Multiple sequence alignment - TraesCS7A01G259900

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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 TraesCS7A01G259900 chr7A 100.000 2435 0 0 1 2435 251759916 251762350 0 4497
1 TraesCS7A01G259900 chr5A 95.037 2438 114 7 1 2435 331790431 331787998 0 3825
2 TraesCS7A01G259900 chr2A 94.998 2439 117 4 1 2435 307407153 307404716 0 3823
3 TraesCS7A01G259900 chr2A 94.636 2442 123 7 1 2435 250852469 250854909 0 3777
4 TraesCS7A01G259900 chr1A 94.959 2440 118 4 1 2435 74500966 74498527 0 3819
5 TraesCS7A01G259900 chr1A 94.458 2436 130 5 2 2435 96122759 96120327 0 3746
6 TraesCS7A01G259900 chr3A 94.875 2439 119 5 1 2435 381958849 381961285 0 3807
7 TraesCS7A01G259900 chr3A 94.625 2437 122 8 1 2435 507690514 507688085 0 3766
8 TraesCS7A01G259900 chr3A 94.501 2437 131 3 1 2435 278604083 278606518 0 3755
9 TraesCS7A01G259900 chr4A 94.460 2437 132 3 1 2435 83139671 83142106 0 3749


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 TraesCS7A01G259900 chr7A 251759916 251762350 2434 False 4497 4497 100.000 1 2435 1 chr7A.!!$F1 2434
1 TraesCS7A01G259900 chr5A 331787998 331790431 2433 True 3825 3825 95.037 1 2435 1 chr5A.!!$R1 2434
2 TraesCS7A01G259900 chr2A 307404716 307407153 2437 True 3823 3823 94.998 1 2435 1 chr2A.!!$R1 2434
3 TraesCS7A01G259900 chr2A 250852469 250854909 2440 False 3777 3777 94.636 1 2435 1 chr2A.!!$F1 2434
4 TraesCS7A01G259900 chr1A 74498527 74500966 2439 True 3819 3819 94.959 1 2435 1 chr1A.!!$R1 2434
5 TraesCS7A01G259900 chr1A 96120327 96122759 2432 True 3746 3746 94.458 2 2435 1 chr1A.!!$R2 2433
6 TraesCS7A01G259900 chr3A 381958849 381961285 2436 False 3807 3807 94.875 1 2435 1 chr3A.!!$F2 2434
7 TraesCS7A01G259900 chr3A 507688085 507690514 2429 True 3766 3766 94.625 1 2435 1 chr3A.!!$R1 2434
8 TraesCS7A01G259900 chr3A 278604083 278606518 2435 False 3755 3755 94.501 1 2435 1 chr3A.!!$F1 2434
9 TraesCS7A01G259900 chr4A 83139671 83142106 2435 False 3749 3749 94.460 1 2435 1 chr4A.!!$F1 2434

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
55 56 0.250727 CCAAGAAGGAAGGCGGTCAA 60.251 55.0 0.0 0.0 41.22 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1846 0.250338 GACTGGGTGAAGCCGAAAGT 60.25 55.0 0.0 0.0 38.44 2.66 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
55 56 0.250727 CCAAGAAGGAAGGCGGTCAA 60.251 55.000 0.00 0.00 41.22 3.18
60 61 0.984230 AAGGAAGGCGGTCAAGATGA 59.016 50.000 0.00 0.00 0.00 2.92
88 89 1.130561 GGCGCAGAGGTATGACAAAAC 59.869 52.381 10.83 0.00 0.00 2.43
148 149 3.994392 GACGTCCATGCTTCTTTAACAGA 59.006 43.478 3.51 0.00 0.00 3.41
366 370 1.004440 GTGACGCTTGCTTCTCCCT 60.004 57.895 1.09 0.00 0.00 4.20
396 400 2.372264 TGATGCCTTCAATTCTGGAGC 58.628 47.619 0.00 0.00 0.00 4.70
443 447 1.140589 CTAGCCAGAGCCACAGACG 59.859 63.158 0.00 0.00 41.25 4.18
479 483 2.851263 ACGGGTAAGCAAATCTGACA 57.149 45.000 0.00 0.00 0.00 3.58
702 708 0.316204 GGTACCATATAGCGTGCGGT 59.684 55.000 7.15 1.16 0.00 5.68
781 787 1.200252 AGCATGCCGTACGATAGCTAG 59.800 52.381 18.76 9.43 42.67 3.42
885 893 0.674895 GATGTTCGAGCCCAGCTTGT 60.675 55.000 3.83 0.00 39.88 3.16
1041 1049 3.785859 GAGATGCCCGGGTCTGCA 61.786 66.667 24.63 14.55 42.52 4.41
1133 1141 1.852157 TTGTGGCCATCAGTCTCCCC 61.852 60.000 9.72 0.00 0.00 4.81
1159 1167 2.101770 GCATTGGAGAGCTTGCGC 59.898 61.111 0.00 0.00 0.00 6.09
1338 1346 7.287512 AGAGATCCCCGTTAAATTAGTCTAC 57.712 40.000 0.00 0.00 0.00 2.59
1356 1364 1.935933 ACGGGCAAGTAGAATTAGCG 58.064 50.000 0.00 0.00 0.00 4.26
1687 1696 1.120530 TCCAGGGAGAATAGTTCCGC 58.879 55.000 0.00 0.00 35.48 5.54
1836 1846 5.987347 CCGAATATTCCCTTAAGAACGCTAA 59.013 40.000 9.87 0.00 0.00 3.09
1960 1970 2.031682 GCATAAATACAAGAGCCAGGCG 60.032 50.000 5.55 0.00 0.00 5.52
2006 2016 6.585416 AGTCATATCGATGCATATAATGGCA 58.415 36.000 8.54 0.00 45.23 4.92
2174 2187 6.074648 TGAAGGCCTTGAGGAAGAATAAAAA 58.925 36.000 26.25 0.00 37.39 1.94
2255 2269 0.179026 ACATAGAGTCCGGCGCTAGA 60.179 55.000 7.64 0.64 33.13 2.43
2267 2281 2.541178 CGGCGCTAGACGTAGAATCTTT 60.541 50.000 7.64 0.00 45.53 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.066143 TCATCTTGACCGCCTTCCTTC 60.066 52.381 0.00 0.00 0.00 3.46
207 210 1.688311 CCTCTATGTCCGGTCCTGGAA 60.688 57.143 0.00 0.00 40.44 3.53
443 447 5.479124 ACCCGTACATCCCTTACATATTC 57.521 43.478 0.00 0.00 0.00 1.75
479 483 7.901322 TCTCAGGGGCTACTGATACATATAATT 59.099 37.037 11.68 0.00 45.67 1.40
621 627 0.532115 GGTTCCTTCAATGCGGCAAT 59.468 50.000 6.82 0.00 0.00 3.56
702 708 2.857186 TTGTTAGATCTGCAGCCACA 57.143 45.000 9.47 4.08 0.00 4.17
741 747 3.556999 CTGGTCTTCCGGATTCTCTCTA 58.443 50.000 4.15 0.00 42.46 2.43
781 787 3.248171 CACGCGTTCGCTAGCCTC 61.248 66.667 10.22 0.00 39.84 4.70
823 831 4.870636 TGGTATTGGCATCTTGGAGATTT 58.129 39.130 0.00 0.00 31.32 2.17
885 893 4.404073 GCTTATTCTCCTTCTCAGAGTCCA 59.596 45.833 0.00 0.00 32.93 4.02
892 900 2.111384 AGCCGCTTATTCTCCTTCTCA 58.889 47.619 0.00 0.00 0.00 3.27
921 929 5.295787 TCGTTCAAGCACTTACTGAAAATGT 59.704 36.000 0.00 0.00 0.00 2.71
1020 1028 2.444895 GACCCGGGCATCTCCTCT 60.445 66.667 24.08 0.00 34.39 3.69
1041 1049 3.153919 GAGCTCGGATAGAAGATCACCT 58.846 50.000 0.00 0.00 0.00 4.00
1297 1305 3.026847 TTTCCCATCGGGCCCCAT 61.027 61.111 18.66 5.97 43.94 4.00
1328 1336 5.927281 TTCTACTTGCCCGTAGACTAATT 57.073 39.130 10.66 0.00 43.95 1.40
1329 1337 6.481434 AATTCTACTTGCCCGTAGACTAAT 57.519 37.500 10.66 2.04 43.95 1.73
1338 1346 1.217882 CCGCTAATTCTACTTGCCCG 58.782 55.000 0.00 0.00 0.00 6.13
1356 1364 2.802719 TCCTGTTGGGAATACTTTGCC 58.197 47.619 0.00 0.00 41.91 4.52
1662 1671 4.384940 GAACTATTCTCCCTGGAAGATGC 58.615 47.826 0.00 0.00 34.07 3.91
1719 1728 1.238439 CAGTCCGGACATGCACTTTT 58.762 50.000 35.00 9.45 0.00 2.27
1836 1846 0.250338 GACTGGGTGAAGCCGAAAGT 60.250 55.000 0.00 0.00 38.44 2.66
1960 1970 1.115326 AGTTTTGGCCAAGCTGGGTC 61.115 55.000 19.48 4.16 38.19 4.46
2006 2016 4.394729 TCTTCCGCATGTACCTTTTCTTT 58.605 39.130 0.00 0.00 0.00 2.52
2217 2231 3.964411 TGTTCGTCTCCTTCCTCTATCA 58.036 45.455 0.00 0.00 0.00 2.15
2220 2234 5.104444 ACTCTATGTTCGTCTCCTTCCTCTA 60.104 44.000 0.00 0.00 0.00 2.43
2255 2269 2.093447 CCAGGCTCCAAAGATTCTACGT 60.093 50.000 0.00 0.00 0.00 3.57
2267 2281 4.704833 GAACGCAGCCAGGCTCCA 62.705 66.667 12.53 0.00 36.40 3.86


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

AutoCloner maintained by Alex Coulton.