989984 732989311 1.610000e-121 446
10 TraesCS2A01G245300 chr6A 94.846 2212 101 7 1 2210 216935637 216933437 0.000000e+00 3441
11 TraesCS2A01G245300 chr5A 91.790 2290 144 23 1 2282 268822488 268820235 0.000000e+00 3147
12 TraesCS2A01G245300 chr5A 91.659 2290 146 24 1 2282 268814514 268812262 0.000000e+00 3129
13 TraesCS2A01G245300 chr5A 87.768 793 79 17 1499 2282 133071031 133070248 0.000000e+00 911
14 TraesCS2A01G245300 chr1A 91.488 2291 146 30 1 2282 201752129 201754379 0.000000e+00 3105
15 TraesCS2A01G245300 chr1A 90.368 789 64 12 1499 2282 322707996 322707215 0.000000e+00 1026
16 TraesCS2A01G245300 chr3A 95.263 1351 61 3 10 1357 701989674 701988324 0.000000e+00 2137
17 TraesCS2A01G245300 chr3A 94.152 1351 75 4 10 1357 701981808 701980459 0.000000e+00 2054


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 TraesCS2A01G245300 chr2A 352643370 352645651 2281 False 4215 4215 100.000 1 2282 1 chr2A.!!$F1 2281
1 TraesCS2A01G245300 chr2A 352651380 352653663 2283 False 3740 3740 96.235 1 2282 1 chr2A.!!$F2 2281
2 TraesCS2A01G245300 chr2A 604016769 604017807 1038 False 1175 1175 87.017 1204 2282 1 chr2A.!!$F3 1078
3 TraesCS2A01G245300 chr2A 604025249 604025994 745 False 911 911 88.642 1204 1965 1 chr2A.!!$F4 761
4 TraesCS2A01G245300 chr4A 85922177 85924433 2256 False 3531 3531 94.790 1 2282 1 chr4A.!!$F1 2281
5 TraesCS2A01G245300 chr4A 85954390 85956647 2257 False 3522 3522 94.705 1 2282 1 chr4A.!!$F2 2281
6 TraesCS2A01G245300 chr4A 409180732 409181330 598 False 732 732 88.907 1688 2282 1 chr4A.!!$F4 594
7 TraesCS2A01G245300 chr4A 374723994 374724593 599 False 699 699 87.914 1688 2282 1 chr4A.!!$F3 594
8 TraesCS2A01G245300 chr4A 494563145 494563815 670 True 453 453 79.624 1617 2282 1 chr4A.!!$R1 665
9 TraesCS2A01G245300 chr4A 732989311 732989984 673 True 446 446 79.424 1617 2282 1 chr4A.!!$R2 665
10 TraesCS2A01G245300 chr6A 216933437 216935637 2200 True 3441 3441 94.846 1 2210 1 chr6A.!!$R1 2209
11 TraesCS2A01G245300 chr5A 268820235 268822488 2253 True 3147 3147 91.790 1 2282 1 chr5A.!!$R3 2281
12 TraesCS2A01G245300 chr5A 268812262 268814514 2252 True 3129 3129 91.659 1 2282 1 chr5A.!!$R2 2281
13 TraesCS2A01G245300 chr5A 133070248 133071031 783 True 911 911 87.768 1499 2282 1 chr5A.!!$R1 783
14 TraesCS2A01G245300 chr1A 201752129 201754379 2250 False 3105 3105 91.488 1 2282 1 chr1A.!!$F1 2281
15 TraesCS2A01G245300 chr1A 322707215 322707996 781 True 1026 1026 90.368 1499 2282 1 chr1A.!!$R1 783
16 TraesCS2A01G245300 chr3A 701988324 701989674 1350 True 2137 2137 95.263 10 1357 1 chr3A.!!$R2 1347
17 TraesCS2A01G245300 chr3A 701980459 701981808 1349 True 2054 2054 94.152 10 1357 1 chr3A.!!$R1 1347

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
506 511 1.075698 GACTCCTCTCCCGATCCCATA 59.924 57.143 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1503 0.673333 TCGAGCGACGGTAGTGGTAA 60.673 55.0 0.0 0.0 42.82 2.85 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
248 251 5.007034 CCCTTCCTCCTCTTTCTTTTCTTC 58.993 45.833 0.00 0.0 0.00 2.87
305 308 6.498538 AGAGTTTAAGAGATGAGAGAGGGAA 58.501 40.000 0.00 0.0 0.00 3.97
340 343 1.118356 CCCTGCCAGCTCTACTAGGG 61.118 65.000 0.00 0.0 38.96 3.53
408 412 4.572223 CCAGTCTCCTTTCCTAACCCTAGA 60.572 50.000 0.00 0.0 0.00 2.43
506 511 1.075698 GACTCCTCTCCCGATCCCATA 59.924 57.143 0.00 0.0 0.00 2.74
535 540 2.067932 CTTCCCTTCCACAGCCACCA 62.068 60.000 0.00 0.0 0.00 4.17
575 580 2.203084 TCCTCTCGATCTCGCGCT 60.203 61.111 5.56 0.0 39.60 5.92
843 848 2.519302 GTGTGCCTGTGCCACCTT 60.519 61.111 0.00 0.0 34.52 3.50
865 870 2.116125 GCCCAACAGGAGCCTTGT 59.884 61.111 0.00 0.0 38.24 3.16
895 900 1.660575 CCTTCGTCGTCTGCGTTGT 60.661 57.895 0.00 0.0 39.49 3.32
925 930 2.811514 GGAGCCCCAGCATCGATCA 61.812 63.158 0.00 0.0 43.56 2.92
945 950 1.745890 CAGTGTCGTCACCTTCCCA 59.254 57.895 9.22 0.0 44.83 4.37
983 988 1.294780 CGAGAGCTTGGCAGGAACT 59.705 57.895 0.00 0.0 43.88 3.01
1196 1202 2.167693 CCACCTCAAGTTCGGCTACATA 59.832 50.000 0.00 0.0 0.00 2.29
1204 1210 5.105269 TCAAGTTCGGCTACATATAACACCA 60.105 40.000 0.00 0.0 0.00 4.17
1364 1370 1.717645 CTTGTACAACTACCGTCGCAC 59.282 52.381 3.59 0.0 0.00 5.34
1495 1501 2.679837 TGTACGACCTACTCCGTGAATC 59.320 50.000 0.00 0.0 39.54 2.52
1497 1503 2.444421 ACGACCTACTCCGTGAATCTT 58.556 47.619 0.00 0.0 37.64 2.40
1631 1637 2.093106 AGCGAGAACGACTACTTCCAT 58.907 47.619 0.00 0.0 42.66 3.41
1808 1824 1.302511 GTCCTCCTCTTTTGCCGCA 60.303 57.895 0.00 0.0 0.00 5.69
1948 2002 1.192757 CACCGTTTCGTTATCGTTGCA 59.807 47.619 0.00 0.0 38.33 4.08
1967 2047 1.127951 CAGTGGCACCGTTTCGTTATC 59.872 52.381 15.27 0.0 0.00 1.75
1972 2052 1.860709 CACCGTTTCGTTATCGTTGC 58.139 50.000 0.00 0.0 38.33 4.17
1973 2053 1.192757 CACCGTTTCGTTATCGTTGCA 59.807 47.619 0.00 0.0 38.33 4.08
2013 2094 2.327568 CGCCACGATGAAAAATGCTTT 58.672 42.857 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 141 4.219115 TGGAGTGGCCATTTTTCAAAGTA 58.781 39.130 9.72 0.00 43.33 2.24
276 279 7.403312 TCTCTCATCTCTTAAACTCTCCTTG 57.597 40.000 0.00 0.00 0.00 3.61
305 308 3.474570 GGACGCTGGGCTCTCCAT 61.475 66.667 0.00 0.00 46.01 3.41
408 412 2.593956 GGGAACGGGCTCAGGAAGT 61.594 63.158 0.00 0.00 0.00 3.01
506 511 1.051556 GGAAGGGAAGCGAGGAGGAT 61.052 60.000 0.00 0.00 0.00 3.24
535 540 1.752608 GGAGGGGATCATGGGAGAAT 58.247 55.000 0.00 0.00 0.00 2.40
655 660 0.909610 CAGGTTGGTAGAGGAGGGCA 60.910 60.000 0.00 0.00 0.00 5.36
843 848 4.704833 GCTCCTGTTGGGCGCTCA 62.705 66.667 5.44 5.44 42.17 4.26
925 930 1.746517 GGAAGGTGACGACACTGGT 59.253 57.895 17.14 3.50 45.32 4.00
983 988 2.000701 ATCGGGGTGGAAGGATGCA 61.001 57.895 0.00 0.00 0.00 3.96
1364 1370 1.006102 ACTTGCTGGTCTCGGTTCG 60.006 57.895 0.00 0.00 0.00 3.95
1495 1501 1.792993 CGAGCGACGGTAGTGGTAAAG 60.793 57.143 0.00 0.00 38.46 1.85
1497 1503 0.673333 TCGAGCGACGGTAGTGGTAA 60.673 55.000 0.00 0.00 42.82 2.85
1948 2002 1.435577 GATAACGAAACGGTGCCACT 58.564 50.000 0.00 0.00 0.00 4.00
1972 2052 2.355007 GGAAATGAAAAGGGGTGCCATG 60.355 50.000 0.00 0.00 0.00 3.66
1973 2053 1.908619 GGAAATGAAAAGGGGTGCCAT 59.091 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.