Multiple sequence alignment - TraesCS5D01G259100

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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 TraesCS5D01G259100 chr5D 100.000 3956 0 0 1 3956 365327015 365323060 0.000000e+00 7306
1 TraesCS5D01G259100 chr5A 94.492 3976 150 23 17 3956 466988452 466984510 0.000000e+00 6065
2 TraesCS5D01G259100 chr5B 94.482 3552 117 25 417 3956 431800606 431797122 0.000000e+00 5400
3 TraesCS5D01G259100 chr5B 96.839 348 11 0 1 348 431807187 431806840 2.050000e-162 582
4 TraesCS5D01G259100 chr5B 96.629 89 3 0 333 421 431806657 431806569 8.860000e-32 148


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 TraesCS5D01G259100 chr5D 365323060 365327015 3955 True 7306 7306 100.000 1 3956 1 chr5D.!!$R1 3955
1 TraesCS5D01G259100 chr5A 466984510 466988452 3942 True 6065 6065 94.492 17 3956 1 chr5A.!!$R1 3939
2 TraesCS5D01G259100 chr5B 431797122 431800606 3484 True 5400 5400 94.482 417 3956 1 chr5B.!!$R1 3539
3 TraesCS5D01G259100 chr5B 431806569 431807187 618 True 365 582 96.734 1 421 2 chr5B.!!$R2 420

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
558 758 1.024271 TGTCTTGTGGCAGCAACTTC 58.976 50.0 0.43 0.0 0.00 3.01 F
1909 2109 0.745845 CCCTGTATCTGCTGTGCACC 60.746 60.0 15.69 0.0 33.79 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2231 0.321564 CGGGCAGACAAAGACCATGA 60.322 55.0 0.0 0.0 31.91 3.07 R
3843 4075 0.034896 GGAAAGCGACCTCCACTGAA 59.965 55.0 0.0 0.0 0.00 3.02 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
118 119 8.461222 TCATGATCATAAGGATTGTTTGTTGTC 58.539 33.333 8.15 0.00 36.00 3.18
133 134 5.581126 TTGTTGTCATGAGAAGCTGTTTT 57.419 34.783 5.37 0.00 0.00 2.43
173 174 2.772102 TGCCAAGAGTGGGAGCTAA 58.228 52.632 0.00 0.00 46.09 3.09
382 582 7.175990 GGGTGGAAGAATTGTCAAGTGTATTTA 59.824 37.037 0.00 0.00 0.00 1.40
421 621 5.625568 ACAACTACCCTGGGTGTATTATC 57.374 43.478 28.64 0.00 36.19 1.75
429 629 5.842874 ACCCTGGGTGTATTATCTTAGTACC 59.157 44.000 19.82 0.00 32.98 3.34
477 677 1.265095 CGGCTATTGCTTGCTATGGTG 59.735 52.381 0.00 0.00 39.59 4.17
542 742 4.331108 AGAAGATCCAAAGAGGCTTTGTC 58.669 43.478 16.11 9.67 37.29 3.18
558 758 1.024271 TGTCTTGTGGCAGCAACTTC 58.976 50.000 0.43 0.00 0.00 3.01
569 769 2.489329 GCAGCAACTTCAGGCTATTTCA 59.511 45.455 0.00 0.00 38.56 2.69
574 774 4.439289 GCAACTTCAGGCTATTTCATGGTC 60.439 45.833 0.00 0.00 0.00 4.02
631 831 8.547967 AACTCATGCCATTACCGTATAATAAG 57.452 34.615 0.00 0.00 0.00 1.73
653 853 5.869579 AGATGTCCTTCTGTTTTGCTTCTA 58.130 37.500 0.00 0.00 0.00 2.10
682 882 6.154877 CCTTCTCATCAGGATATATGTCTGCT 59.845 42.308 0.00 0.00 32.41 4.24
683 883 6.527057 TCTCATCAGGATATATGTCTGCTG 57.473 41.667 0.00 0.64 0.00 4.41
1530 1730 2.354805 GGGTGGTGCCTACTACTTCAAG 60.355 54.545 0.00 0.00 38.26 3.02
1545 1745 4.482990 ACTTCAAGAACATTTGGGGTGAT 58.517 39.130 0.00 0.00 0.00 3.06
1569 1769 4.399004 TGTTGCAATTGTAAAGCCAACT 57.601 36.364 10.72 0.00 34.88 3.16
1751 1951 1.802960 GCTGGTCAAGATCACACACAG 59.197 52.381 0.00 0.00 0.00 3.66
1909 2109 0.745845 CCCTGTATCTGCTGTGCACC 60.746 60.000 15.69 0.00 33.79 5.01
1998 2198 1.073923 GTTGGTCCTGGGTCTGACAAT 59.926 52.381 10.38 0.00 33.09 2.71
2004 2204 2.176798 TCCTGGGTCTGACAATTTTGGT 59.823 45.455 10.38 0.00 0.00 3.67
2031 2231 5.605534 CAGACCGAACTCATTCCTATTGAT 58.394 41.667 0.00 0.00 0.00 2.57
2052 2252 0.036010 ATGGTCTTTGTCTGCCCGAG 60.036 55.000 0.00 0.00 0.00 4.63
2061 2261 1.174783 GTCTGCCCGAGTGTCTAGAA 58.825 55.000 0.00 0.00 0.00 2.10
2073 2273 5.163733 CGAGTGTCTAGAAGACCCTTACTTC 60.164 48.000 0.00 0.00 44.44 3.01
2139 2339 6.267471 AGGAGGAACTTGAATACATTGCAAAA 59.733 34.615 1.71 0.00 41.55 2.44
2274 2474 1.168714 GCCTCTGCTTGTCCGAAATT 58.831 50.000 0.00 0.00 33.53 1.82
2303 2503 2.012673 GATGAGCAGGCAGTTTACTGG 58.987 52.381 11.55 0.00 43.94 4.00
2304 2504 0.036732 TGAGCAGGCAGTTTACTGGG 59.963 55.000 11.55 0.00 43.94 4.45
2305 2505 0.324943 GAGCAGGCAGTTTACTGGGA 59.675 55.000 11.55 0.00 43.94 4.37
2559 2759 3.258872 GTGATGAGGAGGAGGATGATGAG 59.741 52.174 0.00 0.00 0.00 2.90
2622 2822 0.620700 TTCCTAAGCTGGTCCCTCCC 60.621 60.000 0.00 0.00 34.77 4.30
2642 2842 1.069090 TCTCAAAGCTGTCCGCGTT 59.931 52.632 4.92 0.00 45.59 4.84
2841 3041 2.363147 GGCTCCGAGGAGTGGACT 60.363 66.667 19.22 0.00 43.70 3.85
2886 3086 4.521062 CTCCCGAGCGCCTTCCAG 62.521 72.222 2.29 0.00 0.00 3.86
2943 3143 1.743252 GCAGAGGCTGGGAACTTCG 60.743 63.158 0.00 0.00 36.96 3.79
2966 3166 2.623416 GCCAGTTTTGAAGGTAGCAGTT 59.377 45.455 0.00 0.00 0.00 3.16
3041 3246 2.592861 CCGGAAGCAGCCCTATGC 60.593 66.667 0.00 0.00 46.88 3.14
3151 3358 4.409342 CGATCTTCCCGCAGAGTG 57.591 61.111 0.00 0.00 0.00 3.51
3152 3359 1.809869 CGATCTTCCCGCAGAGTGA 59.190 57.895 0.00 0.00 0.00 3.41
3182 3389 3.056821 TCGTGTCTGTGCATAGCTTTAGT 60.057 43.478 5.44 0.00 0.00 2.24
3401 3611 2.689471 TGAATATGCACCTGGATGTTGC 59.311 45.455 0.00 0.00 28.38 4.17
3402 3612 2.742428 ATATGCACCTGGATGTTGCT 57.258 45.000 0.00 0.00 0.00 3.91
3415 3625 1.162800 TGTTGCTACGCATGTGCACA 61.163 50.000 24.08 24.08 38.76 4.57
3421 3631 4.064388 TGCTACGCATGTGCACATATATT 58.936 39.130 30.92 17.56 42.21 1.28
3422 3632 4.083908 TGCTACGCATGTGCACATATATTG 60.084 41.667 30.92 20.97 42.21 1.90
3423 3633 4.083855 GCTACGCATGTGCACATATATTGT 60.084 41.667 30.92 23.59 42.21 2.71
3424 3634 4.472691 ACGCATGTGCACATATATTGTC 57.527 40.909 30.92 14.76 42.21 3.18
3425 3635 3.876320 ACGCATGTGCACATATATTGTCA 59.124 39.130 30.92 0.00 42.21 3.58
3426 3636 4.213674 CGCATGTGCACATATATTGTCAC 58.786 43.478 30.92 11.27 42.21 3.67
3427 3637 4.539870 GCATGTGCACATATATTGTCACC 58.460 43.478 30.92 4.68 41.59 4.02
3428 3638 4.276678 GCATGTGCACATATATTGTCACCT 59.723 41.667 30.92 3.25 41.59 4.00
3429 3639 5.754778 CATGTGCACATATATTGTCACCTG 58.245 41.667 30.92 12.54 36.00 4.00
3431 3641 5.252547 TGTGCACATATATTGTCACCTGTT 58.747 37.500 17.42 0.00 36.00 3.16
3433 3643 6.881602 TGTGCACATATATTGTCACCTGTTTA 59.118 34.615 17.42 0.00 36.00 2.01
3434 3644 7.148323 TGTGCACATATATTGTCACCTGTTTAC 60.148 37.037 17.42 0.00 36.00 2.01
3438 3648 9.330063 CACATATATTGTCACCTGTTTACATCT 57.670 33.333 0.00 0.00 36.00 2.90
3439 3649 9.330063 ACATATATTGTCACCTGTTTACATCTG 57.670 33.333 0.00 0.00 30.89 2.90
3484 3701 2.156891 GCTTTTGATGCGTGAGTCGTTA 59.843 45.455 0.00 0.00 42.13 3.18
3485 3702 3.181520 GCTTTTGATGCGTGAGTCGTTAT 60.182 43.478 0.00 0.00 42.13 1.89
3526 3743 2.742774 TGATGTGATACGAGCGAATGG 58.257 47.619 0.00 0.00 0.00 3.16
3554 3772 2.224209 ACTTGGTTCGGGTAGTGTCAAG 60.224 50.000 0.00 0.00 36.96 3.02
3555 3773 0.682852 TGGTTCGGGTAGTGTCAAGG 59.317 55.000 0.00 0.00 0.00 3.61
3558 3776 1.833787 TTCGGGTAGTGTCAAGGGGC 61.834 60.000 0.00 0.00 0.00 5.80
3562 3780 3.006728 TAGTGTCAAGGGGCCCCG 61.007 66.667 35.78 22.57 41.95 5.73
3563 3781 3.857521 TAGTGTCAAGGGGCCCCGT 62.858 63.158 35.78 30.96 41.95 5.28
3685 3916 5.435686 AGCACAAATCTATTGACCCTGTA 57.564 39.130 0.00 0.00 0.00 2.74
3687 3918 4.335594 GCACAAATCTATTGACCCTGTACC 59.664 45.833 0.00 0.00 0.00 3.34
3780 4012 1.889829 CCTGAAGTGACTTCTCCGAGT 59.110 52.381 24.09 0.00 40.73 4.18
3791 4023 3.898741 ACTTCTCCGAGTCCTTCTTTTCT 59.101 43.478 0.00 0.00 0.00 2.52
3840 4072 2.574399 GGCAGAGTGAGACCGTCC 59.426 66.667 0.00 0.00 0.00 4.79
3843 4075 0.963355 GCAGAGTGAGACCGTCCTCT 60.963 60.000 0.00 0.00 34.75 3.69
3926 4161 0.249120 TCCAAGCCCATCACGTACTG 59.751 55.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 8.349568 ACAATCCTTATGATCATGATTCATGG 57.650 34.615 23.07 16.94 41.66 3.66
118 119 6.267817 TCAAAACTGAAAACAGCTTCTCATG 58.732 36.000 0.00 0.00 0.00 3.07
133 134 6.071952 GGCAGGAATAGAACAATCAAAACTGA 60.072 38.462 0.00 0.00 0.00 3.41
173 174 6.237901 TGCATACAACTCACAAATAGAAGGT 58.762 36.000 0.00 0.00 0.00 3.50
405 605 5.842874 GGTACTAAGATAATACACCCAGGGT 59.157 44.000 4.76 4.76 35.62 4.34
429 629 8.882415 AGCATGGCTTCATAAAATTCTTAATG 57.118 30.769 0.00 0.00 33.89 1.90
480 680 8.778358 CAGTATTTCTGTTCTTTTAGCAAGTCT 58.222 33.333 0.00 0.00 39.17 3.24
491 691 7.750229 TGCTCATTTCAGTATTTCTGTTCTT 57.250 32.000 0.00 0.00 43.97 2.52
542 742 0.313043 CCTGAAGTTGCTGCCACAAG 59.687 55.000 6.63 1.23 0.00 3.16
558 758 2.928334 AGCAGACCATGAAATAGCCTG 58.072 47.619 0.00 0.00 0.00 4.85
569 769 5.622460 CGAGTTAAACAGTCTAGCAGACCAT 60.622 44.000 11.24 0.29 46.18 3.55
574 774 6.764877 TTTTCGAGTTAAACAGTCTAGCAG 57.235 37.500 0.00 0.00 0.00 4.24
631 831 5.389935 CGTAGAAGCAAAACAGAAGGACATC 60.390 44.000 0.00 0.00 0.00 3.06
653 853 6.013379 ACATATATCCTGATGAGAAGGACGT 58.987 40.000 0.00 0.00 46.51 4.34
696 896 8.934023 TTTTTAGACATGTAGAACCAGGAAAT 57.066 30.769 0.00 0.00 0.00 2.17
850 1050 5.480642 AGTAGGCCATAGATGAAGATGTG 57.519 43.478 5.01 0.00 0.00 3.21
1107 1307 4.949856 ACAAAAACTCTCTTCCAGCTCAAA 59.050 37.500 0.00 0.00 0.00 2.69
1530 1730 4.497300 CAACATGATCACCCCAAATGTTC 58.503 43.478 0.00 0.00 38.94 3.18
1545 1745 4.597404 TGGCTTTACAATTGCAACATGA 57.403 36.364 18.17 2.70 0.00 3.07
1569 1769 2.041485 TGGAGCAAATGGTTCCTCATCA 59.959 45.455 0.00 0.00 46.38 3.07
1751 1951 3.052036 GTGGCATTCACATTGAACACAC 58.948 45.455 0.00 0.00 45.39 3.82
1909 2109 1.528586 GATGTCAAGAATGCCGATCCG 59.471 52.381 0.00 0.00 0.00 4.18
1998 2198 0.736053 GTTCGGTCTGCACACCAAAA 59.264 50.000 11.98 2.12 36.01 2.44
2004 2204 1.608025 GGAATGAGTTCGGTCTGCACA 60.608 52.381 0.00 0.00 35.10 4.57
2031 2231 0.321564 CGGGCAGACAAAGACCATGA 60.322 55.000 0.00 0.00 31.91 3.07
2061 2261 4.469945 TGAATCCATTCGAAGTAAGGGTCT 59.530 41.667 3.35 0.00 39.62 3.85
2073 2273 0.734889 GTGGCCAGTGAATCCATTCG 59.265 55.000 5.11 0.00 39.62 3.34
2139 2339 7.121382 TCTCAGCATCTTTTAAAGGATCCAAT 58.879 34.615 15.82 4.38 0.00 3.16
2274 2474 0.757512 GCCTGCTCATCATCTCTCCA 59.242 55.000 0.00 0.00 0.00 3.86
2303 2503 3.244735 ACTTGGCTCTTCTTCTTTCCTCC 60.245 47.826 0.00 0.00 0.00 4.30
2304 2504 3.750652 CACTTGGCTCTTCTTCTTTCCTC 59.249 47.826 0.00 0.00 0.00 3.71
2305 2505 3.392616 TCACTTGGCTCTTCTTCTTTCCT 59.607 43.478 0.00 0.00 0.00 3.36
2559 2759 3.802866 GTCATCCTTGACCATCTCCTTC 58.197 50.000 0.00 0.00 45.45 3.46
2583 2783 0.248289 ACATACCGTTCAAGGGGTCG 59.752 55.000 0.22 0.00 37.75 4.79
2622 2822 2.720758 CGCGGACAGCTTTGAGACG 61.721 63.158 0.00 0.00 45.59 4.18
2642 2842 1.408969 GAAACCAAACCCCTTCAGCA 58.591 50.000 0.00 0.00 0.00 4.41
2676 2876 2.942648 GAATGCCTCCGTGGTAGGGC 62.943 65.000 11.29 11.29 44.31 5.19
2841 3041 0.599204 GGAACTTGTCGAGGAACGCA 60.599 55.000 0.00 0.00 42.26 5.24
2943 3143 1.953686 TGCTACCTTCAAAACTGGCAC 59.046 47.619 0.00 0.00 0.00 5.01
2966 3166 5.682990 GCATCTACATTACCTTTGGGTACGA 60.683 44.000 0.00 0.00 46.62 3.43
3041 3246 0.175760 ACACACCTACAGGCGCATAG 59.824 55.000 10.83 7.69 39.32 2.23
3042 3247 0.108377 CACACACCTACAGGCGCATA 60.108 55.000 10.83 0.00 39.32 3.14
3043 3248 1.375908 CACACACCTACAGGCGCAT 60.376 57.895 10.83 0.00 39.32 4.73
3044 3249 2.030412 CACACACCTACAGGCGCA 59.970 61.111 10.83 0.00 39.32 6.09
3045 3250 1.164041 AAACACACACCTACAGGCGC 61.164 55.000 0.00 0.00 39.32 6.53
3147 3354 2.983136 CAGACACGAAGACACATCACTC 59.017 50.000 0.00 0.00 0.00 3.51
3148 3355 2.362397 ACAGACACGAAGACACATCACT 59.638 45.455 0.00 0.00 0.00 3.41
3149 3356 2.472861 CACAGACACGAAGACACATCAC 59.527 50.000 0.00 0.00 0.00 3.06
3150 3357 2.742774 CACAGACACGAAGACACATCA 58.257 47.619 0.00 0.00 0.00 3.07
3151 3358 1.457303 GCACAGACACGAAGACACATC 59.543 52.381 0.00 0.00 0.00 3.06
3152 3359 1.202521 TGCACAGACACGAAGACACAT 60.203 47.619 0.00 0.00 0.00 3.21
3182 3389 8.428063 AGAACAAACCATTCCATATGTCAAAAA 58.572 29.630 1.24 0.00 0.00 1.94
3230 3437 1.948834 GCGAGGTAGGAGGAGTACTTC 59.051 57.143 0.00 0.00 0.00 3.01
3285 3495 0.808453 AACACTCAACACGACCACCG 60.808 55.000 0.00 0.00 45.44 4.94
3401 3611 5.177327 TGACAATATATGTGCACATGCGTAG 59.823 40.000 36.72 25.50 44.12 3.51
3402 3612 5.050431 GTGACAATATATGTGCACATGCGTA 60.050 40.000 36.72 26.12 44.12 4.42
3415 3625 7.171508 CGCAGATGTAAACAGGTGACAATATAT 59.828 37.037 0.00 0.00 0.00 0.86
3421 3631 2.224185 ACGCAGATGTAAACAGGTGACA 60.224 45.455 0.00 0.00 0.00 3.58
3422 3632 2.157668 CACGCAGATGTAAACAGGTGAC 59.842 50.000 0.00 0.00 0.00 3.67
3423 3633 2.224185 ACACGCAGATGTAAACAGGTGA 60.224 45.455 0.00 0.00 0.00 4.02
3424 3634 2.143122 ACACGCAGATGTAAACAGGTG 58.857 47.619 0.00 0.00 0.00 4.00
3425 3635 2.037251 AGACACGCAGATGTAAACAGGT 59.963 45.455 0.00 0.00 31.24 4.00
3426 3636 2.688507 AGACACGCAGATGTAAACAGG 58.311 47.619 0.00 0.00 31.24 4.00
3427 3637 4.486090 AGTAGACACGCAGATGTAAACAG 58.514 43.478 0.00 0.00 31.24 3.16
3428 3638 4.514781 AGTAGACACGCAGATGTAAACA 57.485 40.909 0.00 0.00 31.24 2.83
3429 3639 5.162075 AGAAGTAGACACGCAGATGTAAAC 58.838 41.667 0.00 0.00 31.24 2.01
3431 3641 4.700692 AGAGAAGTAGACACGCAGATGTAA 59.299 41.667 0.00 0.00 31.24 2.41
3433 3643 3.085533 AGAGAAGTAGACACGCAGATGT 58.914 45.455 0.00 0.00 34.78 3.06
3434 3644 3.433709 CAGAGAAGTAGACACGCAGATG 58.566 50.000 0.00 0.00 0.00 2.90
3438 3648 1.248486 AGCAGAGAAGTAGACACGCA 58.752 50.000 0.00 0.00 0.00 5.24
3439 3649 2.355717 AAGCAGAGAAGTAGACACGC 57.644 50.000 0.00 0.00 0.00 5.34
3484 3701 3.984508 CGTACTATCCCACGTTCTCAT 57.015 47.619 0.00 0.00 33.56 2.90
3526 3743 0.108019 ACCCGAACCAAGTTCCAGAC 59.892 55.000 2.06 0.00 39.14 3.51
3564 3782 1.135689 CAAGTTTCTACGGCACATGGC 60.136 52.381 0.00 0.00 43.74 4.40
3780 4012 4.021368 CCTAACCTGACGAGAAAAGAAGGA 60.021 45.833 0.00 0.00 0.00 3.36
3791 4023 2.642254 CGGCCACCTAACCTGACGA 61.642 63.158 2.24 0.00 0.00 4.20
3824 4056 0.963355 AGAGGACGGTCTCACTCTGC 60.963 60.000 12.66 0.00 38.76 4.26
3840 4072 0.605589 AAGCGACCTCCACTGAAGAG 59.394 55.000 0.00 0.00 0.00 2.85
3843 4075 0.034896 GGAAAGCGACCTCCACTGAA 59.965 55.000 0.00 0.00 0.00 3.02
3926 4161 3.425492 GCTCGCTTGAAGTTTTCTGATCC 60.425 47.826 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.