Multiple sequence alignment - TraesCS3A01G348900

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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 TraesCS3A01G348900 chr3A 100.000 2639 0 0 1 2639 597548730 597546092 0.000000e+00 4874
1 TraesCS3A01G348900 chr3B 91.920 2302 113 31 372 2639 598469232 598466970 0.000000e+00 3153
2 TraesCS3A01G348900 chr3D 92.588 1700 76 24 372 2044 455107566 455105890 0.000000e+00 2396
3 TraesCS3A01G348900 chr3D 92.122 622 20 6 2043 2639 455105823 455105206 0.000000e+00 850
4 TraesCS3A01G348900 chr3D 90.566 477 40 3 1 476 455107893 455107421 6.200000e-176 627
5 TraesCS3A01G348900 chr1B 87.981 416 46 4 1084 1497 422563208 422562795 3.050000e-134 488
6 TraesCS3A01G348900 chr1B 86.553 409 53 2 1082 1489 529288208 529288615 1.440000e-122 449
7 TraesCS3A01G348900 chr1A 87.981 416 46 4 1084 1497 392084936 392084523 3.050000e-134 488
8 TraesCS3A01G348900 chr1A 86.874 419 51 4 1072 1488 492046051 492046467 1.430000e-127 466
9 TraesCS3A01G348900 chr1D 87.740 416 47 4 1084 1497 311988723 311988310 1.420000e-132 483
10 TraesCS3A01G348900 chr1D 87.775 409 48 2 1082 1489 393750478 393750071 6.610000e-131 477
11 TraesCS3A01G348900 chr6D 82.564 390 64 4 1084 1471 94602367 94602754 9.050000e-90 340


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 TraesCS3A01G348900 chr3A 597546092 597548730 2638 True 4874 4874 100.000000 1 2639 1 chr3A.!!$R1 2638
1 TraesCS3A01G348900 chr3B 598466970 598469232 2262 True 3153 3153 91.920000 372 2639 1 chr3B.!!$R1 2267
2 TraesCS3A01G348900 chr3D 455105206 455107893 2687 True 1291 2396 91.758667 1 2639 3 chr3D.!!$R1 2638

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
647 662 0.102481 ATGCTCATACGACCGACACC 59.898 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2442 0.106967 GTCAAATGGAGGAGGAGGGC 60.107 60.0 0.0 0.0 0.0 5.19 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
21 22 0.458889 TCGGGTTTCTGTTATCGCCG 60.459 55.000 0.00 0.00 0.00 6.46
32 33 4.219725 TCTGTTATCGCCGATAATCCATCA 59.780 41.667 21.16 13.24 36.96 3.07
50 51 5.250543 TCCATCAACACTATGGAGGAAGAAA 59.749 40.000 0.67 0.00 46.29 2.52
58 59 3.574354 ATGGAGGAAGAAAGGATGCTC 57.426 47.619 0.00 0.00 33.71 4.26
80 81 0.332972 GGGGGAAAGAAGGCAGATGT 59.667 55.000 0.00 0.00 0.00 3.06
81 82 1.467920 GGGGAAAGAAGGCAGATGTG 58.532 55.000 0.00 0.00 0.00 3.21
86 87 1.901591 AAGAAGGCAGATGTGTGTGG 58.098 50.000 0.00 0.00 0.00 4.17
88 89 0.962356 GAAGGCAGATGTGTGTGGGG 60.962 60.000 0.00 0.00 0.00 4.96
112 113 1.947456 GACGGGTTGAGTGCTTTTTCT 59.053 47.619 0.00 0.00 0.00 2.52
142 143 1.364626 GGTTCTAGACGCGTCGAGGA 61.365 60.000 37.46 31.65 33.85 3.71
155 156 2.129607 GTCGAGGAGTGCGTTTTGTAA 58.870 47.619 0.00 0.00 0.00 2.41
160 161 1.534163 GGAGTGCGTTTTGTAAGGACC 59.466 52.381 0.00 0.00 0.00 4.46
258 260 2.433436 GGACCATGCGTTACCTTTTCT 58.567 47.619 0.00 0.00 0.00 2.52
264 266 2.331194 TGCGTTACCTTTTCTAGCGTC 58.669 47.619 0.00 0.00 0.00 5.19
274 276 3.390521 CTAGCGTCAGGTGGGGCA 61.391 66.667 0.00 0.00 0.00 5.36
275 277 2.687200 TAGCGTCAGGTGGGGCAT 60.687 61.111 0.00 0.00 0.00 4.40
282 284 3.511610 AGGTGGGGCATATGGGGC 61.512 66.667 4.56 0.00 0.00 5.80
287 289 2.606587 GGGGCATATGGGGCGAGAT 61.607 63.158 4.56 0.00 0.00 2.75
294 296 3.057946 GCATATGGGGCGAGATTCTTTTC 60.058 47.826 4.56 0.00 0.00 2.29
295 297 2.058593 ATGGGGCGAGATTCTTTTCC 57.941 50.000 0.00 0.00 0.00 3.13
297 299 1.340017 TGGGGCGAGATTCTTTTCCAG 60.340 52.381 0.00 0.00 0.00 3.86
302 304 4.457949 GGGCGAGATTCTTTTCCAGTTAAA 59.542 41.667 0.00 0.00 0.00 1.52
309 311 7.147976 AGATTCTTTTCCAGTTAAATGTGTGC 58.852 34.615 1.80 0.00 0.00 4.57
318 320 0.250510 TAAATGTGTGCCGTGGAGCA 60.251 50.000 0.00 0.00 41.46 4.26
325 327 1.208293 TGTGCCGTGGAGCAATATACA 59.792 47.619 0.00 0.00 46.19 2.29
333 335 4.878439 GTGGAGCAATATACACGTCCATA 58.122 43.478 0.00 0.00 36.50 2.74
367 369 6.429521 AATATGTATTTACTGGGTAGGCGT 57.570 37.500 0.00 0.00 0.00 5.68
443 445 8.726870 AAACTATAAATACGCACATACCAACT 57.273 30.769 0.00 0.00 0.00 3.16
444 446 8.726870 AACTATAAATACGCACATACCAACTT 57.273 30.769 0.00 0.00 0.00 2.66
445 447 8.726870 ACTATAAATACGCACATACCAACTTT 57.273 30.769 0.00 0.00 0.00 2.66
446 448 9.820725 ACTATAAATACGCACATACCAACTTTA 57.179 29.630 0.00 0.00 0.00 1.85
449 451 9.944663 ATAAATACGCACATACCAACTTTAATG 57.055 29.630 0.00 0.00 0.00 1.90
450 452 4.091453 ACGCACATACCAACTTTAATGC 57.909 40.909 0.00 0.00 0.00 3.56
452 454 3.425625 CGCACATACCAACTTTAATGCGT 60.426 43.478 7.09 0.00 47.00 5.24
453 455 4.481463 GCACATACCAACTTTAATGCGTT 58.519 39.130 0.00 0.00 0.00 4.84
454 456 4.557301 GCACATACCAACTTTAATGCGTTC 59.443 41.667 0.00 0.00 0.00 3.95
455 457 5.694816 CACATACCAACTTTAATGCGTTCA 58.305 37.500 0.00 0.00 0.00 3.18
456 458 6.321717 CACATACCAACTTTAATGCGTTCAT 58.678 36.000 0.00 0.00 33.53 2.57
457 459 7.468441 CACATACCAACTTTAATGCGTTCATA 58.532 34.615 0.00 0.00 31.46 2.15
458 460 8.128582 CACATACCAACTTTAATGCGTTCATAT 58.871 33.333 0.00 0.00 31.46 1.78
459 461 9.332502 ACATACCAACTTTAATGCGTTCATATA 57.667 29.630 0.00 0.00 31.46 0.86
463 465 9.349145 ACCAACTTTAATGCGTTCATATAAAAC 57.651 29.630 0.00 0.00 31.46 2.43
464 466 9.567848 CCAACTTTAATGCGTTCATATAAAACT 57.432 29.630 0.00 0.00 31.46 2.66
545 547 7.690228 TGTTGGATAAGCATGTTCGTATAAAC 58.310 34.615 0.00 0.00 0.00 2.01
642 657 7.027760 ACTATAAATACATGCTCATACGACCG 58.972 38.462 0.00 0.00 0.00 4.79
647 662 0.102481 ATGCTCATACGACCGACACC 59.898 55.000 0.00 0.00 0.00 4.16
683 698 3.832490 CTGCACCAGGTATACCTAGCATA 59.168 47.826 30.36 17.80 46.65 3.14
684 699 4.425772 TGCACCAGGTATACCTAGCATAT 58.574 43.478 28.33 10.68 46.65 1.78
685 700 5.585894 TGCACCAGGTATACCTAGCATATA 58.414 41.667 28.33 14.87 46.65 0.86
686 701 6.202331 TGCACCAGGTATACCTAGCATATAT 58.798 40.000 28.33 6.07 46.65 0.86
729 744 3.501040 AATTGTTCGGGCACGGGGT 62.501 57.895 9.32 0.00 41.39 4.95
814 829 7.103641 TCCATTTCAGTAGTAACATTCACCTC 58.896 38.462 0.00 0.00 0.00 3.85
944 959 2.415224 CCACTGATCACTCACTCGTCAG 60.415 54.545 0.00 0.00 41.47 3.51
1098 1113 2.975732 CTCAGCTGAGCAGGTATGAA 57.024 50.000 29.79 0.00 37.39 2.57
1245 1260 4.235762 ACCAAGGTGCACGTCGCT 62.236 61.111 13.21 0.00 43.06 4.93
1711 1726 3.008835 AGGCATAGCAAGATTTGAGCA 57.991 42.857 0.00 0.00 0.00 4.26
1714 1729 4.404715 AGGCATAGCAAGATTTGAGCATTT 59.595 37.500 0.00 0.00 0.00 2.32
1809 1825 2.615912 AGTACTATTACAGGGCGTCGTC 59.384 50.000 0.00 0.00 0.00 4.20
1810 1826 0.743097 ACTATTACAGGGCGTCGTCC 59.257 55.000 8.12 8.12 0.00 4.79
1838 1854 6.301169 AGTGTTCTAGGGGAAGTGAATTAG 57.699 41.667 0.00 0.00 34.23 1.73
1942 1968 6.824553 TCTTATGCTACATCTCAGCTTGATT 58.175 36.000 0.00 0.00 39.83 2.57
2062 2165 7.061094 GCAAACTAGTAATCAATTCTTGCACAC 59.939 37.037 14.96 0.00 37.26 3.82
2112 2215 4.981674 CGTTTCTTGCTTAATTGGCAGAAA 59.018 37.500 17.49 17.49 40.90 2.52
2117 2223 4.503741 TGCTTAATTGGCAGAAACACTC 57.496 40.909 4.21 0.00 34.56 3.51
2150 2263 9.396022 TGGTTTATTTCTATTTTCTCCTAGCTG 57.604 33.333 0.00 0.00 0.00 4.24
2327 2442 2.355132 GCCAATCTCTTGCTCTGACATG 59.645 50.000 0.00 0.00 0.00 3.21
2331 2446 0.252479 CTCTTGCTCTGACATGCCCT 59.748 55.000 0.00 0.00 0.00 5.19
2418 2533 1.279558 AGACCAGAGAGAGAGCGTGTA 59.720 52.381 0.00 0.00 0.00 2.90
2423 2538 2.421775 CAGAGAGAGAGCGTGTATGTGT 59.578 50.000 0.00 0.00 0.00 3.72
2424 2539 2.421775 AGAGAGAGAGCGTGTATGTGTG 59.578 50.000 0.00 0.00 0.00 3.82
2425 2540 2.162608 GAGAGAGAGCGTGTATGTGTGT 59.837 50.000 0.00 0.00 0.00 3.72
2426 2541 2.095008 AGAGAGAGCGTGTATGTGTGTG 60.095 50.000 0.00 0.00 0.00 3.82
2427 2542 1.613925 AGAGAGCGTGTATGTGTGTGT 59.386 47.619 0.00 0.00 0.00 3.72
2471 2586 1.670811 CTTGCGGTTTCTAATGGCGAT 59.329 47.619 0.00 0.00 0.00 4.58
2472 2587 1.013596 TGCGGTTTCTAATGGCGATG 58.986 50.000 0.00 0.00 0.00 3.84
2478 2593 2.533266 TTCTAATGGCGATGGAGAGC 57.467 50.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.102420 AGTGTTGATGGATTATCGGCGA 59.898 45.455 13.87 13.87 38.71 5.54
32 33 5.749462 CATCCTTTCTTCCTCCATAGTGTT 58.251 41.667 0.00 0.00 0.00 3.32
46 47 2.187946 CCCGCGAGCATCCTTTCT 59.812 61.111 8.23 0.00 0.00 2.52
58 59 4.715523 TGCCTTCTTTCCCCCGCG 62.716 66.667 0.00 0.00 0.00 6.46
86 87 2.606826 ACTCAACCCGTCTCCCCC 60.607 66.667 0.00 0.00 0.00 5.40
88 89 2.047179 GCACTCAACCCGTCTCCC 60.047 66.667 0.00 0.00 0.00 4.30
98 99 3.766591 TCACCCAAAGAAAAAGCACTCAA 59.233 39.130 0.00 0.00 0.00 3.02
112 113 1.982958 GTCTAGAACCCCTCACCCAAA 59.017 52.381 0.00 0.00 0.00 3.28
142 143 2.158871 TCTGGTCCTTACAAAACGCACT 60.159 45.455 0.00 0.00 0.00 4.40
160 161 2.743928 GCACGCCCTTGGACTCTG 60.744 66.667 0.00 0.00 0.00 3.35
187 188 4.024556 CGCTATTTTCACCTGCTTCATAGG 60.025 45.833 0.00 0.00 41.22 2.57
244 246 2.288334 TGACGCTAGAAAAGGTAACGCA 60.288 45.455 0.00 0.00 46.39 5.24
246 248 2.921754 CCTGACGCTAGAAAAGGTAACG 59.078 50.000 0.00 0.00 46.39 3.18
258 260 0.762842 ATATGCCCCACCTGACGCTA 60.763 55.000 0.00 0.00 0.00 4.26
264 266 2.522503 CCCCATATGCCCCACCTG 59.477 66.667 0.00 0.00 0.00 4.00
274 276 3.138283 TGGAAAAGAATCTCGCCCCATAT 59.862 43.478 0.00 0.00 0.00 1.78
275 277 2.507886 TGGAAAAGAATCTCGCCCCATA 59.492 45.455 0.00 0.00 0.00 2.74
282 284 7.535258 CACACATTTAACTGGAAAAGAATCTCG 59.465 37.037 0.00 0.00 0.00 4.04
287 289 5.596845 GGCACACATTTAACTGGAAAAGAA 58.403 37.500 0.00 0.00 0.00 2.52
294 296 1.068610 CCACGGCACACATTTAACTGG 60.069 52.381 0.00 0.00 0.00 4.00
295 297 1.876799 TCCACGGCACACATTTAACTG 59.123 47.619 0.00 0.00 0.00 3.16
297 299 1.401018 GCTCCACGGCACACATTTAAC 60.401 52.381 0.00 0.00 0.00 2.01
302 304 0.035534 TATTGCTCCACGGCACACAT 60.036 50.000 0.00 0.00 42.27 3.21
349 351 3.531934 ACACGCCTACCCAGTAAATAC 57.468 47.619 0.00 0.00 0.00 1.89
352 354 1.693062 TGAACACGCCTACCCAGTAAA 59.307 47.619 0.00 0.00 0.00 2.01
396 398 1.003851 TATAAACGCGTCTTGCCAGC 58.996 50.000 14.44 0.00 42.08 4.85
462 464 9.472361 CAAAGCTGGTATGTACGTATTTATAGT 57.528 33.333 0.00 0.00 0.00 2.12
463 465 9.687210 TCAAAGCTGGTATGTACGTATTTATAG 57.313 33.333 0.00 0.00 0.00 1.31
464 466 9.467258 GTCAAAGCTGGTATGTACGTATTTATA 57.533 33.333 0.00 0.00 0.00 0.98
465 467 7.168637 CGTCAAAGCTGGTATGTACGTATTTAT 59.831 37.037 0.00 0.00 0.00 1.40
466 468 6.473131 CGTCAAAGCTGGTATGTACGTATTTA 59.527 38.462 0.00 0.00 0.00 1.40
467 469 5.290158 CGTCAAAGCTGGTATGTACGTATTT 59.710 40.000 0.00 0.00 0.00 1.40
468 470 4.802039 CGTCAAAGCTGGTATGTACGTATT 59.198 41.667 0.00 0.00 0.00 1.89
469 471 4.357142 CGTCAAAGCTGGTATGTACGTAT 58.643 43.478 0.00 0.00 0.00 3.06
470 472 3.761657 CGTCAAAGCTGGTATGTACGTA 58.238 45.455 0.00 0.00 0.00 3.57
471 473 2.602878 CGTCAAAGCTGGTATGTACGT 58.397 47.619 0.00 0.00 0.00 3.57
472 474 1.323534 GCGTCAAAGCTGGTATGTACG 59.676 52.381 0.00 0.00 0.00 3.67
473 475 1.323534 CGCGTCAAAGCTGGTATGTAC 59.676 52.381 0.00 0.00 34.40 2.90
474 476 1.067425 ACGCGTCAAAGCTGGTATGTA 60.067 47.619 5.58 0.00 34.40 2.29
475 477 0.320421 ACGCGTCAAAGCTGGTATGT 60.320 50.000 5.58 0.00 34.40 2.29
476 478 0.796312 AACGCGTCAAAGCTGGTATG 59.204 50.000 14.44 0.00 34.40 2.39
477 479 1.076332 GAACGCGTCAAAGCTGGTAT 58.924 50.000 14.44 0.00 34.40 2.73
478 480 0.249531 TGAACGCGTCAAAGCTGGTA 60.250 50.000 14.44 0.00 31.51 3.25
479 481 0.884704 ATGAACGCGTCAAAGCTGGT 60.885 50.000 14.44 0.00 40.50 4.00
480 482 1.075542 TATGAACGCGTCAAAGCTGG 58.924 50.000 14.44 0.00 40.50 4.85
481 483 4.514545 TTATATGAACGCGTCAAAGCTG 57.485 40.909 14.44 0.00 40.50 4.24
533 535 8.286800 GCATGCATTTATAGGTTTATACGAACA 58.713 33.333 14.21 0.00 0.00 3.18
586 601 2.030717 ACGCGTTTATCCAACAAATGCA 60.031 40.909 5.58 0.00 44.48 3.96
642 657 2.430921 CGTCTGTGGCTCGGTGTC 60.431 66.667 0.00 0.00 0.00 3.67
683 698 6.040616 GGGCGTATAGAAGTGCATACCTATAT 59.959 42.308 12.12 2.41 0.00 0.86
684 699 5.359009 GGGCGTATAGAAGTGCATACCTATA 59.641 44.000 0.00 0.00 0.00 1.31
685 700 4.159879 GGGCGTATAGAAGTGCATACCTAT 59.840 45.833 0.00 0.00 0.00 2.57
686 701 3.508793 GGGCGTATAGAAGTGCATACCTA 59.491 47.826 0.00 0.00 0.00 3.08
1080 1095 1.134580 GCTTCATACCTGCTCAGCTGA 60.135 52.381 17.19 17.19 0.00 4.26
1398 1413 2.905880 AGGTAGATCCGGACGGCG 60.906 66.667 6.12 4.80 41.99 6.46
1595 1610 2.583441 CCACCGTCTCCAGCTCCAA 61.583 63.158 0.00 0.00 0.00 3.53
1711 1726 4.996758 GCAACAAAGCATACCAAAGGAAAT 59.003 37.500 0.00 0.00 0.00 2.17
1714 1729 2.298729 GGCAACAAAGCATACCAAAGGA 59.701 45.455 0.00 0.00 35.83 3.36
1810 1826 5.507637 TCACTTCCCCTAGAACACTACTAG 58.492 45.833 0.00 0.00 37.61 2.57
1838 1854 3.641437 TGAACAATTAGCTGTGCCAAC 57.359 42.857 0.00 0.00 0.00 3.77
1929 1955 4.202101 CGGAGTACTCAATCAAGCTGAGAT 60.202 45.833 23.91 1.74 42.51 2.75
1942 1968 5.723672 AAGAGAAATGAACGGAGTACTCA 57.276 39.130 23.91 4.69 45.00 3.41
2004 2035 2.447887 GCGAGTGCACCGATCACAG 61.448 63.158 25.37 6.53 42.15 3.66
2105 2208 2.096496 CCATTCATCGAGTGTTTCTGCC 59.904 50.000 0.00 0.00 0.00 4.85
2112 2215 8.964476 ATAGAAATAAACCATTCATCGAGTGT 57.036 30.769 0.00 0.00 0.00 3.55
2150 2263 1.898902 TCCTAGCGATCTACTCCAGC 58.101 55.000 0.00 0.00 0.00 4.85
2273 2388 3.047877 GCCGTCCGGGAACTGTTG 61.048 66.667 7.97 0.00 38.47 3.33
2327 2442 0.106967 GTCAAATGGAGGAGGAGGGC 60.107 60.000 0.00 0.00 0.00 5.19
2331 2446 2.242196 GGAATGGTCAAATGGAGGAGGA 59.758 50.000 0.00 0.00 0.00 3.71
2418 2533 5.504853 TCTATCTCTCTCTCACACACACAT 58.495 41.667 0.00 0.00 0.00 3.21
2423 2538 6.183347 TGTTCATCTATCTCTCTCTCACACA 58.817 40.000 0.00 0.00 0.00 3.72
2424 2539 6.318648 ACTGTTCATCTATCTCTCTCTCACAC 59.681 42.308 0.00 0.00 0.00 3.82
2425 2540 6.422333 ACTGTTCATCTATCTCTCTCTCACA 58.578 40.000 0.00 0.00 0.00 3.58
2426 2541 6.942532 ACTGTTCATCTATCTCTCTCTCAC 57.057 41.667 0.00 0.00 0.00 3.51
2427 2542 7.345691 AGAACTGTTCATCTATCTCTCTCTCA 58.654 38.462 21.50 0.00 0.00 3.27
2471 2586 0.689055 ACTGTTCATGCAGCTCTCCA 59.311 50.000 0.00 0.00 39.96 3.86
2472 2587 1.736681 GAACTGTTCATGCAGCTCTCC 59.263 52.381 15.34 0.00 39.96 3.71
2537 2672 1.296715 CTCTCCGGACAAACCCCTG 59.703 63.158 0.00 0.00 34.64 4.45


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

AutoCloner maintained by Alex Coulton.