Multiple sequence alignment - TraesCS7A01G319600

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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 TraesCS7A01G319600 chr7A 100.000 3602 0 0 1 3602 460116671 460120272 0 6652
1 TraesCS7A01G319600 chr7D 96.135 3648 83 18 1 3602 402148911 402152546 0 5903
2 TraesCS7A01G319600 chr7B 95.334 3622 114 23 1 3602 411749206 411752792 0 5701


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 TraesCS7A01G319600 chr7A 460116671 460120272 3601 False 6652 6652 100.000 1 3602 1 chr7A.!!$F1 3601
1 TraesCS7A01G319600 chr7D 402148911 402152546 3635 False 5903 5903 96.135 1 3602 1 chr7D.!!$F1 3601
2 TraesCS7A01G319600 chr7B 411749206 411752792 3586 False 5701 5701 95.334 1 3602 1 chr7B.!!$F1 3601

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
97 101 1.356124 AGAAGAAGGCCTGCTCTTCA 58.644 50.000 33.73 0.0 46.65 3.02 F
1727 1764 1.294780 GCTCAGGTGTCTGTCCCAG 59.705 63.158 0.00 0.0 41.59 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1801 0.391597 GACAGAGGTGTCCAAACCGA 59.608 55.000 0.00 0.00 46.58 4.69 R
3495 3553 1.442567 TGCCTTTGCAGTTTGCTGG 59.557 52.632 2.48 3.82 45.31 4.85 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
96 100 2.027285 AGAAGAAGAAGGCCTGCTCTTC 60.027 50.000 28.87 28.87 45.26 2.87
97 101 1.356124 AGAAGAAGGCCTGCTCTTCA 58.644 50.000 33.73 0.00 46.65 3.02
329 335 5.591099 TGTCTTGCCTTTCAATTCAGTTTC 58.409 37.500 0.00 0.00 33.57 2.78
330 336 5.126869 TGTCTTGCCTTTCAATTCAGTTTCA 59.873 36.000 0.00 0.00 33.57 2.69
331 337 6.042143 GTCTTGCCTTTCAATTCAGTTTCAA 58.958 36.000 0.00 0.00 33.57 2.69
413 442 4.092383 CGAATCGGACGTTCCAAAATAAGT 59.908 41.667 0.00 0.00 35.91 2.24
489 518 4.434354 AGACGCCGAGAGCCTCCT 62.434 66.667 0.00 0.00 38.78 3.69
517 546 4.264638 GCCTCTCGCTCTCGCTCC 62.265 72.222 0.00 0.00 35.26 4.70
518 547 3.591835 CCTCTCGCTCTCGCTCCC 61.592 72.222 0.00 0.00 35.26 4.30
519 548 3.591835 CTCTCGCTCTCGCTCCCC 61.592 72.222 0.00 0.00 35.26 4.81
520 549 4.426313 TCTCGCTCTCGCTCCCCA 62.426 66.667 0.00 0.00 35.26 4.96
521 550 4.200283 CTCGCTCTCGCTCCCCAC 62.200 72.222 0.00 0.00 35.26 4.61
524 553 4.154347 GCTCTCGCTCCCCACCAG 62.154 72.222 0.00 0.00 0.00 4.00
525 554 4.154347 CTCTCGCTCCCCACCAGC 62.154 72.222 0.00 0.00 0.00 4.85
526 555 4.704103 TCTCGCTCCCCACCAGCT 62.704 66.667 0.00 0.00 34.45 4.24
527 556 3.710722 CTCGCTCCCCACCAGCTT 61.711 66.667 0.00 0.00 34.45 3.74
562 596 3.743636 TGTGATGCGACGGCGAGA 61.744 61.111 18.90 0.00 44.10 4.04
596 630 4.785453 GCGCCCTTCTCCCACCTG 62.785 72.222 0.00 0.00 0.00 4.00
692 726 3.365265 CGCACCTGCCCAAGAACC 61.365 66.667 0.00 0.00 37.91 3.62
693 727 3.365265 GCACCTGCCCAAGAACCG 61.365 66.667 0.00 0.00 34.31 4.44
694 728 3.365265 CACCTGCCCAAGAACCGC 61.365 66.667 0.00 0.00 0.00 5.68
733 770 2.937959 CTTCTCCCCCTCCTCCCTCG 62.938 70.000 0.00 0.00 0.00 4.63
741 778 2.123251 TCCTCCCTCGCCTCCATC 60.123 66.667 0.00 0.00 0.00 3.51
818 855 4.473520 ATTCACGCTCGGCCTGGG 62.474 66.667 0.00 4.54 0.00 4.45
1092 1129 2.569354 GGTCACCATTGGCCGCAAA 61.569 57.895 1.54 0.00 37.89 3.68
1193 1230 2.049618 GGAGCTAGAGGATGCGCG 60.050 66.667 0.00 0.00 0.00 6.86
1313 1350 4.649705 TCAGCGGGTTCCTGGGGA 62.650 66.667 0.00 0.00 0.00 4.81
1397 1434 3.743396 GTGATCAGGTTGTTGTCTCAGAC 59.257 47.826 0.00 0.00 0.00 3.51
1521 1558 3.445857 GGTGGCTGTTCGTCTATACTTC 58.554 50.000 0.00 0.00 0.00 3.01
1606 1643 4.387256 GCTCTGCTGTACTTCTGTTTACAG 59.613 45.833 3.47 3.47 45.45 2.74
1610 1647 6.040054 TCTGCTGTACTTCTGTTTACAGTGTA 59.960 38.462 9.53 0.00 44.79 2.90
1725 1762 1.768684 TTGGCTCAGGTGTCTGTCCC 61.769 60.000 0.00 0.00 41.59 4.46
1727 1764 1.294780 GCTCAGGTGTCTGTCCCAG 59.705 63.158 0.00 0.00 41.59 4.45
1756 1793 1.998315 CTGTCTTGACAATGCTCTCCG 59.002 52.381 4.95 0.00 0.00 4.63
1764 1801 0.877071 CAATGCTCTCCGTTGTTGCT 59.123 50.000 0.00 0.00 36.03 3.91
2273 2310 2.941720 CTCTTATTGAGGCTTGCCTGAC 59.058 50.000 19.84 6.15 39.08 3.51
2583 2620 2.225467 AGTGAGGAAGTGAAAAGCAGC 58.775 47.619 0.00 0.00 0.00 5.25
2899 2943 4.906618 AGGACAAACAATACCGATCACTT 58.093 39.130 0.00 0.00 0.00 3.16
2984 3029 6.125029 AGCATTAATCAGTATGTTGAAGCCT 58.875 36.000 0.00 0.00 37.40 4.58
3016 3061 4.566488 CCCAAGTCATTCCTTGCTAGAACT 60.566 45.833 0.00 0.00 40.40 3.01
3028 3073 7.671302 TCCTTGCTAGAACTGGAATATGATAC 58.329 38.462 0.00 0.00 0.00 2.24
3145 3192 1.678101 AGTGCAGTGAAGCTTTTGGTC 59.322 47.619 0.00 0.00 34.99 4.02
3187 3234 9.474920 CCATGTTAACTTCTTAAAGATTTTGCA 57.525 29.630 7.22 0.00 36.30 4.08
3279 3326 6.650807 TGATTTAAGAGTTGGTGAAGCTGTAG 59.349 38.462 0.00 0.00 0.00 2.74
3307 3354 8.463055 TGTATTATATATGGGAAGGAGGCTTT 57.537 34.615 0.00 0.00 0.00 3.51
3334 3389 5.061853 CCTATGATGAGCATATACATGGCC 58.938 45.833 0.00 0.00 38.72 5.36
3336 3391 2.283298 GATGAGCATATACATGGCCGG 58.717 52.381 0.00 0.00 32.36 6.13
3337 3392 0.321564 TGAGCATATACATGGCCGGC 60.322 55.000 21.18 21.18 32.36 6.13
3423 3481 1.251251 GCCCTTGAGACTTGCACATT 58.749 50.000 0.00 0.00 0.00 2.71
3458 3516 3.785887 TGGGTAGGGAGAAGCATAATGTT 59.214 43.478 0.00 0.00 0.00 2.71
3463 3521 6.547510 GGTAGGGAGAAGCATAATGTTTTGAT 59.452 38.462 0.00 0.00 0.00 2.57
3495 3553 6.412362 TGGTCTTTTCTATGATCTAGGAGC 57.588 41.667 0.00 0.00 0.00 4.70
3500 3558 3.532641 TCTATGATCTAGGAGCCAGCA 57.467 47.619 0.00 0.00 0.00 4.41
3567 3625 3.057526 ACCGTCTTGAGCAAATTTTAGCC 60.058 43.478 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.767375 TCTTCTTGCTGCCAGGAACT 59.233 50.000 0.00 0.00 43.88 3.01
96 100 4.183865 TGGCGAAAATCTCTACATGAGTG 58.816 43.478 0.00 0.00 43.13 3.51
97 101 4.471904 TGGCGAAAATCTCTACATGAGT 57.528 40.909 0.00 0.00 43.13 3.41
413 442 0.320374 ACGCCAAGAGAAATCGGTCA 59.680 50.000 0.00 0.00 0.00 4.02
489 518 1.329256 GCGAGAGGCTAATGGTAGGA 58.671 55.000 0.00 0.00 39.11 2.94
511 540 3.706373 GAAGCTGGTGGGGAGCGA 61.706 66.667 0.00 0.00 41.61 4.93
733 770 0.758123 CAGGAGAAGAGGATGGAGGC 59.242 60.000 0.00 0.00 0.00 4.70
801 838 4.473520 CCCAGGCCGAGCGTGAAT 62.474 66.667 16.67 0.00 45.68 2.57
825 862 2.038975 CTGGGGAGGACGGAAGGA 59.961 66.667 0.00 0.00 0.00 3.36
1193 1230 4.082125 AGACATTTCATCAAACACCCTCC 58.918 43.478 0.00 0.00 0.00 4.30
1313 1350 3.181482 TGCATTCCACGTCACAATGTTTT 60.181 39.130 10.71 0.00 31.29 2.43
1606 1643 3.307242 GTGATGCTCCGAATTGAGTACAC 59.693 47.826 0.00 0.00 34.74 2.90
1610 1647 2.625737 CTGTGATGCTCCGAATTGAGT 58.374 47.619 0.00 0.00 34.74 3.41
1727 1764 5.180117 AGCATTGTCAAGACAGTAACATCAC 59.820 40.000 2.87 0.00 42.94 3.06
1756 1793 0.736053 TGTCCAAACCGAGCAACAAC 59.264 50.000 0.00 0.00 0.00 3.32
1764 1801 0.391597 GACAGAGGTGTCCAAACCGA 59.608 55.000 0.00 0.00 46.58 4.69
2109 2146 5.221322 TGCAATACCAAACACAGCAAACATA 60.221 36.000 0.00 0.00 0.00 2.29
2273 2310 4.648762 TGCCAATTTCTGTATTACCATGGG 59.351 41.667 18.09 0.00 0.00 4.00
2583 2620 6.258160 CAACTATTATCCACCAAAAGCTTCG 58.742 40.000 0.00 0.00 0.00 3.79
2592 2629 6.636454 AGAAGAACCAACTATTATCCACCA 57.364 37.500 0.00 0.00 0.00 4.17
2984 3029 6.364701 CAAGGAATGACTTGGGACCATAATA 58.635 40.000 0.00 0.00 43.14 0.98
3016 3061 5.338626 CCAGCTAGGCATGTATCATATTCCA 60.339 44.000 0.00 0.00 0.00 3.53
3107 3154 7.550551 CACTGCACTTCATTTCCTCTCTAATAA 59.449 37.037 0.00 0.00 0.00 1.40
3187 3234 6.018433 AGCCTATGAAGAAACCATACCATT 57.982 37.500 0.00 0.00 0.00 3.16
3279 3326 8.718656 AGCCTCCTTCCCATATATAATACATTC 58.281 37.037 0.00 0.00 0.00 2.67
3307 3354 6.407752 CCATGTATATGCTCATCATAGGCTGA 60.408 42.308 0.00 0.00 40.69 4.26
3334 3389 4.638421 TCTTTAGTAAATGACAATGGGCCG 59.362 41.667 0.00 0.00 0.00 6.13
3463 3521 9.647918 AGATCATAGAAAAGACCATCAGTACTA 57.352 33.333 0.00 0.00 0.00 1.82
3495 3553 1.442567 TGCCTTTGCAGTTTGCTGG 59.557 52.632 2.48 3.82 45.31 4.85
3567 3625 2.366640 TTGATCCTCTACCTCCTCCG 57.633 55.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.