Multiple sequence alignment - TraesCS7D01G262900

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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 TraesCS7D01G262900 chr7D 100.000 4013 0 0 1 4013 242407640 242411652 0.000000e+00 7411.0
1 TraesCS7D01G262900 chr7B 95.274 3555 119 28 1 3534 218382411 218385937 0.000000e+00 5589.0
2 TraesCS7D01G262900 chr7B 93.515 478 31 0 3533 4010 218385973 218386450 0.000000e+00 712.0
3 TraesCS7D01G262900 chr7B 87.600 250 31 0 3746 3995 540335117 540334868 1.410000e-74 291.0
4 TraesCS7D01G262900 chr7B 92.958 71 5 0 1841 1911 224735982 224735912 1.970000e-18 104.0
5 TraesCS7D01G262900 chr7A 92.991 3524 151 43 1 3505 255581785 255578339 0.000000e+00 5051.0
6 TraesCS7D01G262900 chr7A 82.456 114 16 3 3311 3422 254917264 254917153 3.300000e-16 97.1
7 TraesCS7D01G262900 chr1D 83.436 489 58 11 3525 4011 50706035 50706502 2.220000e-117 433.0
8 TraesCS7D01G262900 chr3B 83.227 471 76 3 3529 3997 28141657 28142126 2.870000e-116 429.0
9 TraesCS7D01G262900 chr1A 84.514 381 53 4 3633 4011 49886845 49887221 4.900000e-99 372.0
10 TraesCS7D01G262900 chr5B 85.818 275 39 0 3737 4011 704832183 704832457 3.920000e-75 292.0
11 TraesCS7D01G262900 chr5B 76.890 463 91 12 3537 3996 564466518 564466069 8.610000e-62 248.0
12 TraesCS7D01G262900 chr4B 86.415 265 36 0 3746 4010 668658568 668658832 1.410000e-74 291.0
13 TraesCS7D01G262900 chrUn 86.590 261 35 0 3737 3997 29317585 29317325 5.070000e-74 289.0
14 TraesCS7D01G262900 chr2B 78.065 465 78 21 3537 3996 738676274 738676719 5.110000e-69 272.0
15 TraesCS7D01G262900 chr6B 92.958 71 5 0 1841 1911 33295876 33295946 1.970000e-18 104.0
16 TraesCS7D01G262900 chr4D 91.549 71 6 0 1841 1911 356511510 356511440 9.180000e-17 99.0


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 TraesCS7D01G262900 chr7D 242407640 242411652 4012 False 7411.0 7411 100.0000 1 4013 1 chr7D.!!$F1 4012
1 TraesCS7D01G262900 chr7B 218382411 218386450 4039 False 3150.5 5589 94.3945 1 4010 2 chr7B.!!$F1 4009
2 TraesCS7D01G262900 chr7A 255578339 255581785 3446 True 5051.0 5051 92.9910 1 3505 1 chr7A.!!$R2 3504

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
602 619 0.570272 GCTGTTTTTCGTGCGGTTTG 59.430 50.0 0.0 0.0 0.0 2.93 F
605 622 0.872451 GTTTTTCGTGCGGTTTGGGG 60.872 55.0 0.0 0.0 0.0 4.96 F
1715 1739 1.456296 TGATTGATCTGCTGGTGTGC 58.544 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1585 2.450476 GCTCCCTGGAATTTGACACAT 58.550 47.619 0.00 0.0 0.00 3.21 R
1976 2005 2.672961 TGCTCGAATTCGTGGATTCT 57.327 45.000 25.93 0.0 40.80 2.40 R
3635 3714 1.081892 CCATCAACTGCTTCCAGACG 58.918 55.000 0.00 0.0 41.77 4.18 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
104 113 3.039526 CCCTCCCTCCCTCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
130 139 1.686110 CTCCCGTCCAAGGTAGCCT 60.686 63.158 0.00 0.00 33.87 4.58
131 140 1.677637 CTCCCGTCCAAGGTAGCCTC 61.678 65.000 0.00 0.00 30.89 4.70
155 167 4.172232 TCCCCCGATCCCTCCCTG 62.172 72.222 0.00 0.00 0.00 4.45
258 270 5.801380 TGTCCCAGTAATTTCTAGGTGTTC 58.199 41.667 0.00 0.00 0.00 3.18
265 277 4.724279 AATTTCTAGGTGTTCTGTGGGT 57.276 40.909 0.00 0.00 0.00 4.51
286 298 1.941325 AGATCTCGCCGAATTTGGTC 58.059 50.000 13.49 2.61 0.00 4.02
291 303 2.202479 GCCGAATTTGGTCAGCGC 60.202 61.111 13.49 0.00 0.00 5.92
308 321 3.595758 CGGATGAAATGCCGGGGC 61.596 66.667 2.18 1.86 43.67 5.80
329 342 2.550208 CGTTTAGTGCTTCCTTGACCCT 60.550 50.000 0.00 0.00 0.00 4.34
370 383 1.735376 GCGGCGGAGTTGGAGATCTA 61.735 60.000 9.78 0.00 0.00 1.98
466 483 3.066291 TGTGGTAGTCATGCGGAAATT 57.934 42.857 0.00 0.00 0.00 1.82
475 492 1.312371 ATGCGGAAATTGGGTCGGTG 61.312 55.000 0.00 0.00 0.00 4.94
490 507 2.754254 GTGAAATCCGGCCCACCC 60.754 66.667 0.00 0.00 0.00 4.61
554 571 5.078411 ACCATGTCACTGATCTAGTTCAC 57.922 43.478 0.00 0.00 37.60 3.18
576 593 0.888736 TGAATTCCTGTGTGGCGGTG 60.889 55.000 2.27 0.00 35.26 4.94
591 608 1.266989 GCGGTGCTTCTAGCTGTTTTT 59.733 47.619 0.00 0.00 42.97 1.94
596 613 2.032030 TGCTTCTAGCTGTTTTTCGTGC 60.032 45.455 0.00 0.00 42.97 5.34
602 619 0.570272 GCTGTTTTTCGTGCGGTTTG 59.430 50.000 0.00 0.00 0.00 2.93
605 622 0.872451 GTTTTTCGTGCGGTTTGGGG 60.872 55.000 0.00 0.00 0.00 4.96
608 625 4.973055 TCGTGCGGTTTGGGGTCG 62.973 66.667 0.00 0.00 0.00 4.79
640 657 9.468532 GGTTATTGGTACCTAGTAAGTATTTCG 57.531 37.037 14.36 0.00 32.75 3.46
744 762 9.309516 GTGTAGTGGAATCGACTTTCATATTTA 57.690 33.333 2.71 0.00 0.00 1.40
827 846 6.094881 ACTTGCACTAGTTTTTGTTGCTTAGA 59.905 34.615 0.00 0.00 0.00 2.10
838 857 5.490139 TTGTTGCTTAGAATAGCTGCATC 57.510 39.130 1.02 0.00 41.76 3.91
1197 1221 2.160822 ATGGATGCGATGCTGTAGTC 57.839 50.000 0.00 0.00 0.00 2.59
1327 1351 4.753107 TGCTTAAAGTTCCTTCTGTAACCG 59.247 41.667 0.00 0.00 0.00 4.44
1715 1739 1.456296 TGATTGATCTGCTGGTGTGC 58.544 50.000 0.00 0.00 0.00 4.57
1976 2005 1.271379 GCAGCCCTACCTCAAGAACAA 60.271 52.381 0.00 0.00 0.00 2.83
2042 2071 1.687660 TGTACCACGCCTTGTAAGTGA 59.312 47.619 0.00 0.00 38.06 3.41
2189 2219 8.443160 ACAGTTGTACAGATTGATAATTTGACG 58.557 33.333 9.45 0.00 0.00 4.35
2235 2265 7.170277 GTCCATGGGGTTTAGTTAAGAGTTTA 58.830 38.462 13.02 0.00 34.93 2.01
2259 2289 6.053005 ACATTGAACGTCTTCCAGAAGTTTA 58.947 36.000 7.26 0.73 44.71 2.01
2423 2454 8.763049 TGTAGTCTGTATGTTCAAAGATCTTG 57.237 34.615 9.17 3.74 0.00 3.02
2508 2543 2.257371 GTCTGCGTGCACCGACTA 59.743 61.111 12.15 0.00 39.56 2.59
2543 2578 9.679661 TTGCTGTTCTAAATATGAGGAATACAA 57.320 29.630 0.00 0.00 0.00 2.41
2739 2775 2.557920 AGTCTCAAGCCTCTGGTTTG 57.442 50.000 6.82 6.82 43.66 2.93
3101 3138 1.202952 TGGTTTATGGGTTGCTCGGTT 60.203 47.619 0.00 0.00 0.00 4.44
3142 3179 1.163554 CTGGAGTTCTTCAGGCTTGC 58.836 55.000 0.41 0.00 0.00 4.01
3143 3180 0.250901 TGGAGTTCTTCAGGCTTGCC 60.251 55.000 2.97 2.97 0.00 4.52
3261 3299 3.931907 TGGTCAATCAGGGAATGTAGG 57.068 47.619 0.00 0.00 0.00 3.18
3441 3483 2.512692 TAAGCTCAATGCACACCCAT 57.487 45.000 0.00 0.00 45.94 4.00
3472 3514 2.625790 GAGTCATAATCAGGAGAGCGGT 59.374 50.000 0.00 0.00 0.00 5.68
3488 3530 0.929615 CGGTGAACGTTTGTAACCGT 59.070 50.000 25.15 0.00 45.96 4.83
3511 3553 3.006323 AGTCATAATCAGCAGATCCGGTC 59.994 47.826 0.00 0.00 31.90 4.79
3545 3624 2.434185 GCGTGCTCGGAACCATGA 60.434 61.111 10.52 0.00 37.56 3.07
3635 3714 4.783621 TGCATCCGGTGGCTCTGC 62.784 66.667 18.26 11.57 0.00 4.26
3644 3723 1.739562 GTGGCTCTGCGTCTGGAAG 60.740 63.158 0.00 0.00 0.00 3.46
3661 3740 2.356535 GGAAGCAGTTGATGGATCTGGT 60.357 50.000 0.00 0.00 40.80 4.00
3679 3758 2.758979 TGGTATCTCGTTCTGGAGGTTC 59.241 50.000 0.00 0.00 34.74 3.62
3695 3774 3.562779 TTCGCCGTCGGTGGTCTTC 62.563 63.158 23.98 0.00 33.43 2.87
3717 3796 1.687840 TGGTGCGGTAGGCTATGGT 60.688 57.895 0.00 0.00 44.05 3.55
3725 3804 1.546476 GGTAGGCTATGGTGGATCTCG 59.454 57.143 0.00 0.00 0.00 4.04
3738 3817 1.339929 GGATCTCGGAGCCTCTTCTTC 59.660 57.143 0.00 0.00 34.95 2.87
3749 3828 1.681166 CCTCTTCTTCGTCGAGGGGTA 60.681 57.143 5.12 0.00 40.47 3.69
3756 3835 2.124403 GTCGAGGGGTAGCTCCGA 60.124 66.667 0.00 1.90 37.00 4.55
3776 3855 2.520741 GTGGTGGTGGTTGGTGGG 60.521 66.667 0.00 0.00 0.00 4.61
3782 3861 1.760480 GGTGGTTGGTGGGCTTGTT 60.760 57.895 0.00 0.00 0.00 2.83
3787 3866 4.514585 TGGTGGGCTTGTTGGCGT 62.515 61.111 0.00 0.00 42.84 5.68
3793 3872 4.683334 GCTTGTTGGCGTCGGTGC 62.683 66.667 0.00 0.00 0.00 5.01
3794 3873 4.368808 CTTGTTGGCGTCGGTGCG 62.369 66.667 0.00 0.00 35.06 5.34
3830 3909 0.475632 AGGTGGTGTGGGAGATTGGA 60.476 55.000 0.00 0.00 0.00 3.53
3840 3919 2.654385 TGGGAGATTGGATGAAAACCCT 59.346 45.455 0.00 0.00 37.25 4.34
3847 3926 1.003118 TGGATGAAAACCCTGTCTCGG 59.997 52.381 0.00 0.00 0.00 4.63
3862 3941 3.077705 CGGTGTTATGCCGTGACG 58.922 61.111 0.00 0.00 43.84 4.35
3909 3988 0.250234 TGACCTTCTTGGAGGCATCG 59.750 55.000 0.00 0.00 40.65 3.84
3921 4000 4.950744 GCATCGTTGCTTTGCTGT 57.049 50.000 11.21 0.00 45.77 4.40
3996 4075 3.848347 CTGGGATCGGACGATGGCG 62.848 68.421 12.40 0.00 44.79 5.69
3998 4077 2.651361 GGATCGGACGATGGCGAT 59.349 61.111 12.40 0.00 41.64 4.58
4001 4080 1.004277 GATCGGACGATGGCGATGTC 61.004 60.000 12.40 0.00 41.64 3.06
4010 4089 0.740868 ATGGCGATGTCTTGGTGTCG 60.741 55.000 0.00 0.00 37.17 4.35
4012 4091 4.260194 CGATGTCTTGGTGTCGCA 57.740 55.556 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 2.197324 CGAGAGGGAGGGAGGGAG 59.803 72.222 0.00 0.0 0.00 4.30
147 159 4.888325 AGGGATCGCCAGGGAGGG 62.888 72.222 6.09 0.0 38.09 4.30
258 270 0.249073 CGGCGAGATCTAACCCACAG 60.249 60.000 0.00 0.0 0.00 3.66
265 277 3.118920 TGACCAAATTCGGCGAGATCTAA 60.119 43.478 10.46 0.0 0.00 2.10
286 298 2.025156 GGCATTTCATCCGCGCTG 59.975 61.111 5.56 0.0 0.00 5.18
291 303 3.595758 GCCCCGGCATTTCATCCG 61.596 66.667 0.00 0.0 44.89 4.18
308 321 1.804748 GGGTCAAGGAAGCACTAAACG 59.195 52.381 0.00 0.0 0.00 3.60
448 461 2.364632 CCAATTTCCGCATGACTACCA 58.635 47.619 0.00 0.0 0.00 3.25
475 492 1.917336 TAGTGGGTGGGCCGGATTTC 61.917 60.000 5.05 0.0 34.97 2.17
485 502 1.432251 CGAGCGTAGTAGTGGGTGG 59.568 63.158 0.00 0.0 0.00 4.61
490 507 1.860399 GCATCACCGAGCGTAGTAGTG 60.860 57.143 0.00 0.0 0.00 2.74
554 571 1.875963 GCCACACAGGAATTCACCG 59.124 57.895 7.93 0.0 41.22 4.94
576 593 2.575363 GCACGAAAAACAGCTAGAAGC 58.425 47.619 0.00 0.0 42.84 3.86
591 608 4.973055 CGACCCCAAACCGCACGA 62.973 66.667 0.00 0.0 0.00 4.35
596 613 0.952010 CCACTTACGACCCCAAACCG 60.952 60.000 0.00 0.0 0.00 4.44
602 619 2.026915 ACCAATAACCACTTACGACCCC 60.027 50.000 0.00 0.0 0.00 4.95
605 622 5.077134 AGGTACCAATAACCACTTACGAC 57.923 43.478 15.94 0.0 39.64 4.34
608 625 8.753133 ACTTACTAGGTACCAATAACCACTTAC 58.247 37.037 15.94 0.0 39.64 2.34
659 676 8.062065 TCCTCTGTAAACAAACACTTCATTTT 57.938 30.769 0.00 0.0 0.00 1.82
744 762 0.249911 GACTGCAAACGACTCCCACT 60.250 55.000 0.00 0.0 0.00 4.00
827 846 5.528690 ACAACAATATGACGATGCAGCTATT 59.471 36.000 0.00 0.0 0.00 1.73
838 857 8.577939 GTCATTCAATCAAACAACAATATGACG 58.422 33.333 0.00 0.0 31.98 4.35
1010 1034 4.497006 GCAATGCACTATCTGACATGTTCC 60.497 45.833 0.00 0.0 0.00 3.62
1316 1340 4.131596 TGGAAAACCTTCGGTTACAGAAG 58.868 43.478 16.30 16.3 46.20 2.85
1353 1377 5.298989 TCCAACCTTGTAAGCAAAGTCTA 57.701 39.130 0.00 0.0 33.73 2.59
1365 1389 4.284234 CCAATCCTTTGAATCCAACCTTGT 59.716 41.667 0.00 0.0 34.60 3.16
1561 1585 2.450476 GCTCCCTGGAATTTGACACAT 58.550 47.619 0.00 0.0 0.00 3.21
1976 2005 2.672961 TGCTCGAATTCGTGGATTCT 57.327 45.000 25.93 0.0 40.80 2.40
2042 2071 8.477419 TCAGATAAATTTTTGGGTGAGACTTT 57.523 30.769 0.00 0.0 0.00 2.66
2189 2219 4.826556 ACAGAGAAGAATAGCACAAGGAC 58.173 43.478 0.00 0.0 0.00 3.85
2235 2265 4.073293 ACTTCTGGAAGACGTTCAATGT 57.927 40.909 16.06 0.0 43.62 2.71
2259 2289 8.874744 AGCATCTGCATATCCAAATAAAGTAT 57.125 30.769 4.79 0.0 45.16 2.12
2423 2454 3.008049 ACCCTACTGAAATGACTGGTGTC 59.992 47.826 0.00 0.0 43.20 3.67
2505 2540 4.423625 AGAACAGCAACCAAGAGTTAGT 57.576 40.909 0.00 0.0 36.18 2.24
2508 2543 7.665559 TCATATTTAGAACAGCAACCAAGAGTT 59.334 33.333 0.00 0.0 40.16 3.01
2739 2775 3.567797 GCGCTGTCATCTTCGCCC 61.568 66.667 0.00 0.0 41.53 6.13
2863 2899 2.600470 GCCGCCTTCTTTTGGGGT 60.600 61.111 0.00 0.0 36.96 4.95
3101 3138 5.123820 CAGCAAAAGGAGATTCGATTTACCA 59.876 40.000 0.00 0.0 0.00 3.25
3143 3180 2.493273 ATTAACACCCACCCCAGGCG 62.493 60.000 0.00 0.0 0.00 5.52
3247 3285 5.946486 GGAAGAAATCCTACATTCCCTGAT 58.054 41.667 0.00 0.0 45.56 2.90
3261 3299 7.497909 TCCAAATATCTAACGGTGGAAGAAATC 59.502 37.037 0.00 0.0 32.31 2.17
3277 3315 4.593634 GGGGCTGTAGTACTCCAAATATCT 59.406 45.833 0.00 0.0 0.00 1.98
3333 3374 9.606631 AAAACTAAAGACCACAAAATGCAAATA 57.393 25.926 0.00 0.0 0.00 1.40
3472 3514 4.039151 TGACTACGGTTACAAACGTTCA 57.961 40.909 10.66 6.6 43.79 3.18
3488 3530 4.152647 ACCGGATCTGCTGATTATGACTA 58.847 43.478 9.46 0.0 32.19 2.59
3545 3624 1.678970 GCCCGAAGCCAAGAACCAT 60.679 57.895 0.00 0.0 34.35 3.55
3635 3714 1.081892 CCATCAACTGCTTCCAGACG 58.918 55.000 0.00 0.0 41.77 4.18
3644 3723 4.314121 GAGATACCAGATCCATCAACTGC 58.686 47.826 0.00 0.0 0.00 4.40
3661 3740 1.404391 GCGAACCTCCAGAACGAGATA 59.596 52.381 0.00 0.0 30.97 1.98
3695 3774 2.292794 ATAGCCTACCGCACCACACG 62.293 60.000 0.00 0.0 41.38 4.49
3717 3796 0.260230 AGAAGAGGCTCCGAGATCCA 59.740 55.000 11.71 0.0 0.00 3.41
3725 3804 0.099791 CTCGACGAAGAAGAGGCTCC 59.900 60.000 11.71 0.0 32.96 4.70
3738 3817 3.584052 CGGAGCTACCCCTCGACG 61.584 72.222 0.00 0.0 34.64 5.12
3749 3828 2.607750 ACCACCACCATCGGAGCT 60.608 61.111 0.00 0.0 0.00 4.09
3756 3835 1.152567 CACCAACCACCACCACCAT 60.153 57.895 0.00 0.0 0.00 3.55
3776 3855 4.683334 GCACCGACGCCAACAAGC 62.683 66.667 0.00 0.0 0.00 4.01
3787 3866 4.889856 CGCATCATCCCGCACCGA 62.890 66.667 0.00 0.0 0.00 4.69
3793 3872 3.333189 CAGTCGCGCATCATCCCG 61.333 66.667 8.75 0.0 0.00 5.14
3794 3873 1.953138 CTCAGTCGCGCATCATCCC 60.953 63.158 8.75 0.0 0.00 3.85
3830 3909 1.420138 ACACCGAGACAGGGTTTTCAT 59.580 47.619 0.00 0.0 34.97 2.57
3847 3926 1.708027 GCTCGTCACGGCATAACAC 59.292 57.895 0.00 0.0 0.00 3.32
3960 4039 2.359900 CAGATCAAAGGTTTCCCTCGG 58.640 52.381 0.00 0.0 41.56 4.63
3962 4041 2.308866 TCCCAGATCAAAGGTTTCCCTC 59.691 50.000 0.00 0.0 41.56 4.30
3982 4061 1.004277 GACATCGCCATCGTCCGATC 61.004 60.000 0.00 0.0 41.76 3.69


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

AutoCloner maintained by Alex Coulton.