Multiple sequence alignment - TraesCS7A01G183300

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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 TraesCS7A01G183300 chr7A 100.000 2258 0 0 1 2258 138162688 138164945 0.000000e+00 4170
1 TraesCS7A01G183300 chr7D 92.191 2241 143 10 22 2258 138192540 138194752 0.000000e+00 3140
2 TraesCS7A01G183300 chr7D 86.631 561 58 6 1709 2253 511648466 511647907 2.480000e-169 604
3 TraesCS7A01G183300 chr7B 95.762 1463 57 3 1 1462 103571601 103573059 0.000000e+00 2353
4 TraesCS7A01G183300 chr7B 85.616 584 62 14 1694 2258 544409399 544408819 5.370000e-166 593
5 TraesCS7A01G183300 chr7B 88.636 132 3 4 1504 1635 103574453 103574572 1.400000e-32 150
6 TraesCS7A01G183300 chr2D 84.543 634 86 10 1634 2258 552066951 552067581 3.190000e-173 617
7 TraesCS7A01G183300 chr4A 84.211 627 86 9 1640 2258 595823589 595822968 4.150000e-167 597
8 TraesCS7A01G183300 chr4A 83.604 616 94 4 1640 2251 668277537 668276925 2.520000e-159 571
9 TraesCS7A01G183300 chr3A 83.625 629 90 7 1640 2257 605832759 605833385 1.500000e-161 579
10 TraesCS7A01G183300 chr4D 83.307 635 90 10 1634 2258 295427215 295426587 2.520000e-159 571
11 TraesCS7A01G183300 chr1D 83.360 631 87 11 1634 2258 303020325 303020943 3.250000e-158 568
12 TraesCS7A01G183300 chr6B 84.925 199 22 6 1132 1323 41410120 41410317 6.360000e-46 195
13 TraesCS7A01G183300 chr1B 77.904 353 50 24 988 1323 683538250 683538591 6.360000e-46 195


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 TraesCS7A01G183300 chr7A 138162688 138164945 2257 False 4170.0 4170 100.000 1 2258 1 chr7A.!!$F1 2257
1 TraesCS7A01G183300 chr7D 138192540 138194752 2212 False 3140.0 3140 92.191 22 2258 1 chr7D.!!$F1 2236
2 TraesCS7A01G183300 chr7D 511647907 511648466 559 True 604.0 604 86.631 1709 2253 1 chr7D.!!$R1 544
3 TraesCS7A01G183300 chr7B 103571601 103574572 2971 False 1251.5 2353 92.199 1 1635 2 chr7B.!!$F1 1634
4 TraesCS7A01G183300 chr7B 544408819 544409399 580 True 593.0 593 85.616 1694 2258 1 chr7B.!!$R1 564
5 TraesCS7A01G183300 chr2D 552066951 552067581 630 False 617.0 617 84.543 1634 2258 1 chr2D.!!$F1 624
6 TraesCS7A01G183300 chr4A 595822968 595823589 621 True 597.0 597 84.211 1640 2258 1 chr4A.!!$R1 618
7 TraesCS7A01G183300 chr4A 668276925 668277537 612 True 571.0 571 83.604 1640 2251 1 chr4A.!!$R2 611
8 TraesCS7A01G183300 chr3A 605832759 605833385 626 False 579.0 579 83.625 1640 2257 1 chr3A.!!$F1 617
9 TraesCS7A01G183300 chr4D 295426587 295427215 628 True 571.0 571 83.307 1634 2258 1 chr4D.!!$R1 624
10 TraesCS7A01G183300 chr1D 303020325 303020943 618 False 568.0 568 83.360 1634 2258 1 chr1D.!!$F1 624

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
374 376 0.528017 TTCTTCTCAGTCAGCGCGAT 59.472 50.0 12.1 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 3441 0.885196 GAGGAACACGTGCTCTCTCT 59.115 55.0 17.22 5.66 41.36 3.1 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
27 28 3.304928 GCATGTTCACTGGAAAACTGGAG 60.305 47.826 0.00 0.00 34.13 3.86
52 53 3.367498 GGCACTCCACGATCCATATCTAC 60.367 52.174 0.00 0.00 0.00 2.59
75 76 3.441244 GTGCTGATCACATCCGTCA 57.559 52.632 0.00 0.00 44.98 4.35
87 88 2.760650 ACATCCGTCACTCTGCTATTCA 59.239 45.455 0.00 0.00 0.00 2.57
123 125 3.939740 ACACAAGATCACCCATAGCAT 57.060 42.857 0.00 0.00 0.00 3.79
137 139 8.268605 TCACCCATAGCATACTGTTTAACATTA 58.731 33.333 0.00 0.00 0.00 1.90
196 198 2.920724 TTCCAACACGACAATCCAGA 57.079 45.000 0.00 0.00 0.00 3.86
212 214 1.004044 CCAGAAACATGCTCCCAGACT 59.996 52.381 0.00 0.00 0.00 3.24
231 233 2.564504 ACTAAGCATGCACAGAGTCTCA 59.435 45.455 21.98 0.00 0.00 3.27
374 376 0.528017 TTCTTCTCAGTCAGCGCGAT 59.472 50.000 12.10 0.00 0.00 4.58
377 379 1.849219 CTTCTCAGTCAGCGCGATAAC 59.151 52.381 12.10 0.00 0.00 1.89
480 482 4.180057 GCTCATAGCTATACATGACCAGC 58.820 47.826 5.77 4.34 38.45 4.85
495 497 1.900016 CAGCACTGGCCTTTGAGCA 60.900 57.895 3.32 0.00 42.56 4.26
636 638 2.224018 TGACCAACCAAGCATTTCAAGC 60.224 45.455 0.00 0.00 0.00 4.01
674 676 4.704057 GTCAATTTTCTCCTGGCTCTGAAT 59.296 41.667 0.00 0.00 0.00 2.57
676 678 4.581309 ATTTTCTCCTGGCTCTGAATCA 57.419 40.909 0.00 0.00 0.00 2.57
755 757 1.594862 GATGTACAGCACGGCATTCTC 59.405 52.381 6.17 0.00 0.00 2.87
773 775 2.439883 GACGTACTCGGGGAGCCT 60.440 66.667 0.00 0.00 41.85 4.58
811 813 9.274206 GGGTAAGGTATGTATCTGAAAATTCTC 57.726 37.037 0.00 0.00 0.00 2.87
948 950 1.677552 GAAGACCGGGAGCCAGAAA 59.322 57.895 6.32 0.00 0.00 2.52
986 988 4.021925 GGAGCTGCGGAAGGTGGT 62.022 66.667 0.00 0.00 36.52 4.16
1028 1030 1.068753 CGATCTGGGAGCGCTTGAT 59.931 57.895 13.26 13.28 34.07 2.57
1036 1038 1.593750 GAGCGCTTGATGCCGAGAT 60.594 57.895 13.26 0.00 38.78 2.75
1329 1331 4.667935 TGGAGCGGGGAAAGGGGA 62.668 66.667 0.00 0.00 0.00 4.81
1479 2671 2.902423 TTTGCACTCCAAGTGGCCGT 62.902 55.000 9.01 0.00 46.01 5.68
1550 2905 8.645814 AGGTGTCGTAGGTATAATTCATATCA 57.354 34.615 0.00 0.00 0.00 2.15
1551 2906 9.256228 AGGTGTCGTAGGTATAATTCATATCAT 57.744 33.333 0.00 0.00 0.00 2.45
1674 3036 0.612732 TGCAAATCTGGCCCCTCAAG 60.613 55.000 0.00 0.00 0.00 3.02
1797 3164 7.334858 TCCATACAAACTCATGCAACTATGTA 58.665 34.615 0.00 0.00 0.00 2.29
1813 3180 4.690748 ACTATGTAGTTGCACACACATCAC 59.309 41.667 8.97 0.00 32.60 3.06
2118 3495 4.108299 AATGTGGGCGCGGATGGA 62.108 61.111 8.83 0.00 0.00 3.41
2127 3504 1.816863 GCGCGGATGGATTCCTCCTA 61.817 60.000 8.83 0.00 42.99 2.94
2201 3589 2.939261 GCCTCGACGACCCTTTCCA 61.939 63.158 0.00 0.00 0.00 3.53
2203 3591 1.080025 CTCGACGACCCTTTCCACC 60.080 63.158 0.00 0.00 0.00 4.61
2215 3604 4.585216 TCCACCCCTTCCCACGGT 62.585 66.667 0.00 0.00 0.00 4.83
2253 3643 1.742768 GGACTCATAGTCTGCCCGG 59.257 63.158 6.99 0.00 44.46 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 6.392625 TCGCTAGTTAATGAATAGCAGAGT 57.607 37.500 5.42 0.00 41.60 3.24
123 125 9.968870 GACCCATGTTTTTAATGTTAAACAGTA 57.031 29.630 8.64 0.00 44.61 2.74
137 139 1.061735 ACCCCCTTGACCCATGTTTTT 60.062 47.619 0.00 0.00 0.00 1.94
196 198 2.040278 TGCTTAGTCTGGGAGCATGTTT 59.960 45.455 0.00 0.00 41.15 2.83
212 214 3.900966 ATGAGACTCTGTGCATGCTTA 57.099 42.857 20.33 6.77 0.00 3.09
231 233 8.923270 TCTACCTGAAAAGACAAAATGGAAAAT 58.077 29.630 0.00 0.00 0.00 1.82
374 376 6.437477 TCCTGAGCTTGACTTCTATTCTGTTA 59.563 38.462 0.00 0.00 0.00 2.41
377 379 5.336150 TCCTGAGCTTGACTTCTATTCTG 57.664 43.478 0.00 0.00 0.00 3.02
480 482 3.567164 CCTATATTGCTCAAAGGCCAGTG 59.433 47.826 5.01 1.58 0.00 3.66
495 497 4.435977 TGGGCTGGAGATACCCTATATT 57.564 45.455 0.00 0.00 44.56 1.28
636 638 5.425196 AAATTGACAGGAAAATGGGGATG 57.575 39.130 0.00 0.00 0.00 3.51
704 706 2.368192 TGCCCCGGGATTCCTCAT 60.368 61.111 26.32 0.00 0.00 2.90
773 775 0.974010 CCTTACCCGGGTGCTCACTA 60.974 60.000 36.97 11.79 0.00 2.74
811 813 0.937304 CAATGCGGGATAAGTGTCCG 59.063 55.000 0.00 0.00 45.84 4.79
1028 1030 2.755876 AGCTCACGGATCTCGGCA 60.756 61.111 8.20 0.00 44.45 5.69
1061 1063 0.036952 CGATGTGGAGCTGAACCTGT 60.037 55.000 0.00 0.00 0.00 4.00
1123 1125 2.190578 CGGCATCTCCCCCTCAAC 59.809 66.667 0.00 0.00 0.00 3.18
1124 1126 2.040442 TCGGCATCTCCCCCTCAA 59.960 61.111 0.00 0.00 0.00 3.02
1329 1331 2.681778 CGCACACCCTCCCTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
1414 1416 1.403687 GCCTAGCGGTCAATCCTCCT 61.404 60.000 0.00 0.00 0.00 3.69
1479 2671 1.100463 TCAGCGGCACAGCAAGAAAA 61.100 50.000 1.45 0.00 40.15 2.29
1797 3164 1.165907 CGGGTGATGTGTGTGCAACT 61.166 55.000 0.00 0.00 38.04 3.16
1813 3180 2.494471 TGTAGTGTGATGGAGTAACGGG 59.506 50.000 0.00 0.00 0.00 5.28
1896 3264 3.984732 GGGAAGGGCAAGGGCAGT 61.985 66.667 0.00 0.00 43.71 4.40
2064 3441 0.885196 GAGGAACACGTGCTCTCTCT 59.115 55.000 17.22 5.66 41.36 3.10
2068 3445 2.651361 CGGAGGAACACGTGCTCT 59.349 61.111 17.22 10.57 43.96 4.09
2070 3447 3.616721 AGCGGAGGAACACGTGCT 61.617 61.111 17.22 2.15 33.72 4.40
2118 3495 2.743718 CGGCCGCATAGGAGGAAT 59.256 61.111 14.67 0.00 45.00 3.01


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

AutoCloner maintained by Alex Coulton.