AutoCloner

Multiple sequence alignment - TraesCS5D01G400300

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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	TraesCS5D01G400300	chr5D	100.000	2808	0	0	1	2808	465449914	465447107	0.000000e+00	5186
1	TraesCS5D01G400300	chr5D	96.262	535	19	1	1	535	465465062	465464529	0.000000e+00	876
2	TraesCS5D01G400300	chr5D	83.369	463	53	13	1	443	258892534	258892992	9.360000e-110	407
3	TraesCS5D01G400300	chr5B	91.445	2104	93	39	730	2808	572856145	572854104	0.000000e+00	2808
4	TraesCS5D01G400300	chr5B	91.451	2082	86	34	537	2564	572856361	572854318	0.000000e+00	2774
5	TraesCS5D01G400300	chr5B	89.405	538	50	6	1	535	561005379	561004846	0.000000e+00	671
6	TraesCS5D01G400300	chr5B	82.973	370	44	5	167	535	182470487	182470136	1.620000e-82	316
7	TraesCS5D01G400300	chr5B	94.079	152	7	2	1	151	182470704	182470554	2.180000e-56	230
8	TraesCS5D01G400300	chr5A	90.437	1579	80	23	639	2153	585739869	585738298	0.000000e+00	2013
9	TraesCS5D01G400300	chr5A	91.544	272	9	7	2157	2417	585738172	585737904	2.060000e-96	363
10	TraesCS5D01G400300	chr5A	91.824	159	8	4	1	155	210842413	210842570	1.690000e-52	217
11	TraesCS5D01G400300	chr5A	94.048	84	4	1	2444	2526	585737906	585737823	2.940000e-25	126
12	TraesCS5D01G400300	chr6A	83.063	555	63	15	1	535	132936625	132936082	2.530000e-130	475
13	TraesCS5D01G400300	chr6A	82.251	462	62	10	1	443	264272091	264271631	5.680000e-102	381
14	TraesCS5D01G400300	chrUn	82.319	526	62	13	30	535	301066018	301065504	7.190000e-116	427
15	TraesCS5D01G400300	chrUn	82.319	526	62	13	30	535	301084562	301084048	7.190000e-116	427
16	TraesCS5D01G400300	chr6B	82.171	516	61	13	40	535	5304736	5305240	5.600000e-112	414
17	TraesCS5D01G400300	chr7A	82.119	453	55	20	9	444	516156574	516156131	5.720000e-97	364
18	TraesCS5D01G400300	chr7A	81.662	349	49	7	201	546	55829577	55829241	2.760000e-70	276
19	TraesCS5D01G400300	chr7B	81.466	464	64	11	1	445	255784987	255784527	7.390000e-96	361
20	TraesCS5D01G400300	chr7B	86.517	89	12	0	447	535	712955258	712955346	6.400000e-17	99
21	TraesCS5D01G400300	chr1A	81.236	453	61	14	14	445	228110565	228110116	7.450000e-91	344
22	TraesCS5D01G400300	chr6D	84.452	283	21	12	9	271	3140664	3140943	9.980000e-65	257

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	TraesCS5D01G400300	chr5D	465447107	465449914	2807	True	5186	5186	100.000000	1	2808	1	chr5D.!!$R1	2807
1	TraesCS5D01G400300	chr5D	465464529	465465062	533	True	876	876	96.262000	1	535	1	chr5D.!!$R2	534
2	TraesCS5D01G400300	chr5B	572854104	572856361	2257	True	2791	2808	91.448000	537	2808	2	chr5B.!!$R3	2271
3	TraesCS5D01G400300	chr5B	561004846	561005379	533	True	671	671	89.405000	1	535	1	chr5B.!!$R1	534
4	TraesCS5D01G400300	chr5B	182470136	182470704	568	True	273	316	88.526000	1	535	2	chr5B.!!$R2	534
5	TraesCS5D01G400300	chr5A	585737823	585739869	2046	True	834	2013	92.009667	639	2526	3	chr5A.!!$R1	1887
6	TraesCS5D01G400300	chr6A	132936082	132936625	543	True	475	475	83.063000	1	535	1	chr6A.!!$R1	534
7	TraesCS5D01G400300	chrUn	301065504	301066018	514	True	427	427	82.319000	30	535	1	chrUn.!!$R1	505
8	TraesCS5D01G400300	chrUn	301084048	301084562	514	True	427	427	82.319000	30	535	1	chrUn.!!$R2	505
9	TraesCS5D01G400300	chr6B	5304736	5305240	504	False	414	414	82.171000	40	535	1	chr6B.!!$F1	495

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
589	645	0.255890	GTGACATGGTGGGTAGGCAT	59.744	55.0	0.0	0.0	0.0	4.40	F
1239	1332	0.931005	CCGAGCTGGATTTCTTACGC	59.069	55.0	0.0	0.0	42.0	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1601	1704	0.249398	GAGCGGTCTTGGCCTTCTTA	59.751	55.000	7.51	0.0	0.00	2.10	R
2634	2922	1.339055	TGATCTACTGTTGCAGCCCAC	60.339	52.381	0.00	0.0	34.37	4.61	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
114	115	4.799419	ACAAACTTCAAAATGTGCATGC	57.201	36.364	11.82	11.82	0.00	4.06
181	225	5.165961	TGACCTCTTATGCAGCTTTTAGT	57.834	39.130	0.00	0.00	0.00	2.24
245	300	3.748568	GGCAGAAAGGAATATAAGCGGAG	59.251	47.826	0.00	0.00	0.00	4.63
347	403	0.741574	TCTTCCGTTGCAACACACGT	60.742	50.000	28.01	0.00	0.00	4.49
356	412	1.267782	TGCAACACACGTGAACATTCG	60.268	47.619	25.01	4.70	0.00	3.34
405	461	9.136323	GAATACCCATTACTGAATTTCTTCCAT	57.864	33.333	0.00	0.00	0.00	3.41
514	570	3.482436	TGTTTACTTCTCCCGTTGCAAT	58.518	40.909	0.59	0.00	0.00	3.56
515	571	3.500680	TGTTTACTTCTCCCGTTGCAATC	59.499	43.478	0.59	0.00	0.00	2.67
573	629	7.877612	TCTGAATAGCTTCATGTTTACAAGTGA	59.122	33.333	0.00	0.00	40.52	3.41
574	630	7.806690	TGAATAGCTTCATGTTTACAAGTGAC	58.193	34.615	0.00	0.00	36.46	3.67
576	632	7.928307	ATAGCTTCATGTTTACAAGTGACAT	57.072	32.000	0.00	0.00	34.52	3.06
579	635	5.278463	GCTTCATGTTTACAAGTGACATGGT	60.278	40.000	20.97	0.00	46.54	3.55
580	636	5.687770	TCATGTTTACAAGTGACATGGTG	57.312	39.130	20.97	7.47	46.54	4.17
581	637	4.518590	TCATGTTTACAAGTGACATGGTGG	59.481	41.667	20.97	6.21	46.54	4.61
582	638	3.218453	TGTTTACAAGTGACATGGTGGG	58.782	45.455	0.00	0.00	0.00	4.61
584	640	4.141459	TGTTTACAAGTGACATGGTGGGTA	60.141	41.667	0.00	0.00	0.00	3.69
585	641	2.859165	ACAAGTGACATGGTGGGTAG	57.141	50.000	0.00	0.00	0.00	3.18
586	642	1.351017	ACAAGTGACATGGTGGGTAGG	59.649	52.381	0.00	0.00	0.00	3.18
587	643	0.328258	AAGTGACATGGTGGGTAGGC	59.672	55.000	0.00	0.00	0.00	3.93
588	644	0.840288	AGTGACATGGTGGGTAGGCA	60.840	55.000	0.00	0.00	0.00	4.75
589	645	0.255890	GTGACATGGTGGGTAGGCAT	59.744	55.000	0.00	0.00	0.00	4.40
590	646	0.998928	TGACATGGTGGGTAGGCATT	59.001	50.000	0.00	0.00	0.00	3.56
591	647	1.357420	TGACATGGTGGGTAGGCATTT	59.643	47.619	0.00	0.00	0.00	2.32
592	648	2.024414	GACATGGTGGGTAGGCATTTC	58.976	52.381	0.00	0.00	0.00	2.17
593	649	1.640670	ACATGGTGGGTAGGCATTTCT	59.359	47.619	0.00	0.00	0.00	2.52
609	665	8.260270	AGGCATTTCTAAGAAATTTCAAATGC	57.740	30.769	33.02	33.02	44.03	3.56
613	669	7.636259	TTTCTAAGAAATTTCAAATGCCACG	57.364	32.000	19.99	0.00	0.00	4.94
643	699	9.713338	TGCACTCATGGGACAAATATTGAATGC	62.713	40.741	0.00	0.00	43.12	3.56
749	839	2.200373	AAACCAGGCGCACTTTCTAT	57.800	45.000	10.83	0.00	0.00	1.98
754	844	4.076394	ACCAGGCGCACTTTCTATAAAAA	58.924	39.130	10.83	0.00	0.00	1.94
806	896	2.009774	CCACGCATAAAGAACTCCTGG	58.990	52.381	0.00	0.00	0.00	4.45
863	953	2.908015	GTCCGATTAGGCCAGCCA	59.092	61.111	12.03	0.00	40.77	4.75
885	975	2.036992	GAGCAATCTCATCCGTCCATCT	59.963	50.000	0.00	0.00	39.16	2.90
888	978	3.742327	GCAATCTCATCCGTCCATCTTCA	60.742	47.826	0.00	0.00	0.00	3.02
892	982	6.617782	ATCTCATCCGTCCATCTTCATTAT	57.382	37.500	0.00	0.00	0.00	1.28
1125	1216	2.089980	CCATATCCCGAGGTACTACCG	58.910	57.143	0.00	0.00	44.90	4.02
1152	1244	1.862201	CCGTTTCTCGCTGTGTTGTAA	59.138	47.619	0.00	0.00	38.35	2.41
1208	1301	4.154015	GCCAAGATTTACATTTTGTTGGGC	59.846	41.667	0.00	0.00	34.71	5.36
1239	1332	0.931005	CCGAGCTGGATTTCTTACGC	59.069	55.000	0.00	0.00	42.00	4.42
1249	1342	4.184629	GGATTTCTTACGCTGATCTGTGT	58.815	43.478	20.56	20.56	34.78	3.72
1280	1374	3.027412	ACGAGTTCAGATGATACTGGCT	58.973	45.455	0.00	0.00	38.31	4.75
2005	2136	2.936498	CGGTGGATGGATTAACTGTGTC	59.064	50.000	0.00	0.00	0.00	3.67
2054	2194	0.178932	ACCAGGTGTCTGCTCCAGTA	60.179	55.000	0.00	0.00	39.61	2.74
2069	2225	6.864342	TGCTCCAGTATTTTGTAGTCTACTC	58.136	40.000	11.28	0.00	0.00	2.59
2071	2227	7.832685	TGCTCCAGTATTTTGTAGTCTACTCTA	59.167	37.037	11.28	0.00	0.00	2.43
2072	2228	8.130469	GCTCCAGTATTTTGTAGTCTACTCTAC	58.870	40.741	11.28	7.39	40.22	2.59
2080	2236	8.930846	TTTTGTAGTCTACTCTACCTAGTTGT	57.069	34.615	11.28	0.00	39.39	3.32
2082	2238	7.250032	TGTAGTCTACTCTACCTAGTTGTGA	57.750	40.000	11.28	0.00	39.39	3.58
2083	2239	7.683578	TGTAGTCTACTCTACCTAGTTGTGAA	58.316	38.462	11.28	0.00	39.39	3.18
2103	2259	5.000591	TGAATTGTGATCGAGCCTGTTAAA	58.999	37.500	0.00	0.00	0.00	1.52
2110	2266	4.693566	TGATCGAGCCTGTTAAAATTCGTT	59.306	37.500	0.00	0.00	0.00	3.85
2111	2267	4.398549	TCGAGCCTGTTAAAATTCGTTG	57.601	40.909	0.00	0.00	0.00	4.10
2175	2453	4.864334	GTGATGGGCTGCCGAGGG	62.864	72.222	13.40	0.00	0.00	4.30
2243	2521	3.330720	GCTGGCCTGGTACCTGGT	61.331	66.667	31.72	4.05	37.37	4.00
2342	2629	5.630121	ACCACAACACAATCTTGAGGAATA	58.370	37.500	0.00	0.00	34.47	1.75
2417	2704	6.357367	AGGCAACCTCATTTATCTACGAAAT	58.643	36.000	0.00	0.00	37.17	2.17
2512	2799	2.874664	GCACACCGTGGGAGGTACA	61.875	63.158	4.51	0.00	43.89	2.90
2634	2922	2.544685	CGGCAGACAGGTTATCTGAAG	58.455	52.381	0.00	0.00	45.46	3.02
2636	2924	3.265791	GGCAGACAGGTTATCTGAAGTG	58.734	50.000	0.00	0.00	45.46	3.16
2647	2935	0.535780	TCTGAAGTGGGCTGCAACAG	60.536	55.000	0.50	1.79	27.90	3.16
2650	2938	1.160137	GAAGTGGGCTGCAACAGTAG	58.840	55.000	0.50	0.00	33.43	2.57
2713	3002	9.886132	ACAAAGTAACGAGAGATAAAACCATAT	57.114	29.630	0.00	0.00	0.00	1.78
2730	3019	8.840833	AAACCATATTTTACACCACCAAAATC	57.159	30.769	0.00	0.00	36.18	2.17
2742	3031	3.449737	CCACCAAAATCAGATGAGGCATT	59.550	43.478	0.00	0.00	0.00	3.56
2775	3064	2.264794	GTGACAATCCCCGACGCT	59.735	61.111	0.00	0.00	0.00	5.07
2784	3073	2.476126	TCCCCGACGCTGAAATAAAA	57.524	45.000	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
181	225	2.027653	TGTCCACCTTGCGTCAATCATA	60.028	45.455	0.00	0.00	0.00	2.15
245	300	5.189928	TCAACACAATACCCCACATGTATC	58.810	41.667	0.00	0.00	0.00	2.24
347	403	3.501445	TGACATGCACATTCGAATGTTCA	59.499	39.130	34.55	34.55	46.95	3.18
405	461	7.880713	TGCAAGAACATAAGTGGTCAACTATAA	59.119	33.333	0.00	0.00	44.77	0.98
514	570	2.778299	ACTAGCAAAAATGCTCGTGGA	58.222	42.857	6.59	0.00	45.00	4.02
515	571	3.058293	TGAACTAGCAAAAATGCTCGTGG	60.058	43.478	6.59	0.00	45.00	4.94
559	615	4.321156	CCCACCATGTCACTTGTAAACATG	60.321	45.833	15.58	15.58	46.25	3.21
573	629	1.640670	AGAAATGCCTACCCACCATGT	59.359	47.619	0.00	0.00	0.00	3.21
574	630	2.442236	AGAAATGCCTACCCACCATG	57.558	50.000	0.00	0.00	0.00	3.66
576	632	3.186283	TCTTAGAAATGCCTACCCACCA	58.814	45.455	0.00	0.00	0.00	4.17
579	635	6.951198	TGAAATTTCTTAGAAATGCCTACCCA	59.049	34.615	19.35	8.26	0.00	4.51
580	636	7.404671	TGAAATTTCTTAGAAATGCCTACCC	57.595	36.000	19.35	6.24	0.00	3.69
581	637	9.875691	ATTTGAAATTTCTTAGAAATGCCTACC	57.124	29.630	19.35	7.36	0.00	3.18
584	640	8.260270	GCATTTGAAATTTCTTAGAAATGCCT	57.740	30.769	32.01	8.53	44.99	4.75
587	643	8.164153	CGTGGCATTTGAAATTTCTTAGAAATG	58.836	33.333	24.02	24.02	35.07	2.32
588	644	7.331687	CCGTGGCATTTGAAATTTCTTAGAAAT	59.668	33.333	18.64	13.82	0.00	2.17
589	645	6.644592	CCGTGGCATTTGAAATTTCTTAGAAA	59.355	34.615	18.64	9.99	0.00	2.52
590	646	6.155827	CCGTGGCATTTGAAATTTCTTAGAA	58.844	36.000	18.64	8.95	0.00	2.10
591	647	5.242838	ACCGTGGCATTTGAAATTTCTTAGA	59.757	36.000	18.64	3.30	0.00	2.10
592	648	5.345741	CACCGTGGCATTTGAAATTTCTTAG	59.654	40.000	18.64	7.70	0.00	2.18
593	649	5.221342	ACACCGTGGCATTTGAAATTTCTTA	60.221	36.000	18.64	7.40	0.00	2.10
609	665	2.327343	CCATGAGTGCACACCGTGG	61.327	63.158	25.85	25.85	34.63	4.94
613	669	0.537143	TTGTCCCATGAGTGCACACC	60.537	55.000	21.04	10.95	0.00	4.16
706	762	3.118542	GTGAAAGGCAAGCTGTTCAAAG	58.881	45.455	10.84	0.00	32.12	2.77
806	896	4.148825	ATCGGTGACCTGGCGAGC	62.149	66.667	0.00	0.00	0.00	5.03
863	953	1.489481	TGGACGGATGAGATTGCTCT	58.511	50.000	0.00	0.00	41.84	4.09
885	975	2.553602	GCATGGTGGCGATGATAATGAA	59.446	45.455	0.00	0.00	0.00	2.57
1107	1198	1.988107	TCCGGTAGTACCTCGGGATAT	59.012	52.381	17.29	0.00	43.54	1.63
1140	1231	6.305399	CCAGAAACAAATATTACAACACAGCG	59.695	38.462	0.00	0.00	0.00	5.18
1143	1234	7.283625	AGCCAGAAACAAATATTACAACACA	57.716	32.000	0.00	0.00	0.00	3.72
1152	1244	5.242838	TCGAACCAAAGCCAGAAACAAATAT	59.757	36.000	0.00	0.00	0.00	1.28
1221	1314	1.590238	CAGCGTAAGAAATCCAGCTCG	59.410	52.381	0.00	0.00	43.02	5.03
1561	1664	3.646715	CGGGGTCCTTGGGCTTGA	61.647	66.667	0.00	0.00	0.00	3.02
1601	1704	0.249398	GAGCGGTCTTGGCCTTCTTA	59.751	55.000	7.51	0.00	0.00	2.10
1762	1893	5.934625	AGCACTACAGAACAAGATTAACCAG	59.065	40.000	0.00	0.00	0.00	4.00
2054	2194	9.531158	ACAACTAGGTAGAGTAGACTACAAAAT	57.469	33.333	14.95	0.59	42.91	1.82
2069	2225	6.330278	TCGATCACAATTCACAACTAGGTAG	58.670	40.000	0.00	0.00	0.00	3.18
2071	2227	5.147330	TCGATCACAATTCACAACTAGGT	57.853	39.130	0.00	0.00	0.00	3.08
2072	2228	4.033358	GCTCGATCACAATTCACAACTAGG	59.967	45.833	0.00	0.00	0.00	3.02
2076	2232	2.744202	AGGCTCGATCACAATTCACAAC	59.256	45.455	0.00	0.00	0.00	3.32
2077	2233	2.743664	CAGGCTCGATCACAATTCACAA	59.256	45.455	0.00	0.00	0.00	3.33
2078	2234	2.289631	ACAGGCTCGATCACAATTCACA	60.290	45.455	0.00	0.00	0.00	3.58
2079	2235	2.350522	ACAGGCTCGATCACAATTCAC	58.649	47.619	0.00	0.00	0.00	3.18
2080	2236	2.768253	ACAGGCTCGATCACAATTCA	57.232	45.000	0.00	0.00	0.00	2.57
2082	2238	5.957842	TTTTAACAGGCTCGATCACAATT	57.042	34.783	0.00	0.00	0.00	2.32
2083	2239	6.515272	AATTTTAACAGGCTCGATCACAAT	57.485	33.333	0.00	0.00	0.00	2.71
2103	2259	5.064707	CGGAAGTGATCATTACCAACGAATT	59.935	40.000	0.00	0.00	0.00	2.17
2243	2521	5.502079	TCCCTCAAACTGACTTAAAACACA	58.498	37.500	0.00	0.00	0.00	3.72
2342	2629	1.509463	CATGTTGCCTGCTGCGATT	59.491	52.632	0.00	0.00	45.60	3.34
2395	2682	7.798982	GCTTATTTCGTAGATAAATGAGGTTGC	59.201	37.037	0.00	0.00	35.04	4.17
2417	2704	6.791867	TCTATAAAGCAGGACAAGAGCTTA	57.208	37.500	0.00	0.00	46.95	3.09
2468	2755	7.231317	CCATTGTATGTCCAAGCTTATATGGTT	59.769	37.037	0.00	0.00	37.94	3.67
2471	2758	6.207221	TGCCATTGTATGTCCAAGCTTATATG	59.793	38.462	0.00	0.00	0.00	1.78
2479	2766	2.164219	GGTGTGCCATTGTATGTCCAAG	59.836	50.000	0.00	0.00	34.09	3.61
2570	2858	9.927081	ACTCATTTTTATCCCAGTTATTCTGAT	57.073	29.630	0.00	0.00	46.27	2.90
2571	2859	9.396022	GACTCATTTTTATCCCAGTTATTCTGA	57.604	33.333	0.00	0.00	46.27	3.27
2572	2860	9.177608	TGACTCATTTTTATCCCAGTTATTCTG	57.822	33.333	0.00	0.00	43.27	3.02
2573	2861	9.927081	ATGACTCATTTTTATCCCAGTTATTCT	57.073	29.630	0.00	0.00	0.00	2.40
2579	2867	9.561069	GTGTATATGACTCATTTTTATCCCAGT	57.439	33.333	0.00	0.00	0.00	4.00
2580	2868	9.784531	AGTGTATATGACTCATTTTTATCCCAG	57.215	33.333	0.00	0.00	0.00	4.45
2609	2897	1.681793	GATAACCTGTCTGCCGCTCTA	59.318	52.381	0.00	0.00	0.00	2.43
2634	2922	1.339055	TGATCTACTGTTGCAGCCCAC	60.339	52.381	0.00	0.00	34.37	4.61
2636	2924	2.338577	ATGATCTACTGTTGCAGCCC	57.661	50.000	0.00	0.00	34.37	5.19
2696	2984	9.104965	TGGTGTAAAATATGGTTTTATCTCTCG	57.895	33.333	0.00	0.00	0.00	4.04
2701	2989	9.930693	TTTGGTGGTGTAAAATATGGTTTTATC	57.069	29.630	0.00	0.00	0.00	1.75
2713	3002	6.015519	CCTCATCTGATTTTGGTGGTGTAAAA	60.016	38.462	0.00	0.00	0.00	1.52
2714	3003	5.476599	CCTCATCTGATTTTGGTGGTGTAAA	59.523	40.000	0.00	0.00	0.00	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.