Multiple sequence alignment - TraesCS2D01G412200

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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 TraesCS2D01G412200 chr2D 100.000 2645 0 0 1 2645 527005330 527002686 0.000000e+00 4885.0
1 TraesCS2D01G412200 chr2D 88.014 292 32 2 1083 1371 527272591 527272300 2.520000e-90 342.0
2 TraesCS2D01G412200 chr2B 93.795 2208 74 27 487 2642 623870615 623868419 0.000000e+00 3260.0
3 TraesCS2D01G412200 chr2B 94.043 470 24 4 1 466 623871071 623870602 0.000000e+00 710.0
4 TraesCS2D01G412200 chr2B 87.415 294 30 5 1083 1371 624287333 624287042 5.460000e-87 331.0
5 TraesCS2D01G412200 chr2A 91.063 2182 114 44 494 2628 672235501 672233354 0.000000e+00 2874.0
6 TraesCS2D01G412200 chr2A 87.205 297 33 4 1077 1371 672265711 672265418 1.520000e-87 333.0
7 TraesCS2D01G412200 chr2A 90.164 183 14 2 267 445 672235671 672235489 4.400000e-58 235.0
8 TraesCS2D01G412200 chr6A 81.315 578 75 19 1090 1643 465389760 465390328 3.130000e-119 438.0
9 TraesCS2D01G412200 chr6A 89.157 249 21 3 1117 1359 465316702 465316950 3.310000e-79 305.0
10 TraesCS2D01G412200 chr6D 80.844 569 82 20 1090 1643 326760684 326761240 3.150000e-114 422.0
11 TraesCS2D01G412200 chr6B 80.274 583 84 15 1090 1643 495543800 495543220 6.810000e-111 411.0
12 TraesCS2D01G412200 chr5A 82.105 95 11 3 1338 1432 8111600 8111512 2.820000e-10 76.8


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 TraesCS2D01G412200 chr2D 527002686 527005330 2644 True 4885.0 4885 100.0000 1 2645 1 chr2D.!!$R1 2644
1 TraesCS2D01G412200 chr2B 623868419 623871071 2652 True 1985.0 3260 93.9190 1 2642 2 chr2B.!!$R2 2641
2 TraesCS2D01G412200 chr2A 672233354 672235671 2317 True 1554.5 2874 90.6135 267 2628 2 chr2A.!!$R2 2361
3 TraesCS2D01G412200 chr6A 465389760 465390328 568 False 438.0 438 81.3150 1090 1643 1 chr6A.!!$F2 553
4 TraesCS2D01G412200 chr6D 326760684 326761240 556 False 422.0 422 80.8440 1090 1643 1 chr6D.!!$F1 553
5 TraesCS2D01G412200 chr6B 495543220 495543800 580 True 411.0 411 80.2740 1090 1643 1 chr6B.!!$R1 553

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
202 205 1.338769 CGGGAGATTTCGGGAAGTTGT 60.339 52.381 0.00 0.0 0.00 3.32 F
1080 1125 0.094901 CATCGTCGTCGTCTTCGTCT 59.905 55.000 1.33 0.0 38.33 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1326 1.003718 GTCCGGGAAGTTGAGGTGG 60.004 63.158 0.0 0.0 0.0 4.61 R
1945 2043 1.216178 CCCAAATCAAGCAAGGCCG 59.784 57.895 0.0 0.0 0.0 6.13 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
26 27 1.597663 CGAACTGTCTCCCAACACAAC 59.402 52.381 0.00 0.00 0.00 3.32
95 96 2.418197 CCTGTCGTCGGGTCATTTATGT 60.418 50.000 0.00 0.00 35.48 2.29
102 103 4.007659 GTCGGGTCATTTATGTGAGGTTT 58.992 43.478 0.00 0.00 0.00 3.27
128 129 3.897122 AGTTGGGCCGCTTTGGGA 61.897 61.111 0.00 0.00 38.63 4.37
184 187 6.955963 CGATCATAGTTTTTCTGTTCTTTCGG 59.044 38.462 0.00 0.00 0.00 4.30
198 201 2.093658 TCTTTCGGGAGATTTCGGGAAG 60.094 50.000 0.00 0.00 39.57 3.46
202 205 1.338769 CGGGAGATTTCGGGAAGTTGT 60.339 52.381 0.00 0.00 0.00 3.32
219 222 7.488150 GGGAAGTTGTTGTCTTTGTAAAAAGAG 59.512 37.037 8.41 0.00 39.26 2.85
438 447 9.627123 CAAATGGATACTAGGTTCAAGGAATTA 57.373 33.333 0.00 0.00 37.61 1.40
449 458 7.497595 AGGTTCAAGGAATTAAACACCTTTTC 58.502 34.615 0.00 0.00 41.33 2.29
463 472 3.646736 CCTTTTCTAGGGGTTCGGAAT 57.353 47.619 0.00 0.00 40.67 3.01
464 473 3.964411 CCTTTTCTAGGGGTTCGGAATT 58.036 45.455 0.00 0.00 40.67 2.17
465 474 5.106876 CCTTTTCTAGGGGTTCGGAATTA 57.893 43.478 0.00 0.00 40.67 1.40
466 475 5.691896 CCTTTTCTAGGGGTTCGGAATTAT 58.308 41.667 0.00 0.00 40.67 1.28
467 476 6.127101 CCTTTTCTAGGGGTTCGGAATTATT 58.873 40.000 0.00 0.00 40.67 1.40
468 477 7.284820 CCTTTTCTAGGGGTTCGGAATTATTA 58.715 38.462 0.00 0.00 40.67 0.98
469 478 7.942894 CCTTTTCTAGGGGTTCGGAATTATTAT 59.057 37.037 0.00 0.00 40.67 1.28
470 479 9.350951 CTTTTCTAGGGGTTCGGAATTATTATT 57.649 33.333 0.00 0.00 0.00 1.40
477 486 9.649316 AGGGGTTCGGAATTATTATTATTTTGA 57.351 29.630 0.00 0.00 0.00 2.69
483 492 9.160576 TCGGAATTATTATTATTTTGAAACGCG 57.839 29.630 3.53 3.53 0.00 6.01
484 493 8.414173 CGGAATTATTATTATTTTGAAACGCGG 58.586 33.333 12.47 0.00 0.00 6.46
485 494 9.240159 GGAATTATTATTATTTTGAAACGCGGT 57.760 29.630 12.47 0.00 0.00 5.68
487 496 7.972623 TTATTATTATTTTGAAACGCGGTGG 57.027 32.000 12.47 0.00 0.00 4.61
507 516 3.159472 GGGGTTCGGAATTAAACACCTT 58.841 45.455 10.45 0.00 44.12 3.50
832 875 3.308530 GGTTCAAATTTCAGCACTTCCG 58.691 45.455 0.00 0.00 0.00 4.30
948 993 2.681778 CGACCACTCTCCCCTGCT 60.682 66.667 0.00 0.00 0.00 4.24
950 995 1.610673 GACCACTCTCCCCTGCTCA 60.611 63.158 0.00 0.00 0.00 4.26
1071 1116 0.586748 CCTCGTCTTCATCGTCGTCG 60.587 60.000 0.00 0.00 38.55 5.12
1077 1122 1.172700 CTTCATCGTCGTCGTCTTCG 58.827 55.000 1.33 0.00 38.33 3.79
1080 1125 0.094901 CATCGTCGTCGTCTTCGTCT 59.905 55.000 1.33 0.00 38.33 4.18
1081 1126 0.369589 ATCGTCGTCGTCTTCGTCTC 59.630 55.000 1.33 0.00 38.33 3.36
1302 1347 1.296715 CCTCAACTTCCCGGACCTG 59.703 63.158 0.73 0.00 0.00 4.00
1758 1848 0.389948 GCACCTCGTTCCGTCAATCT 60.390 55.000 0.00 0.00 0.00 2.40
1764 1854 4.159879 ACCTCGTTCCGTCAATCTTCTTAT 59.840 41.667 0.00 0.00 0.00 1.73
1945 2043 9.511272 TGTATAAAGTTAGTTTCTTTTCCTCCC 57.489 33.333 0.00 0.00 36.65 4.30
1946 2044 7.683437 ATAAAGTTAGTTTCTTTTCCTCCCG 57.317 36.000 0.00 0.00 36.65 5.14
2111 2223 5.335191 GCATACTTTTCCTGACTTGACAAGG 60.335 44.000 19.16 2.28 0.00 3.61
2152 2264 3.622166 TTCCATTTTACTCTCCGGTCC 57.378 47.619 0.00 0.00 0.00 4.46
2155 2267 2.500098 CCATTTTACTCTCCGGTCCTCA 59.500 50.000 0.00 0.00 0.00 3.86
2158 2270 1.676746 TTACTCTCCGGTCCTCATCG 58.323 55.000 0.00 0.00 0.00 3.84
2189 2301 1.143969 CGCAACGGTAGGATTCGTCC 61.144 60.000 0.00 0.00 38.78 4.79
2289 2401 4.367023 GCAGTGGCGGTGGTACGA 62.367 66.667 0.00 0.00 35.47 3.43
2386 2498 1.065926 GGGTTCCCGGGTTACTGTAAG 60.066 57.143 22.86 0.00 42.29 2.34
2435 2553 2.025418 CGTTCTCGTCAAACCCCCG 61.025 63.158 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.932699 TTTTGCAATTTAACATTTGTTGATCAG 57.067 25.926 0.00 0.00 38.90 2.90
76 77 2.231721 TCACATAAATGACCCGACGACA 59.768 45.455 0.00 0.00 0.00 4.35
95 96 3.194542 CCCAACTGTTTCACAAAACCTCA 59.805 43.478 0.00 0.00 43.44 3.86
102 103 2.010582 GCGGCCCAACTGTTTCACAA 62.011 55.000 0.00 0.00 0.00 3.33
111 112 3.224007 ATCCCAAAGCGGCCCAACT 62.224 57.895 0.00 0.00 0.00 3.16
182 185 1.338769 ACAACTTCCCGAAATCTCCCG 60.339 52.381 0.00 0.00 0.00 5.14
184 187 3.146847 ACAACAACTTCCCGAAATCTCC 58.853 45.455 0.00 0.00 0.00 3.71
202 205 9.445786 CGCTTAAATCTCTTTTTACAAAGACAA 57.554 29.630 0.00 0.00 42.99 3.18
219 222 8.620533 AGCAAATGATTTTACTCGCTTAAATC 57.379 30.769 0.00 0.00 38.27 2.17
252 256 7.535489 ACTAATTTATTACAACGTCTCTGCC 57.465 36.000 0.00 0.00 0.00 4.85
253 257 9.897349 GTTACTAATTTATTACAACGTCTCTGC 57.103 33.333 0.00 0.00 0.00 4.26
438 447 3.483421 CGAACCCCTAGAAAAGGTGTTT 58.517 45.455 0.00 0.00 44.99 2.83
457 466 9.160576 CGCGTTTCAAAATAATAATAATTCCGA 57.839 29.630 0.00 0.00 0.00 4.55
458 467 8.414173 CCGCGTTTCAAAATAATAATAATTCCG 58.586 33.333 4.92 0.00 0.00 4.30
459 468 9.240159 ACCGCGTTTCAAAATAATAATAATTCC 57.760 29.630 4.92 0.00 0.00 3.01
461 470 9.026074 CCACCGCGTTTCAAAATAATAATAATT 57.974 29.630 4.92 0.00 0.00 1.40
462 471 7.650104 CCCACCGCGTTTCAAAATAATAATAAT 59.350 33.333 4.92 0.00 0.00 1.28
463 472 6.973474 CCCACCGCGTTTCAAAATAATAATAA 59.027 34.615 4.92 0.00 0.00 1.40
464 473 6.459848 CCCCACCGCGTTTCAAAATAATAATA 60.460 38.462 4.92 0.00 0.00 0.98
465 474 5.344884 CCCACCGCGTTTCAAAATAATAAT 58.655 37.500 4.92 0.00 0.00 1.28
466 475 4.380655 CCCCACCGCGTTTCAAAATAATAA 60.381 41.667 4.92 0.00 0.00 1.40
467 476 3.128938 CCCCACCGCGTTTCAAAATAATA 59.871 43.478 4.92 0.00 0.00 0.98
468 477 2.094442 CCCCACCGCGTTTCAAAATAAT 60.094 45.455 4.92 0.00 0.00 1.28
469 478 1.269998 CCCCACCGCGTTTCAAAATAA 59.730 47.619 4.92 0.00 0.00 1.40
470 479 0.882474 CCCCACCGCGTTTCAAAATA 59.118 50.000 4.92 0.00 0.00 1.40
471 480 1.110518 ACCCCACCGCGTTTCAAAAT 61.111 50.000 4.92 0.00 0.00 1.82
472 481 1.321074 AACCCCACCGCGTTTCAAAA 61.321 50.000 4.92 0.00 0.00 2.44
473 482 1.726533 GAACCCCACCGCGTTTCAAA 61.727 55.000 4.92 0.00 0.00 2.69
474 483 2.124236 AACCCCACCGCGTTTCAA 60.124 55.556 4.92 0.00 0.00 2.69
475 484 2.592287 GAACCCCACCGCGTTTCA 60.592 61.111 4.92 0.00 0.00 2.69
476 485 3.719144 CGAACCCCACCGCGTTTC 61.719 66.667 4.92 0.00 0.00 2.78
480 489 2.855880 TAATTCCGAACCCCACCGCG 62.856 60.000 0.00 0.00 0.00 6.46
481 490 0.677414 TTAATTCCGAACCCCACCGC 60.677 55.000 0.00 0.00 0.00 5.68
482 491 1.469703 GTTTAATTCCGAACCCCACCG 59.530 52.381 0.00 0.00 0.00 4.94
483 492 2.229543 GTGTTTAATTCCGAACCCCACC 59.770 50.000 0.00 0.00 0.00 4.61
484 493 2.229543 GGTGTTTAATTCCGAACCCCAC 59.770 50.000 0.00 0.00 0.00 4.61
485 494 2.108601 AGGTGTTTAATTCCGAACCCCA 59.891 45.455 0.00 0.00 0.00 4.96
486 495 2.799017 AGGTGTTTAATTCCGAACCCC 58.201 47.619 0.00 0.00 0.00 4.95
487 496 3.613193 GCAAGGTGTTTAATTCCGAACCC 60.613 47.826 0.00 0.00 0.00 4.11
507 516 7.175467 CCAATATAAGAGTATCAAATGCCTGCA 59.825 37.037 0.00 0.00 37.82 4.41
633 650 1.405105 CGGCCCATGAAAACTATGTGG 59.595 52.381 0.00 0.00 0.00 4.17
640 657 0.609681 TACACCCGGCCCATGAAAAC 60.610 55.000 0.00 0.00 0.00 2.43
832 875 4.754618 AGAAAATTGCGGGGAAAAACAATC 59.245 37.500 0.00 0.00 31.75 2.67
1077 1122 2.430244 TTGTTCGCGGCGAGAGAC 60.430 61.111 25.02 20.28 37.14 3.36
1281 1326 1.003718 GTCCGGGAAGTTGAGGTGG 60.004 63.158 0.00 0.00 0.00 4.61
1725 1815 2.679059 CGAGGTGCATTTCCATGTCTCT 60.679 50.000 0.00 0.00 32.28 3.10
1764 1854 6.089476 CGACGACGTCCTAGATAGATAGTAA 58.911 44.000 21.63 0.00 34.56 2.24
1945 2043 1.216178 CCCAAATCAAGCAAGGCCG 59.784 57.895 0.00 0.00 0.00 6.13
1946 2044 1.598517 CCCCAAATCAAGCAAGGCC 59.401 57.895 0.00 0.00 0.00 5.19
2111 2223 2.024176 TGCTTAAATGTCGCTCTCCC 57.976 50.000 0.00 0.00 0.00 4.30
2152 2264 3.916544 TGGGCCGCTAGCGATGAG 61.917 66.667 37.39 21.55 45.17 2.90
2189 2301 1.503542 GTTGCATGGCCTTGACGAG 59.496 57.895 22.21 0.00 0.00 4.18
2289 2401 4.022849 GCTTTCAAGCCATTGTAGACTTGT 60.023 41.667 0.00 0.00 46.20 3.16
2291 2403 4.773323 GCTTTCAAGCCATTGTAGACTT 57.227 40.909 0.00 0.00 46.20 3.01
2401 2513 5.347907 ACGAGAACGGACATCAATAACTTTC 59.652 40.000 0.00 0.00 44.46 2.62
2411 2524 1.725164 GGTTTGACGAGAACGGACATC 59.275 52.381 0.00 0.00 44.46 3.06
2415 2533 1.368579 GGGGTTTGACGAGAACGGA 59.631 57.895 0.00 0.00 44.46 4.69
2419 2537 2.031465 GCGGGGGTTTGACGAGAA 59.969 61.111 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.