Multiple sequence alignment - TraesCS1D01G261500

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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 TraesCS1D01G261500 chr1D 100.000 2582 0 0 1 2582 355509453 355506872 0.000000e+00 4769
1 TraesCS1D01G261500 chr1B 94.046 2553 105 22 1 2540 478482804 478480286 0.000000e+00 3829
2 TraesCS1D01G261500 chr1A 93.079 2355 99 27 1 2331 456233285 456230971 0.000000e+00 3387
3 TraesCS1D01G261500 chr1A 90.315 826 56 13 1727 2540 456230009 456229196 0.000000e+00 1061
4 TraesCS1D01G261500 chr1A 87.363 182 11 3 2327 2508 456230700 456230531 5.640000e-47 198


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 TraesCS1D01G261500 chr1D 355506872 355509453 2581 True 4769.000000 4769 100.000000 1 2582 1 chr1D.!!$R1 2581
1 TraesCS1D01G261500 chr1B 478480286 478482804 2518 True 3829.000000 3829 94.046000 1 2540 1 chr1B.!!$R1 2539
2 TraesCS1D01G261500 chr1A 456229196 456233285 4089 True 1548.666667 3387 90.252333 1 2540 3 chr1A.!!$R1 2539

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
455 466 0.324923 AACCTCATGCACATGGCCAT 60.325 50.0 14.09 14.09 43.89 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 3814 0.326048 ATGGACAGCACTAGAGGGCT 60.326 55.0 0.0 0.0 42.06 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
50 51 4.389890 ACAGCTGTGATTCTGAGATCTC 57.610 45.455 20.97 16.21 34.57 2.75
276 282 3.379372 AGGATTGGAGCAAATCATGAACG 59.621 43.478 0.00 0.00 38.14 3.95
281 287 1.732259 GAGCAAATCATGAACGTCGGT 59.268 47.619 0.00 0.00 0.00 4.69
291 297 2.129607 TGAACGTCGGTCAGCTTTAAC 58.870 47.619 9.38 0.00 0.00 2.01
297 303 0.798776 CGGTCAGCTTTAACTGCAGG 59.201 55.000 19.93 0.00 37.59 4.85
440 451 7.310175 GCCCATGTGGTAAACTTTAATTAACCT 60.310 37.037 0.00 0.00 36.04 3.50
455 466 0.324923 AACCTCATGCACATGGCCAT 60.325 50.000 14.09 14.09 43.89 4.40
457 468 0.467474 CCTCATGCACATGGCCATCT 60.467 55.000 17.61 0.00 43.89 2.90
487 498 1.457455 ACAACCCAACCCTGCCTTG 60.457 57.895 0.00 0.00 0.00 3.61
489 500 3.387609 AACCCAACCCTGCCTTGCA 62.388 57.895 0.00 0.00 36.92 4.08
495 506 0.760189 AACCCTGCCTTGCATGTTGT 60.760 50.000 0.00 0.00 38.13 3.32
504 515 3.243301 GCCTTGCATGTTGTCATCCTATG 60.243 47.826 0.00 0.00 31.15 2.23
683 694 6.377146 ACCAGAAAGTTTCAGTTTTCTAAGCA 59.623 34.615 17.65 0.00 40.62 3.91
684 695 7.068716 ACCAGAAAGTTTCAGTTTTCTAAGCAT 59.931 33.333 17.65 0.00 40.62 3.79
685 696 7.922811 CCAGAAAGTTTCAGTTTTCTAAGCATT 59.077 33.333 17.65 0.00 40.62 3.56
686 697 9.950680 CAGAAAGTTTCAGTTTTCTAAGCATTA 57.049 29.630 17.65 0.00 40.62 1.90
790 805 0.926293 CTCCTCCCTCTCTGGTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
1035 1050 2.824936 CCAAATGGCCATACAACTCACA 59.175 45.455 21.15 0.00 0.00 3.58
1107 1122 1.153939 CACGTCCTCCTCTCTTGCG 60.154 63.158 0.00 0.00 0.00 4.85
1203 1218 2.965147 CCACAAAACTTCCATGGAGGTT 59.035 45.455 30.87 30.87 44.50 3.50
1255 1270 0.326618 AGATGGGGTGTCCGAGGATT 60.327 55.000 0.00 0.00 38.76 3.01
1344 1359 3.092301 TGAAGTCTCGGTGTCTGATGAT 58.908 45.455 0.00 0.00 0.00 2.45
1445 1460 4.821589 GCAAGACCTCCTCGCCGG 62.822 72.222 0.00 0.00 0.00 6.13
1567 1582 1.321016 CATCAAGTGCGCAAACTTCG 58.679 50.000 14.00 7.66 38.34 3.79
1631 1646 6.896021 AATCATTCTATGAATTGCTCCTGG 57.104 37.500 0.00 0.00 43.50 4.45
1764 1783 2.274920 GCCTTTGCTGCATCTCTTTC 57.725 50.000 1.84 0.00 33.53 2.62
1770 1789 3.701205 TGCTGCATCTCTTTCCTTGTA 57.299 42.857 0.00 0.00 0.00 2.41
1784 1803 7.930217 TCTTTCCTTGTACTTTCTGAATGTTG 58.070 34.615 13.24 3.86 0.00 3.33
1788 1807 7.168219 TCCTTGTACTTTCTGAATGTTGCTAT 58.832 34.615 13.24 0.00 0.00 2.97
1928 3511 5.674052 ATGTCAGGGCTAGCTATATCAAG 57.326 43.478 15.72 0.00 0.00 3.02
1960 3543 9.551734 GGTGGGGTATACTTAAGTTACTTTATG 57.448 37.037 14.49 0.00 0.00 1.90
1983 3569 7.307493 TGATTAGTGCACTAATACAAAGCTG 57.693 36.000 39.09 0.00 46.07 4.24
2035 3621 6.952773 TGTTAGCTACTTGATGTGGTTTTT 57.047 33.333 0.00 0.00 0.00 1.94
2068 3654 6.716628 AGCTCAACCTTTTGTCATTCTGAATA 59.283 34.615 1.98 0.00 34.02 1.75
2137 3733 7.390718 AGAATAATCGGTCTTTTAGTTTGTGCT 59.609 33.333 0.00 0.00 0.00 4.40
2150 3746 0.467106 TTGTGCTGCTGGGTGCTTTA 60.467 50.000 0.00 0.00 43.37 1.85
2183 3779 8.811017 TGATGTTTGATTTGGAAAAAGGCTATA 58.189 29.630 0.00 0.00 0.00 1.31
2211 3807 7.792374 TCTTCATGATTTGCACCTCTATTAC 57.208 36.000 0.00 0.00 0.00 1.89
2213 3809 7.496920 TCTTCATGATTTGCACCTCTATTACTG 59.503 37.037 0.00 0.00 0.00 2.74
2214 3810 6.653020 TCATGATTTGCACCTCTATTACTGT 58.347 36.000 0.00 0.00 0.00 3.55
2215 3811 7.791029 TCATGATTTGCACCTCTATTACTGTA 58.209 34.615 0.00 0.00 0.00 2.74
2216 3812 7.928167 TCATGATTTGCACCTCTATTACTGTAG 59.072 37.037 0.00 0.00 0.00 2.74
2217 3813 7.182817 TGATTTGCACCTCTATTACTGTAGT 57.817 36.000 0.00 0.00 0.00 2.73
2218 3814 8.301252 TGATTTGCACCTCTATTACTGTAGTA 57.699 34.615 0.00 0.00 0.00 1.82
2219 3815 8.414003 TGATTTGCACCTCTATTACTGTAGTAG 58.586 37.037 10.21 10.21 0.00 2.57
2220 3816 5.769484 TGCACCTCTATTACTGTAGTAGC 57.231 43.478 11.32 3.04 0.00 3.58
2221 3817 4.583489 TGCACCTCTATTACTGTAGTAGCC 59.417 45.833 11.32 1.06 0.00 3.93
2222 3818 4.022155 GCACCTCTATTACTGTAGTAGCCC 60.022 50.000 11.32 0.00 0.00 5.19
2249 3845 5.804639 AGTGCTGTCCATAACAAATGTAGA 58.195 37.500 0.00 0.00 37.45 2.59
2322 3918 7.922837 ACATTTTAGCGTACTACTGTTTTTGT 58.077 30.769 0.00 0.00 0.00 2.83
2324 3920 6.907206 TTTAGCGTACTACTGTTTTTGTGT 57.093 33.333 0.00 0.00 0.00 3.72
2391 3987 4.407365 TCCACTTTGGATCTTTTTCTCCC 58.593 43.478 0.00 0.00 42.67 4.30
2411 4007 8.754991 TCTCCCTGTTTTAAGTACAAAAATCA 57.245 30.769 8.75 6.52 0.00 2.57
2463 4060 2.874701 ACATGCTGACACTTGACACTTC 59.125 45.455 0.00 0.00 0.00 3.01
2482 4079 7.044980 CACTTCAGATAAGTGTGCACATGCA 62.045 44.000 24.69 11.17 42.61 3.96
2541 4138 4.796231 CGGCTAACGCTCGCCTGT 62.796 66.667 0.00 0.00 44.11 4.00
2542 4139 2.493030 GGCTAACGCTCGCCTGTA 59.507 61.111 0.00 0.00 42.98 2.74
2543 4140 1.067582 GGCTAACGCTCGCCTGTAT 59.932 57.895 0.00 0.00 42.98 2.29
2544 4141 0.529992 GGCTAACGCTCGCCTGTATT 60.530 55.000 0.00 0.00 42.98 1.89
2545 4142 0.577269 GCTAACGCTCGCCTGTATTG 59.423 55.000 0.00 0.00 0.00 1.90
2546 4143 1.922570 CTAACGCTCGCCTGTATTGT 58.077 50.000 0.00 0.00 0.00 2.71
2547 4144 1.588404 CTAACGCTCGCCTGTATTGTG 59.412 52.381 0.00 0.00 0.00 3.33
2548 4145 1.019278 AACGCTCGCCTGTATTGTGG 61.019 55.000 0.00 0.00 0.00 4.17
2549 4146 1.153647 CGCTCGCCTGTATTGTGGA 60.154 57.895 0.00 0.00 0.00 4.02
2550 4147 0.530650 CGCTCGCCTGTATTGTGGAT 60.531 55.000 0.00 0.00 0.00 3.41
2551 4148 1.269569 CGCTCGCCTGTATTGTGGATA 60.270 52.381 0.00 0.00 0.00 2.59
2552 4149 2.610479 CGCTCGCCTGTATTGTGGATAT 60.610 50.000 0.00 0.00 0.00 1.63
2553 4150 3.403038 GCTCGCCTGTATTGTGGATATT 58.597 45.455 0.00 0.00 0.00 1.28
2554 4151 3.815401 GCTCGCCTGTATTGTGGATATTT 59.185 43.478 0.00 0.00 0.00 1.40
2555 4152 4.319766 GCTCGCCTGTATTGTGGATATTTG 60.320 45.833 0.00 0.00 0.00 2.32
2556 4153 3.563808 TCGCCTGTATTGTGGATATTTGC 59.436 43.478 0.00 0.00 0.00 3.68
2557 4154 3.565482 CGCCTGTATTGTGGATATTTGCT 59.435 43.478 0.00 0.00 0.00 3.91
2558 4155 4.555313 CGCCTGTATTGTGGATATTTGCTG 60.555 45.833 0.00 0.00 0.00 4.41
2559 4156 4.794003 GCCTGTATTGTGGATATTTGCTGC 60.794 45.833 0.00 0.00 0.00 5.25
2560 4157 4.261741 CCTGTATTGTGGATATTTGCTGCC 60.262 45.833 0.00 0.00 0.00 4.85
2561 4158 3.636300 TGTATTGTGGATATTTGCTGCCC 59.364 43.478 0.00 0.00 0.00 5.36
2562 4159 2.530460 TTGTGGATATTTGCTGCCCT 57.470 45.000 0.00 0.00 0.00 5.19
2563 4160 3.660970 TTGTGGATATTTGCTGCCCTA 57.339 42.857 0.00 0.00 0.00 3.53
2564 4161 3.882102 TGTGGATATTTGCTGCCCTAT 57.118 42.857 0.00 0.00 0.00 2.57
2565 4162 4.183223 TGTGGATATTTGCTGCCCTATT 57.817 40.909 0.00 0.00 0.00 1.73
2566 4163 4.545678 TGTGGATATTTGCTGCCCTATTT 58.454 39.130 0.00 0.00 0.00 1.40
2567 4164 4.961730 TGTGGATATTTGCTGCCCTATTTT 59.038 37.500 0.00 0.00 0.00 1.82
2568 4165 5.424895 TGTGGATATTTGCTGCCCTATTTTT 59.575 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.447406 TCATTTCGCGGCACAAGATG 59.553 50.000 6.13 0.00 0.00 2.90
276 282 1.461127 CTGCAGTTAAAGCTGACCGAC 59.539 52.381 5.25 0.00 38.70 4.79
281 287 0.038166 CCCCCTGCAGTTAAAGCTGA 59.962 55.000 13.81 0.00 38.70 4.26
297 303 1.304617 CTTTCTCTTGCCCTCCCCC 59.695 63.158 0.00 0.00 0.00 5.40
358 368 3.831715 ACCTTATCAAAAGCAGCGTTC 57.168 42.857 0.00 0.00 0.00 3.95
440 451 1.064240 AGAAGATGGCCATGTGCATGA 60.064 47.619 26.56 0.00 43.89 3.07
487 498 3.316308 GGTTCCATAGGATGACAACATGC 59.684 47.826 0.00 0.00 43.55 4.06
489 500 4.860802 TGGTTCCATAGGATGACAACAT 57.139 40.909 0.00 0.00 39.67 2.71
495 506 3.331591 CCATCCATGGTTCCATAGGATGA 59.668 47.826 33.69 18.12 44.05 2.92
754 769 1.044611 GAGGAGTAGGGCTCACCATC 58.955 60.000 0.00 0.00 45.88 3.51
790 805 6.376864 TGTGAATTGACACAAAGAGGAAAAGA 59.623 34.615 0.00 0.00 45.81 2.52
1035 1050 4.463186 AGGCTACACGAAATGAGTAGAAGT 59.537 41.667 0.00 0.00 42.38 3.01
1107 1122 1.740025 GAGATAACCAGCACCAGCAAC 59.260 52.381 0.00 0.00 45.49 4.17
1172 1187 1.194218 AGTTTTGTGGCTGCTGGTTT 58.806 45.000 0.00 0.00 0.00 3.27
1203 1218 3.606595 CTCTTCTCCTGATGAGCAACA 57.393 47.619 0.00 0.00 41.18 3.33
1241 1256 2.202892 GCGAATCCTCGGACACCC 60.203 66.667 0.00 0.00 45.55 4.61
1344 1359 2.070262 TAAGACTCTCGTCGTCGTCA 57.930 50.000 1.33 0.00 44.93 4.35
1629 1644 3.126703 TTGCCCTGACGAAAGCCCA 62.127 57.895 0.00 0.00 0.00 5.36
1631 1646 2.335712 CCTTGCCCTGACGAAAGCC 61.336 63.158 0.00 0.00 0.00 4.35
1704 1722 6.767902 ACTAATGAAACTGAGCTCTTTGTGAA 59.232 34.615 16.19 2.07 0.00 3.18
1705 1723 6.203530 CACTAATGAAACTGAGCTCTTTGTGA 59.796 38.462 16.19 0.00 0.00 3.58
1750 1769 2.574006 ACAAGGAAAGAGATGCAGCA 57.426 45.000 4.07 0.00 0.00 4.41
1764 1783 5.695851 AGCAACATTCAGAAAGTACAAGG 57.304 39.130 0.00 0.00 0.00 3.61
1770 1789 9.507329 TTTCTTCTATAGCAACATTCAGAAAGT 57.493 29.630 0.00 0.00 0.00 2.66
1784 1803 5.366752 CACGCGCTTTATTTCTTCTATAGC 58.633 41.667 5.73 0.00 0.00 2.97
1788 1807 2.997303 TGCACGCGCTTTATTTCTTCTA 59.003 40.909 5.73 0.00 39.64 2.10
1842 3425 0.612732 AAGGGCCATCCACACACATG 60.613 55.000 6.18 0.00 38.24 3.21
1852 3435 3.903467 AGGTATGAAAAGAAGGGCCATC 58.097 45.455 6.18 2.46 0.00 3.51
1928 3511 4.163649 ACTTAAGTATACCCCACCTTGAGC 59.836 45.833 6.26 0.00 0.00 4.26
1960 3543 6.183360 TGCAGCTTTGTATTAGTGCACTAATC 60.183 38.462 41.35 32.60 43.57 1.75
2015 3601 7.575414 TTTCAAAAACCACATCAAGTAGCTA 57.425 32.000 0.00 0.00 0.00 3.32
2035 3621 7.106439 TGACAAAAGGTTGAGCTTAATTTCA 57.894 32.000 0.00 0.00 38.20 2.69
2077 3663 7.232534 TGAACCATATGCCACTACTTTTTCTTT 59.767 33.333 0.00 0.00 0.00 2.52
2078 3664 6.719370 TGAACCATATGCCACTACTTTTTCTT 59.281 34.615 0.00 0.00 0.00 2.52
2079 3665 6.245408 TGAACCATATGCCACTACTTTTTCT 58.755 36.000 0.00 0.00 0.00 2.52
2080 3666 6.509418 TGAACCATATGCCACTACTTTTTC 57.491 37.500 0.00 0.00 0.00 2.29
2081 3667 6.266558 TGTTGAACCATATGCCACTACTTTTT 59.733 34.615 0.00 0.00 0.00 1.94
2082 3668 5.772672 TGTTGAACCATATGCCACTACTTTT 59.227 36.000 0.00 0.00 0.00 2.27
2083 3669 5.321102 TGTTGAACCATATGCCACTACTTT 58.679 37.500 0.00 0.00 0.00 2.66
2085 3671 4.568072 TGTTGAACCATATGCCACTACT 57.432 40.909 0.00 0.00 0.00 2.57
2150 3746 2.353011 CCAAATCAAACATCAGCCGCTT 60.353 45.455 0.00 0.00 0.00 4.68
2183 3779 5.507637 AGAGGTGCAAATCATGAAGATCTT 58.492 37.500 7.95 7.95 35.39 2.40
2211 3807 2.621055 CAGCACTAGAGGGCTACTACAG 59.379 54.545 5.84 0.00 38.56 2.74
2213 3809 2.619646 GACAGCACTAGAGGGCTACTAC 59.380 54.545 5.84 0.00 38.56 2.73
2214 3810 2.423088 GGACAGCACTAGAGGGCTACTA 60.423 54.545 5.84 0.00 38.56 1.82
2215 3811 1.686741 GGACAGCACTAGAGGGCTACT 60.687 57.143 5.84 0.00 38.56 2.57
2216 3812 0.747852 GGACAGCACTAGAGGGCTAC 59.252 60.000 5.84 3.94 38.56 3.58
2217 3813 0.335019 TGGACAGCACTAGAGGGCTA 59.665 55.000 5.84 0.00 38.56 3.93
2218 3814 0.326048 ATGGACAGCACTAGAGGGCT 60.326 55.000 0.00 0.00 42.06 5.19
2219 3815 1.414158 TATGGACAGCACTAGAGGGC 58.586 55.000 0.00 0.00 0.00 5.19
2220 3816 2.766263 TGTTATGGACAGCACTAGAGGG 59.234 50.000 0.00 0.00 33.40 4.30
2221 3817 4.471904 TTGTTATGGACAGCACTAGAGG 57.528 45.455 0.00 0.00 39.94 3.69
2222 3818 5.877012 ACATTTGTTATGGACAGCACTAGAG 59.123 40.000 0.00 0.00 39.94 2.43
2249 3845 6.028780 TCCAATAAACAAAGGATCCCCAAAT 58.971 36.000 8.55 0.00 33.88 2.32
2352 3948 8.087750 CCAAAGTGGAGTTAAAATAAGCATTCA 58.912 33.333 0.00 0.00 40.96 2.57
2381 3977 9.863845 TTTTGTACTTAAAACAGGGAGAAAAAG 57.136 29.630 0.00 0.00 0.00 2.27
2418 4014 7.281999 TGTCAGATTACAAATGTTCACACTCAA 59.718 33.333 0.00 0.00 0.00 3.02
2482 4079 4.646492 GCCTATTTCCAACAGTGAATGGAT 59.354 41.667 18.67 10.52 44.83 3.41
2540 4137 3.891366 AGGGCAGCAAATATCCACAATAC 59.109 43.478 0.00 0.00 0.00 1.89
2541 4138 4.183223 AGGGCAGCAAATATCCACAATA 57.817 40.909 0.00 0.00 0.00 1.90
2542 4139 3.036452 AGGGCAGCAAATATCCACAAT 57.964 42.857 0.00 0.00 0.00 2.71
2543 4140 2.530460 AGGGCAGCAAATATCCACAA 57.470 45.000 0.00 0.00 0.00 3.33
2544 4141 3.882102 ATAGGGCAGCAAATATCCACA 57.118 42.857 0.00 0.00 0.00 4.17
2545 4142 5.535753 AAAATAGGGCAGCAAATATCCAC 57.464 39.130 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.