AutoCloner

Multiple sequence alignment - TraesCS7D01G284000

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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	TraesCS7D01G284000	chr7D	100.000	2877	0	0	1	2877	296515638	296512762	0.000000e+00	5313.0
1	TraesCS7D01G284000	chr7D	83.731	713	37	28	12	719	47518738	47519376	4.100000e-168	601.0
2	TraesCS7D01G284000	chr7D	85.350	157	18	5	568	723	240521450	240521602	1.070000e-34	158.0
3	TraesCS7D01G284000	chrUn	93.252	1971	91	15	717	2654	116439783	116437822	0.000000e+00	2865.0
4	TraesCS7D01G284000	chrUn	80.980	694	62	25	14	706	302507013	302507637	1.200000e-133	486.0
5	TraesCS7D01G284000	chrUn	80.980	694	61	24	14	706	302525119	302525742	4.310000e-133	484.0
6	TraesCS7D01G284000	chrUn	87.500	296	20	4	411	706	393322211	393321933	2.760000e-85	326.0
7	TraesCS7D01G284000	chrUn	87.500	296	20	4	411	706	393331978	393332256	2.760000e-85	326.0
8	TraesCS7D01G284000	chrUn	92.135	178	13	1	2700	2877	116437751	116437575	1.710000e-62	250.0
9	TraesCS7D01G284000	chr7B	92.526	1659	72	14	718	2346	339645947	339644311	0.000000e+00	2329.0
10	TraesCS7D01G284000	chr7B	90.274	329	17	6	2327	2654	339644288	339643974	1.590000e-112	416.0
11	TraesCS7D01G284000	chr7B	93.007	143	9	1	2700	2842	339643903	339643762	1.040000e-49	207.0
12	TraesCS7D01G284000	chr7A	92.105	570	33	4	152	713	705368057	705367492	0.000000e+00	793.0
13	TraesCS7D01G284000	chr7A	97.297	148	4	0	1	148	705369468	705369321	4.760000e-63	252.0
14	TraesCS7D01G284000	chr3D	88.755	498	27	11	217	712	383215247	383215717	1.490000e-162	582.0
15	TraesCS7D01G284000	chr3D	88.043	184	13	4	1	176	383215067	383215249	2.900000e-50	209.0
16	TraesCS7D01G284000	chr3D	82.482	137	21	3	584	719	372637476	372637610	1.810000e-22	117.0
17	TraesCS7D01G284000	chr3D	92.857	56	4	0	664	719	497712592	497712647	6.610000e-12	82.4
18	TraesCS7D01G284000	chr4B	88.247	502	37	11	215	712	88428371	88427888	5.340000e-162	580.0
19	TraesCS7D01G284000	chr4B	92.174	115	8	1	1	114	88840317	88840203	8.250000e-36	161.0
20	TraesCS7D01G284000	chr5D	97.445	274	7	0	1	274	496011429	496011702	4.340000e-128	468.0
21	TraesCS7D01G284000	chr5D	90.291	309	26	4	37	344	367524090	367524395	4.470000e-108	401.0
22	TraesCS7D01G284000	chr5D	86.032	315	22	6	347	646	367524612	367524919	4.630000e-83	318.0
23	TraesCS7D01G284000	chr5D	96.667	60	2	0	338	397	367524575	367524634	1.820000e-17	100.0
24	TraesCS7D01G284000	chr5A	90.237	338	22	8	13	344	469486814	469487146	5.690000e-117	431.0
25	TraesCS7D01G284000	chr5A	88.487	304	26	4	343	646	469487835	469488129	2.730000e-95	359.0
26	TraesCS7D01G284000	chr5A	84.564	149	19	2	571	719	663916967	663916823	8.310000e-31	145.0
27	TraesCS7D01G284000	chr5B	87.566	378	31	7	342	712	403192918	403192550	9.530000e-115	424.0
28	TraesCS7D01G284000	chr5B	86.111	180	12	9	546	720	42264822	42264651	6.330000e-42	182.0
29	TraesCS7D01G284000	chr1D	80.545	257	27	17	475	723	99412896	99412655	2.950000e-40	176.0
30	TraesCS7D01G284000	chr1D	82.468	154	22	2	570	721	200345362	200345512	2.330000e-26	130.0
31	TraesCS7D01G284000	chr1D	95.385	65	3	0	1	65	212084956	212084892	1.410000e-18	104.0
32	TraesCS7D01G284000	chr1B	79.149	235	25	11	489	721	678284673	678284461	1.070000e-29	141.0
33	TraesCS7D01G284000	chr6D	98.305	59	1	0	1	59	21113050	21113108	1.410000e-18	104.0
34	TraesCS7D01G284000	chr6D	95.385	65	3	0	1	65	364856810	364856746	1.410000e-18	104.0

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	TraesCS7D01G284000	chr7D	296512762	296515638	2876	True	5313.0	5313	100.000000	1	2877	1	chr7D.!!$R1	2876
1	TraesCS7D01G284000	chr7D	47518738	47519376	638	False	601.0	601	83.731000	12	719	1	chr7D.!!$F1	707
2	TraesCS7D01G284000	chrUn	116437575	116439783	2208	True	1557.5	2865	92.693500	717	2877	2	chrUn.!!$R2	2160
3	TraesCS7D01G284000	chrUn	302507013	302507637	624	False	486.0	486	80.980000	14	706	1	chrUn.!!$F1	692
4	TraesCS7D01G284000	chrUn	302525119	302525742	623	False	484.0	484	80.980000	14	706	1	chrUn.!!$F2	692
5	TraesCS7D01G284000	chr7B	339643762	339645947	2185	True	984.0	2329	91.935667	718	2842	3	chr7B.!!$R1	2124
6	TraesCS7D01G284000	chr7A	705367492	705369468	1976	True	522.5	793	94.701000	1	713	2	chr7A.!!$R1	712
7	TraesCS7D01G284000	chr3D	383215067	383215717	650	False	395.5	582	88.399000	1	712	2	chr3D.!!$F3	711
8	TraesCS7D01G284000	chr5D	367524090	367524919	829	False	273.0	401	90.996667	37	646	3	chr5D.!!$F2	609
9	TraesCS7D01G284000	chr5A	469486814	469488129	1315	False	395.0	431	89.362000	13	646	2	chr5A.!!$F1	633

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
690	2760	0.178873	AGGGGAGCAGGAACCTTACA	60.179	55.0	0.0	0.0	0.0	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2296	4417	1.02833	CGGCAAGCATGTCCACAGAT	61.028	55.0	0.0	0.0	0.0	2.9	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
316	1615	1.224592	GAAGTGGTGGGATCGGCAT	59.775	57.895	0.00	0.00	0.00	4.40
403	2029	6.287525	GGTGATAGAAGAAAGGAAGGAGATG	58.712	44.000	0.00	0.00	0.00	2.90
566	2635	9.981114	GATAGAAGAAAGGAATTGAAAACCAAA	57.019	29.630	0.00	0.00	38.43	3.28
646	2716	1.246737	GGGGTCGTACGAGAGGTTGT	61.247	60.000	20.18	0.00	0.00	3.32
647	2717	0.600057	GGGTCGTACGAGAGGTTGTT	59.400	55.000	20.18	0.00	0.00	2.83
648	2718	1.668047	GGGTCGTACGAGAGGTTGTTG	60.668	57.143	20.18	0.00	0.00	3.33
666	2736	0.896940	TGGACGAAGCGAGGGTAACT	60.897	55.000	0.00	0.00	0.00	2.24
678	2748	2.435069	GAGGGTAACTTAAGAGGGGAGC	59.565	54.545	10.09	0.00	0.00	4.70
679	2749	2.193993	GGGTAACTTAAGAGGGGAGCA	58.806	52.381	10.09	0.00	0.00	4.26
690	2760	0.178873	AGGGGAGCAGGAACCTTACA	60.179	55.000	0.00	0.00	0.00	2.41
821	2900	0.756294	TCCTCAAACTGCTCCAACGA	59.244	50.000	0.00	0.00	0.00	3.85
829	2908	1.961394	ACTGCTCCAACGACTAACTGA	59.039	47.619	0.00	0.00	0.00	3.41
868	2947	7.592938	TCATCACAAACTAAAAATAGCCACAG	58.407	34.615	0.00	0.00	0.00	3.66
899	2978	6.624917	CACTTGTCATCGCGTATTTTAATCAG	59.375	38.462	5.77	0.00	0.00	2.90
933	3012	7.119846	AGGAACAGTGCATCAGAAAACTATTAC	59.880	37.037	0.00	0.00	0.00	1.89
934	3013	7.094805	GGAACAGTGCATCAGAAAACTATTACA	60.095	37.037	0.00	0.00	0.00	2.41
935	3014	7.369803	ACAGTGCATCAGAAAACTATTACAG	57.630	36.000	0.00	0.00	0.00	2.74
980	3059	5.260027	AGTTTACTCGTCGTTGTAATTGC	57.740	39.130	11.88	0.00	0.00	3.56
1005	3084	7.596494	CAATTAGTTGTTGTCCATTCATGTCT	58.404	34.615	0.00	0.00	0.00	3.41
1006	3085	6.558771	TTAGTTGTTGTCCATTCATGTCTG	57.441	37.500	0.00	0.00	0.00	3.51
1007	3086	3.822735	AGTTGTTGTCCATTCATGTCTGG	59.177	43.478	9.26	9.26	0.00	3.86
1426	3517	3.329889	TCACCATGCCGGCCTTCT	61.330	61.111	26.77	2.51	39.03	2.85
1551	3642	6.356190	GCTGACTGAAAATTTTGTACGTGTAC	59.644	38.462	8.47	3.21	36.63	2.90
1636	3727	3.258123	ACAAATACTTCAACATGGTGGCC	59.742	43.478	11.68	0.00	0.00	5.36
1879	3970	1.804748	GCACCCAAGAACTTCTAACCG	59.195	52.381	0.00	0.00	0.00	4.44
1884	3975	2.235402	CCAAGAACTTCTAACCGCCCTA	59.765	50.000	0.00	0.00	0.00	3.53
1927	4018	6.183360	GCCAAGTGTAAATTCATCGAATCTCA	60.183	38.462	0.00	0.00	30.29	3.27
2000	4091	3.253432	GCGTCAAGAAACAAGATTCCCTT	59.747	43.478	0.00	0.00	34.91	3.95
2007	4098	6.149129	AGAAACAAGATTCCCTTTGACAAC	57.851	37.500	0.00	0.00	31.42	3.32
2053	4157	2.561569	AGAAACAAGACTTGTGTCCGG	58.438	47.619	27.75	0.00	46.84	5.14
2055	4159	0.107410	AACAAGACTTGTGTCCGGCA	60.107	50.000	21.24	0.00	44.59	5.69
2062	4166	2.476534	CTTGTGTCCGGCATTGCACC	62.477	60.000	11.39	0.00	0.00	5.01
2247	4359	2.781681	TTCCTTTCCTCCACGATTCC	57.218	50.000	0.00	0.00	0.00	3.01
2296	4417	3.385749	GATCCTCCTTCCCGCGCAA	62.386	63.158	8.75	0.00	0.00	4.85
2336	4457	1.082117	GGCGTCAATGGAGGTACACG	61.082	60.000	0.00	0.00	0.00	4.49
2543	4701	6.645003	ACTTTCAAAACTGTTGAGAACAAACC	59.355	34.615	7.23	0.00	41.61	3.27
2614	4772	1.064166	CCAGCCCACCAGAGATCAAAT	60.064	52.381	0.00	0.00	0.00	2.32
2615	4773	2.622452	CCAGCCCACCAGAGATCAAATT	60.622	50.000	0.00	0.00	0.00	1.82
2616	4774	2.426024	CAGCCCACCAGAGATCAAATTG	59.574	50.000	0.00	0.00	0.00	2.32
2658	4816	8.870160	TGTCTCATGATAAAAACAAAACAAGG	57.130	30.769	0.00	0.00	0.00	3.61
2659	4817	7.925483	TGTCTCATGATAAAAACAAAACAAGGG	59.075	33.333	0.00	0.00	0.00	3.95
2660	4818	7.926018	GTCTCATGATAAAAACAAAACAAGGGT	59.074	33.333	0.00	0.00	0.00	4.34
2661	4819	8.141268	TCTCATGATAAAAACAAAACAAGGGTC	58.859	33.333	0.00	0.00	0.00	4.46
2662	4820	7.786030	TCATGATAAAAACAAAACAAGGGTCA	58.214	30.769	0.00	0.00	0.00	4.02
2674	4832	8.650490	ACAAAACAAGGGTCATATTCTTTCAAT	58.350	29.630	0.00	0.00	0.00	2.57
2704	4868	3.751246	CGAGTACGACGCCCCCAA	61.751	66.667	0.00	0.00	42.66	4.12
2751	4943	9.206870	ACAACAAATATGCAAATTTAAGAGGTG	57.793	29.630	0.00	0.00	0.00	4.00
2786	4978	8.034804	GCATTACCCATAAAAACTCATCAAACT	58.965	33.333	0.00	0.00	0.00	2.66
2790	4982	6.323739	ACCCATAAAAACTCATCAAACTGTGT	59.676	34.615	0.00	0.00	0.00	3.72
2799	4991	4.609947	TCATCAAACTGTGTGCATGTTTC	58.390	39.130	0.00	0.00	32.42	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
316	1615	2.247637	CGAATTCGCACTCGTCAGTTA	58.752	47.619	15.93	0.00	36.96	2.24
403	2029	6.743575	TCTTTCGATCAATTCCTTTCTTCC	57.256	37.500	0.00	0.00	0.00	3.46
556	2625	3.851098	CCGGTTTTGTCTTTGGTTTTCA	58.149	40.909	0.00	0.00	0.00	2.69
566	2635	1.073199	CTCCCTGCCGGTTTTGTCT	59.927	57.895	1.90	0.00	0.00	3.41
646	2716	0.037975	GTTACCCTCGCTTCGTCCAA	60.038	55.000	0.00	0.00	0.00	3.53
647	2717	0.896940	AGTTACCCTCGCTTCGTCCA	60.897	55.000	0.00	0.00	0.00	4.02
648	2718	0.245813	AAGTTACCCTCGCTTCGTCC	59.754	55.000	0.00	0.00	0.00	4.79
666	2736	1.203440	AGGTTCCTGCTCCCCTCTTAA	60.203	52.381	0.00	0.00	0.00	1.85
678	2748	7.761038	ACCTAAAAGAAATGTAAGGTTCCTG	57.239	36.000	0.00	0.00	33.59	3.86
679	2749	8.666821	ACTACCTAAAAGAAATGTAAGGTTCCT	58.333	33.333	0.00	0.00	38.31	3.36
715	2785	4.083802	GCAAACGCTGACCTGGAATATATC	60.084	45.833	0.00	0.00	0.00	1.63
717	2787	3.118408	AGCAAACGCTGACCTGGAATATA	60.118	43.478	0.00	0.00	38.67	0.86
718	2788	2.017049	GCAAACGCTGACCTGGAATAT	58.983	47.619	0.00	0.00	0.00	1.28
719	2789	1.003118	AGCAAACGCTGACCTGGAATA	59.997	47.619	0.00	0.00	38.67	1.75
720	2790	0.250901	AGCAAACGCTGACCTGGAAT	60.251	50.000	0.00	0.00	38.67	3.01
721	2791	0.884704	GAGCAAACGCTGACCTGGAA	60.885	55.000	0.00	0.00	40.78	3.53
868	2947	3.084579	CGATGACAAGTGCGAGGC	58.915	61.111	0.00	0.00	0.00	4.70
914	2993	7.278868	AGCTACTGTAATAGTTTTCTGATGCAC	59.721	37.037	0.00	0.00	40.89	4.57
970	3049	7.436673	TGGACAACAACTAATTGCAATTACAAC	59.563	33.333	24.63	11.60	39.66	3.32
980	3059	7.539710	CAGACATGAATGGACAACAACTAATTG	59.460	37.037	0.00	0.00	41.98	2.32
1006	3085	4.459089	GAGAGGCGCCCACAGACC	62.459	72.222	26.15	3.65	0.00	3.85
1007	3086	4.803426	CGAGAGGCGCCCACAGAC	62.803	72.222	26.15	11.96	0.00	3.51
1164	3255	1.447838	CGTGTCCTTGTAGCCGCAT	60.448	57.895	0.00	0.00	0.00	4.73
1426	3517	1.604147	TTCTCCTCCGCGATCTGCAA	61.604	55.000	8.23	0.00	46.97	4.08
1551	3642	4.782116	CACTGCATCGCACGCACG	62.782	66.667	0.00	0.00	35.08	5.34
1609	3700	5.243730	CACCATGTTGAAGTATTTGTTCCCT	59.756	40.000	0.00	0.00	0.00	4.20
1879	3970	1.871676	GCTAGCACGGTTTTATAGGGC	59.128	52.381	10.63	0.00	33.87	5.19
1906	3997	8.498054	AACATGAGATTCGATGAATTTACACT	57.502	30.769	0.00	0.00	31.89	3.55
1927	4018	1.420138	ACTCCGAGGGACACAAAACAT	59.580	47.619	0.00	0.00	0.00	2.71
2000	4091	6.567687	TCTTTGTTTCTTGTCAGTTGTCAA	57.432	33.333	0.00	0.00	0.00	3.18
2007	4098	8.861033	TTCATTCATTCTTTGTTTCTTGTCAG	57.139	30.769	0.00	0.00	0.00	3.51
2055	4159	4.666253	AGTGCCCAGCGGTGCAAT	62.666	61.111	9.63	0.89	39.57	3.56
2062	4166	2.180017	GCATGAAAGTGCCCAGCG	59.820	61.111	0.00	0.00	39.18	5.18
2131	4236	2.048503	GGACGTCCCGTTCTGTGG	60.049	66.667	24.75	0.00	41.37	4.17
2247	4359	1.131218	CGACTGCAGCGTCAACATG	59.869	57.895	15.27	0.00	33.54	3.21
2296	4417	1.028330	CGGCAAGCATGTCCACAGAT	61.028	55.000	0.00	0.00	0.00	2.90
2336	4457	4.374399	CAAAGGCATTATCAAGATTGGCC	58.626	43.478	0.00	0.00	40.18	5.36
2519	4677	6.868339	AGGTTTGTTCTCAACAGTTTTGAAAG	59.132	34.615	0.00	0.00	43.27	2.62
2543	4701	4.618920	ACCACTAACCTTCCAACTACAG	57.381	45.455	0.00	0.00	0.00	2.74
2570	4728	1.732259	GGTTTGATACGTGGTGAGCTG	59.268	52.381	0.00	0.00	0.00	4.24
2606	4764	6.199937	AGCGTAAAATCTGCAATTTGATCT	57.800	33.333	0.00	1.70	0.00	2.75
2614	4772	4.455533	AGACATCAAGCGTAAAATCTGCAA	59.544	37.500	0.00	0.00	0.00	4.08
2615	4773	4.002982	AGACATCAAGCGTAAAATCTGCA	58.997	39.130	0.00	0.00	0.00	4.41
2616	4774	4.093408	TGAGACATCAAGCGTAAAATCTGC	59.907	41.667	0.00	0.00	30.61	4.26
2654	4812	5.658190	ACCCATTGAAAGAATATGACCCTTG	59.342	40.000	0.00	0.00	0.00	3.61
2655	4813	5.842339	ACCCATTGAAAGAATATGACCCTT	58.158	37.500	0.00	0.00	0.00	3.95
2656	4814	5.472301	ACCCATTGAAAGAATATGACCCT	57.528	39.130	0.00	0.00	0.00	4.34
2657	4815	7.039714	GGAATACCCATTGAAAGAATATGACCC	60.040	40.741	0.00	0.00	34.14	4.46
2658	4816	7.886338	GGAATACCCATTGAAAGAATATGACC	58.114	38.462	0.00	0.00	34.14	4.02
2690	4854	1.004679	TTTCTTGGGGGCGTCGTAC	60.005	57.895	0.00	0.00	0.00	3.67
2693	4857	1.574702	GAACTTTCTTGGGGGCGTCG	61.575	60.000	0.00	0.00	0.00	5.12
2702	4866	8.964420	TGTAAAACAGTTTGAGAACTTTCTTG	57.036	30.769	0.00	0.00	43.48	3.02
2704	4868	8.573035	TGTTGTAAAACAGTTTGAGAACTTTCT	58.427	29.630	19.49	0.00	43.48	2.52
2751	4943	7.334171	AGTTTTTATGGGTAATGCATTCAAAGC	59.666	33.333	16.86	8.29	0.00	3.51
2786	4978	0.943673	CACTCCGAAACATGCACACA	59.056	50.000	0.00	0.00	0.00	3.72
2790	4982	0.250252	TGAGCACTCCGAAACATGCA	60.250	50.000	0.00	0.00	40.63	3.96
2799	4991	0.037882	TTTCAGAGCTGAGCACTCCG	60.038	55.000	7.39	0.00	41.13	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.