Multiple sequence alignment - TraesCS1D01G305200

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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 TraesCS1D01G305200 chr1D 100.000 3948 0 0 1 3948 402827380 402823433 0.000000e+00 7291.0
1 TraesCS1D01G305200 chr1D 100.000 37 0 0 418 454 402826927 402826891 7.080000e-08 69.4
2 TraesCS1D01G305200 chr1D 100.000 37 0 0 454 490 402826963 402826927 7.080000e-08 69.4
3 TraesCS1D01G305200 chr1B 95.211 3529 116 24 454 3948 540722875 540719366 0.000000e+00 5531.0
4 TraesCS1D01G305200 chr1B 95.435 460 15 3 1 454 540723298 540722839 0.000000e+00 728.0
5 TraesCS1D01G305200 chr1A 95.850 2024 54 10 1950 3948 498049725 498047707 0.000000e+00 3245.0
6 TraesCS1D01G305200 chr1A 98.285 1458 21 4 454 1910 498051188 498049734 0.000000e+00 2551.0
7 TraesCS1D01G305200 chr1A 95.445 461 13 5 1 454 498051611 498051152 0.000000e+00 728.0
8 TraesCS1D01G305200 chr5D 85.039 127 14 5 581 705 505091794 505091671 1.490000e-24 124.0
9 TraesCS1D01G305200 chr3D 100.000 34 0 0 3915 3948 444681688 444681721 3.290000e-06 63.9
10 TraesCS1D01G305200 chr3B 100.000 34 0 0 3915 3948 582476565 582476598 3.290000e-06 63.9
11 TraesCS1D01G305200 chr3A 100.000 34 0 0 3915 3948 585502362 585502395 3.290000e-06 63.9


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 TraesCS1D01G305200 chr1D 402823433 402827380 3947 True 2476.600000 7291 100.000000 1 3948 3 chr1D.!!$R1 3947
1 TraesCS1D01G305200 chr1B 540719366 540723298 3932 True 3129.500000 5531 95.323000 1 3948 2 chr1B.!!$R1 3947
2 TraesCS1D01G305200 chr1A 498047707 498051611 3904 True 2174.666667 3245 96.526667 1 3948 3 chr1A.!!$R1 3947

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
568 577 1.073763 TGCAGAGAAAGCTAAAGGGCA 59.926 47.619 0.0 0.0 34.17 5.36 F
803 813 3.458118 TCAACCTGAGAAGACCAAAAGGA 59.542 43.478 0.0 0.0 0.00 3.36 F
1943 1956 1.238439 CACTCTCGTGCCAACCAAAT 58.762 50.000 0.0 0.0 33.82 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1751 3.719268 TTGCATAGTTCTGTCACCCAT 57.281 42.857 0.0 0.0 0.0 4.00 R
2022 2035 8.613482 GGTTCTTTAATTGCTAGACTGTATTCC 58.387 37.037 0.0 0.0 0.0 3.01 R
3643 3677 0.183492 ACTCTTGCCTTGCCTGTTGA 59.817 50.000 0.0 0.0 0.0 3.18 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
146 147 7.721286 ACAGAAAAATTGTGTTTTTGTGTGA 57.279 28.000 20.64 0.00 46.80 3.58
148 149 8.782144 ACAGAAAAATTGTGTTTTTGTGTGAAT 58.218 25.926 20.64 4.13 46.80 2.57
320 327 4.557205 ACTAAGGTAACAGAGAAGTTGCG 58.443 43.478 0.00 0.00 35.32 4.85
450 459 7.195374 TGCTCCAGTTGTAGGTATTTATTCT 57.805 36.000 0.00 0.00 0.00 2.40
451 460 7.047891 TGCTCCAGTTGTAGGTATTTATTCTG 58.952 38.462 0.00 0.00 0.00 3.02
452 461 7.048512 GCTCCAGTTGTAGGTATTTATTCTGT 58.951 38.462 0.00 0.00 0.00 3.41
453 462 8.202137 GCTCCAGTTGTAGGTATTTATTCTGTA 58.798 37.037 0.00 0.00 0.00 2.74
470 479 9.905713 TTATTCTGTAAGATAAATTGCTCCAGT 57.094 29.630 0.00 0.00 46.36 4.00
471 480 8.814038 ATTCTGTAAGATAAATTGCTCCAGTT 57.186 30.769 0.00 0.00 46.36 3.16
472 481 7.615582 TCTGTAAGATAAATTGCTCCAGTTG 57.384 36.000 0.00 0.00 38.67 3.16
473 482 7.168219 TCTGTAAGATAAATTGCTCCAGTTGT 58.832 34.615 0.00 0.00 38.67 3.32
474 483 8.318412 TCTGTAAGATAAATTGCTCCAGTTGTA 58.682 33.333 0.00 0.00 38.67 2.41
475 484 8.492673 TGTAAGATAAATTGCTCCAGTTGTAG 57.507 34.615 0.00 0.00 0.00 2.74
476 485 7.552687 TGTAAGATAAATTGCTCCAGTTGTAGG 59.447 37.037 0.00 0.00 0.00 3.18
477 486 6.067217 AGATAAATTGCTCCAGTTGTAGGT 57.933 37.500 0.00 0.00 0.00 3.08
478 487 7.195374 AGATAAATTGCTCCAGTTGTAGGTA 57.805 36.000 0.00 0.00 0.00 3.08
479 488 7.806180 AGATAAATTGCTCCAGTTGTAGGTAT 58.194 34.615 0.00 0.00 0.00 2.73
480 489 8.275040 AGATAAATTGCTCCAGTTGTAGGTATT 58.725 33.333 0.00 0.00 0.00 1.89
481 490 8.823220 ATAAATTGCTCCAGTTGTAGGTATTT 57.177 30.769 0.00 0.00 0.00 1.40
482 491 9.914834 ATAAATTGCTCCAGTTGTAGGTATTTA 57.085 29.630 0.00 0.00 0.00 1.40
483 492 8.823220 AAATTGCTCCAGTTGTAGGTATTTAT 57.177 30.769 0.00 0.00 0.00 1.40
484 493 8.823220 AATTGCTCCAGTTGTAGGTATTTATT 57.177 30.769 0.00 0.00 0.00 1.40
485 494 7.859325 TTGCTCCAGTTGTAGGTATTTATTC 57.141 36.000 0.00 0.00 0.00 1.75
492 501 9.095065 CCAGTTGTAGGTATTTATTCTGTACAC 57.905 37.037 0.00 0.00 0.00 2.90
566 575 4.704057 AGAAATGCAGAGAAAGCTAAAGGG 59.296 41.667 0.00 0.00 0.00 3.95
568 577 1.073763 TGCAGAGAAAGCTAAAGGGCA 59.926 47.619 0.00 0.00 34.17 5.36
636 646 8.361139 GTCACAGGTTGCTATTAGTACTGATAT 58.639 37.037 5.39 0.00 0.00 1.63
717 727 5.157067 GGTTAAAGATTGTTCTTCTGCTGC 58.843 41.667 0.00 0.00 41.42 5.25
803 813 3.458118 TCAACCTGAGAAGACCAAAAGGA 59.542 43.478 0.00 0.00 0.00 3.36
1047 1057 4.302559 TGAGCTCTTCACTACTAGGACA 57.697 45.455 16.19 0.00 0.00 4.02
1056 1066 4.748701 TCACTACTAGGACAACCTTTCCT 58.251 43.478 0.00 0.00 45.36 3.36
1837 1849 4.401022 TCGAGGTGAGGTACTGAAACTAA 58.599 43.478 0.00 0.00 41.55 2.24
1936 1949 1.606601 AGCTACCACTCTCGTGCCA 60.607 57.895 0.00 0.00 39.86 4.92
1943 1956 1.238439 CACTCTCGTGCCAACCAAAT 58.762 50.000 0.00 0.00 33.82 2.32
2002 2015 1.444119 TTTGAACGCTGCGCTTCCTT 61.444 50.000 23.51 8.38 0.00 3.36
2074 2087 2.738314 GAGCGAAAAAGCAATTTGGCAT 59.262 40.909 18.41 7.85 43.73 4.40
2893 2906 5.294306 TGATCTGAACACTCAAAACACTGAC 59.706 40.000 0.00 0.00 0.00 3.51
3050 3063 3.331150 TGGTGATTAAACTGCGTAGGTG 58.669 45.455 5.26 0.00 0.00 4.00
3058 3072 6.680874 TTAAACTGCGTAGGTGAAGAAAAA 57.319 33.333 5.26 0.00 0.00 1.94
3247 3262 6.352516 CAAAGATAGCTAGAGAACCACCAAT 58.647 40.000 0.00 0.00 0.00 3.16
3258 3273 0.739813 ACCACCAATCGAGTAAGCGC 60.740 55.000 0.00 0.00 0.00 5.92
3421 3436 3.009916 AGAAGCTATCCCTGCCATTATGG 59.990 47.826 6.92 6.92 41.55 2.74
3442 3457 1.795286 GGAGACTTTCAGCTCAACACG 59.205 52.381 0.00 0.00 32.83 4.49
3491 3513 6.578163 TCAATTGATGCAGACTTCATGAAA 57.422 33.333 9.88 0.00 30.75 2.69
3499 3521 6.060028 TGCAGACTTCATGAAAACAACTAC 57.940 37.500 9.88 1.09 0.00 2.73
3575 3609 5.580691 TCGTTCAACCAGCATATAAACTGAG 59.419 40.000 6.88 1.43 35.90 3.35
3603 3637 4.998671 ATTCATCCACACAACACAAACA 57.001 36.364 0.00 0.00 0.00 2.83
3614 3648 5.411053 ACACAACACAAACAATTTTTGAGGG 59.589 36.000 15.45 9.47 33.83 4.30
3615 3649 5.411053 CACAACACAAACAATTTTTGAGGGT 59.589 36.000 15.45 9.88 33.83 4.34
3629 3663 0.824759 GAGGGTAAGTCCATCGCAGT 59.175 55.000 0.00 0.00 37.27 4.40
3634 3668 3.187700 GGTAAGTCCATCGCAGTACTTG 58.812 50.000 0.00 0.00 34.23 3.16
3643 3677 6.479001 GTCCATCGCAGTACTTGTTTGTATAT 59.521 38.462 0.00 0.00 0.00 0.86
3646 3680 7.011016 CCATCGCAGTACTTGTTTGTATATCAA 59.989 37.037 0.00 0.00 0.00 2.57
3837 3881 7.062839 GCAAGAGCACTGTATTATAGAGTATGC 59.937 40.741 1.63 3.29 41.58 3.14
3886 3940 2.341543 CAGTGAGCGCTGGTGTCT 59.658 61.111 18.48 2.30 33.11 3.41
3887 3941 2.025969 CAGTGAGCGCTGGTGTCTG 61.026 63.158 18.48 11.80 33.11 3.51
3888 3942 2.029666 GTGAGCGCTGGTGTCTGT 59.970 61.111 18.48 0.00 0.00 3.41
3889 3943 2.024319 GTGAGCGCTGGTGTCTGTC 61.024 63.158 18.48 0.00 0.00 3.51
3900 3954 3.440127 TGGTGTCTGTCATCCACTCATA 58.560 45.455 0.00 0.00 0.00 2.15
3909 3963 2.630098 TCATCCACTCATAGCTGCTACC 59.370 50.000 12.26 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.678947 ATTCTCATTGTAGTCCAGAAAAGTG 57.321 36.000 0.00 0.00 0.00 3.16
146 147 3.181440 TGCCTTCTTGGAGAGTGACAATT 60.181 43.478 0.00 0.00 38.35 2.32
148 149 1.768275 TGCCTTCTTGGAGAGTGACAA 59.232 47.619 0.00 0.00 38.35 3.18
264 267 5.682943 TTAGTGTTGCTGGTTCATGTTAC 57.317 39.130 0.00 0.00 0.00 2.50
320 327 3.988379 TGCCGAGATGGAAATATTTGC 57.012 42.857 12.39 12.39 42.00 3.68
413 422 9.383519 CTACAACTGGAGCAATTTATCTTTCTA 57.616 33.333 0.00 0.00 0.00 2.10
450 459 7.552687 CCTACAACTGGAGCAATTTATCTTACA 59.447 37.037 0.00 0.00 0.00 2.41
451 460 7.553044 ACCTACAACTGGAGCAATTTATCTTAC 59.447 37.037 0.00 0.00 0.00 2.34
452 461 7.630082 ACCTACAACTGGAGCAATTTATCTTA 58.370 34.615 0.00 0.00 0.00 2.10
453 462 6.485171 ACCTACAACTGGAGCAATTTATCTT 58.515 36.000 0.00 0.00 0.00 2.40
454 463 6.067217 ACCTACAACTGGAGCAATTTATCT 57.933 37.500 0.00 0.00 0.00 1.98
455 464 8.451908 AATACCTACAACTGGAGCAATTTATC 57.548 34.615 0.00 0.00 0.00 1.75
456 465 8.823220 AAATACCTACAACTGGAGCAATTTAT 57.177 30.769 0.00 0.00 0.00 1.40
457 466 9.914834 ATAAATACCTACAACTGGAGCAATTTA 57.085 29.630 8.33 8.33 0.00 1.40
458 467 8.823220 ATAAATACCTACAACTGGAGCAATTT 57.177 30.769 0.00 5.54 0.00 1.82
459 468 8.823220 AATAAATACCTACAACTGGAGCAATT 57.177 30.769 0.00 0.00 0.00 2.32
460 469 8.275040 AGAATAAATACCTACAACTGGAGCAAT 58.725 33.333 0.00 0.00 0.00 3.56
461 470 7.552687 CAGAATAAATACCTACAACTGGAGCAA 59.447 37.037 0.00 0.00 0.00 3.91
462 471 7.047891 CAGAATAAATACCTACAACTGGAGCA 58.952 38.462 0.00 0.00 0.00 4.26
463 472 7.048512 ACAGAATAAATACCTACAACTGGAGC 58.951 38.462 0.00 0.00 0.00 4.70
464 473 9.530633 GTACAGAATAAATACCTACAACTGGAG 57.469 37.037 0.00 0.00 0.00 3.86
465 474 9.038072 TGTACAGAATAAATACCTACAACTGGA 57.962 33.333 0.00 0.00 0.00 3.86
466 475 9.095065 GTGTACAGAATAAATACCTACAACTGG 57.905 37.037 0.00 0.00 0.00 4.00
467 476 9.647797 TGTGTACAGAATAAATACCTACAACTG 57.352 33.333 0.00 0.00 0.00 3.16
480 489 9.470399 TCAGTAGAAGGTATGTGTACAGAATAA 57.530 33.333 0.00 0.00 32.25 1.40
481 490 9.642343 ATCAGTAGAAGGTATGTGTACAGAATA 57.358 33.333 0.00 0.00 32.25 1.75
482 491 7.956328 TCAGTAGAAGGTATGTGTACAGAAT 57.044 36.000 0.00 0.00 32.25 2.40
483 492 7.834681 AGATCAGTAGAAGGTATGTGTACAGAA 59.165 37.037 0.00 0.00 32.25 3.02
484 493 7.347252 AGATCAGTAGAAGGTATGTGTACAGA 58.653 38.462 0.00 0.00 32.25 3.41
485 494 7.575414 AGATCAGTAGAAGGTATGTGTACAG 57.425 40.000 0.00 0.00 32.25 2.74
566 575 3.421844 ACCCCTCAGTAATGAAACTTGC 58.578 45.455 0.00 0.00 0.00 4.01
568 577 5.836024 TGTACCCCTCAGTAATGAAACTT 57.164 39.130 0.00 0.00 0.00 2.66
717 727 9.979578 ACATAGAATCTAGCATCTTAGAACAAG 57.020 33.333 0.00 0.00 33.64 3.16
803 813 4.878397 GTGTGAGCTTAAGCCTGTTGATAT 59.122 41.667 23.71 1.50 43.38 1.63
1047 1057 2.562296 TGCCTCTCCATAGGAAAGGTT 58.438 47.619 7.23 0.00 41.78 3.50
1056 1066 3.432749 GCAGAAACAGATGCCTCTCCATA 60.433 47.826 0.00 0.00 36.41 2.74
1558 1570 4.128643 CAAAATTTCATGGCCTGTGTGTT 58.871 39.130 3.32 0.00 0.00 3.32
1739 1751 3.719268 TTGCATAGTTCTGTCACCCAT 57.281 42.857 0.00 0.00 0.00 4.00
1837 1849 8.947115 GTCTTGGTTAAGAGCTTATTACACAAT 58.053 33.333 0.00 0.00 43.29 2.71
2022 2035 8.613482 GGTTCTTTAATTGCTAGACTGTATTCC 58.387 37.037 0.00 0.00 0.00 3.01
2893 2906 3.617531 GCCTATACCCTTGATCACCATCG 60.618 52.174 0.00 0.00 0.00 3.84
2988 3001 9.956640 AAATGCCAGGAAAAATTATTTGTATGA 57.043 25.926 0.00 0.00 0.00 2.15
3058 3072 7.015877 TGGTTGAACTCTGGTGTACTAGTATTT 59.984 37.037 5.75 0.00 0.00 1.40
3247 3262 0.883153 TAAGTGTGGCGCTTACTCGA 59.117 50.000 7.64 0.00 35.69 4.04
3258 3273 6.094881 CCATGGTTTACCTGTATTAAGTGTGG 59.905 42.308 2.57 0.00 36.82 4.17
3421 3436 2.147150 GTGTTGAGCTGAAAGTCTCCC 58.853 52.381 0.00 0.00 36.63 4.30
3442 3457 6.147985 TGAACTGTTTGGTTTTGTTTTAAGCC 59.852 34.615 0.00 0.00 0.00 4.35
3487 3509 6.419484 TCTCTGAGATGGTAGTTGTTTTCA 57.581 37.500 2.58 0.00 0.00 2.69
3491 3513 8.816894 TCTTTATTCTCTGAGATGGTAGTTGTT 58.183 33.333 8.42 0.00 0.00 2.83
3575 3609 6.112734 TGTGTTGTGTGGATGAATAGATACC 58.887 40.000 0.00 0.00 0.00 2.73
3603 3637 4.157840 GCGATGGACTTACCCTCAAAAATT 59.842 41.667 0.00 0.00 38.00 1.82
3614 3648 3.846360 ACAAGTACTGCGATGGACTTAC 58.154 45.455 0.00 0.00 31.05 2.34
3615 3649 4.530710 AACAAGTACTGCGATGGACTTA 57.469 40.909 0.00 0.00 31.05 2.24
3629 3663 7.120579 CCTTGCCTGTTGATATACAAACAAGTA 59.879 37.037 13.79 0.00 40.36 2.24
3634 3668 4.157656 TGCCTTGCCTGTTGATATACAAAC 59.842 41.667 0.00 0.00 40.36 2.93
3643 3677 0.183492 ACTCTTGCCTTGCCTGTTGA 59.817 50.000 0.00 0.00 0.00 3.18
3646 3680 0.536006 GTGACTCTTGCCTTGCCTGT 60.536 55.000 0.00 0.00 0.00 4.00
3886 3940 2.113807 AGCAGCTATGAGTGGATGACA 58.886 47.619 0.00 0.00 0.00 3.58
3887 3941 2.906691 AGCAGCTATGAGTGGATGAC 57.093 50.000 0.00 0.00 0.00 3.06
3888 3942 2.630098 GGTAGCAGCTATGAGTGGATGA 59.370 50.000 5.14 0.00 0.00 2.92
3889 3943 2.366590 TGGTAGCAGCTATGAGTGGATG 59.633 50.000 5.14 0.00 0.00 3.51
3900 3954 3.970842 AGAAGTAGTAGTGGTAGCAGCT 58.029 45.455 0.00 0.00 0.00 4.24
3909 3963 3.707793 GCCGGATCAAGAAGTAGTAGTG 58.292 50.000 5.05 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.