AutoCloner

Multiple sequence alignment - TraesCS6D01G291300

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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	TraesCS6D01G291300	chr6D	100.000	3107	0	0	1	3107	401736053	401739159	0.000000e+00	5738.0
1	TraesCS6D01G291300	chr6D	96.629	89	3	0	2704	2792	401738668	401738756	6.940000e-32	148.0
2	TraesCS6D01G291300	chr6D	96.629	89	3	0	2616	2704	401738756	401738844	6.940000e-32	148.0
3	TraesCS6D01G291300	chr6B	91.868	3185	142	45	2	3107	602503157	602506303	0.000000e+00	4338.0
4	TraesCS6D01G291300	chr6B	93.289	298	17	1	1156	1450	85848898	85849195	1.320000e-118	436.0
5	TraesCS6D01G291300	chr6B	91.892	111	4	5	2682	2792	602505779	602505884	1.930000e-32	150.0
6	TraesCS6D01G291300	chr6B	93.814	97	5	1	2616	2711	602505884	602505980	8.980000e-31	145.0
7	TraesCS6D01G291300	chr6B	95.122	82	4	0	1647	1728	85849197	85849278	2.510000e-26	130.0
8	TraesCS6D01G291300	chr6A	93.262	2538	79	42	608	3106	548110307	548112791	0.000000e+00	3655.0
9	TraesCS6D01G291300	chr6A	88.755	498	37	8	2	483	548109719	548110213	2.670000e-165	592.0
10	TraesCS6D01G291300	chr6A	97.753	89	2	0	2704	2792	548112314	548112402	1.490000e-33	154.0
11	TraesCS6D01G291300	chr6A	92.784	97	6	1	2616	2711	548112402	548112498	4.180000e-29	139.0
12	TraesCS6D01G291300	chr4D	95.803	834	30	2	1156	1986	399420202	399419371	0.000000e+00	1341.0
13	TraesCS6D01G291300	chr1B	92.354	824	43	12	1157	1973	668249327	668250137	0.000000e+00	1155.0
14	TraesCS6D01G291300	chr7D	87.904	959	100	13	1063	2019	159062801	159063745	0.000000e+00	1114.0
15	TraesCS6D01G291300	chr7B	86.911	955	111	11	1066	2019	119700558	119701499	0.000000e+00	1059.0
16	TraesCS6D01G291300	chr7A	87.039	949	109	10	1072	2019	159558343	159557408	0.000000e+00	1059.0
17	TraesCS6D01G291300	chr2B	94.483	145	5	2	1645	1789	196347126	196347267	1.450000e-53	220.0
18	TraesCS6D01G291300	chr3D	88.060	67	7	1	2	68	390410265	390410200	9.240000e-11	78.7

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	TraesCS6D01G291300	chr6D	401736053	401739159	3106	False	2011.333333	5738	97.752667	1	3107	3	chr6D.!!$F1	3106
1	TraesCS6D01G291300	chr6B	602503157	602506303	3146	False	1544.333333	4338	92.524667	2	3107	3	chr6B.!!$F2	3105
2	TraesCS6D01G291300	chr6A	548109719	548112791	3072	False	1135.000000	3655	93.138500	2	3106	4	chr6A.!!$F1	3104
3	TraesCS6D01G291300	chr4D	399419371	399420202	831	True	1341.000000	1341	95.803000	1156	1986	1	chr4D.!!$R1	830
4	TraesCS6D01G291300	chr1B	668249327	668250137	810	False	1155.000000	1155	92.354000	1157	1973	1	chr1B.!!$F1	816
5	TraesCS6D01G291300	chr7D	159062801	159063745	944	False	1114.000000	1114	87.904000	1063	2019	1	chr7D.!!$F1	956
6	TraesCS6D01G291300	chr7B	119700558	119701499	941	False	1059.000000	1059	86.911000	1066	2019	1	chr7B.!!$F1	953
7	TraesCS6D01G291300	chr7A	159557408	159558343	935	True	1059.000000	1059	87.039000	1072	2019	1	chr7A.!!$R1	947

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
395	413	0.449388	CATTCCGTCCTGCAGCTTTC	59.551	55.000	8.66	0.0	0.0	2.62	F
835	905	1.612739	ACTTCGTTCCCCTCCCCTC	60.613	63.158	0.00	0.0	0.0	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1917	2020	0.538584	CTGACCAGTGCATCAGGCTA	59.461	55.000	12.62	0.0	45.15	3.93	R
2572	2688	1.066152	GAATTTCCGCATCAAGGGAGC	59.934	52.381	0.00	0.0	33.01	4.70	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
58	59	9.970395	TCAATAAAGTAAATCATGATGGCATTC	57.030	29.630	9.46	0.00	30.68	2.67
121	125	7.081976	GCGGCGTCCTTCATTAATTTATTTAT	58.918	34.615	9.37	0.00	0.00	1.40
148	152	4.595762	ATCATCACAAATAATGGCAGCC	57.404	40.909	3.66	3.66	0.00	4.85
212	221	7.928307	TTGAGAAATTGTCCTCTCCAAATAG	57.072	36.000	3.08	0.00	37.82	1.73
214	223	7.334090	TGAGAAATTGTCCTCTCCAAATAGAG	58.666	38.462	3.08	0.00	42.30	2.43
299	313	8.826765	ACTTATATTCCATCTGGGTATTCGATT	58.173	33.333	0.00	0.00	38.11	3.34
385	403	6.438763	GTTGATTGATTATTCCATTCCGTCC	58.561	40.000	0.00	0.00	0.00	4.79
395	413	0.449388	CATTCCGTCCTGCAGCTTTC	59.551	55.000	8.66	0.00	0.00	2.62
434	452	6.040247	GCACAAGCAGTAACTAAAACCTTTT	58.960	36.000	0.00	0.00	41.58	2.27
570	611	2.036958	TGACCGATGCAATTCCGATT	57.963	45.000	0.00	0.00	0.00	3.34
588	629	5.912360	CGATTCCGGTTTACTTATAACCC	57.088	43.478	0.00	0.00	41.62	4.11
589	630	4.445385	CGATTCCGGTTTACTTATAACCCG	59.555	45.833	0.00	0.00	43.89	5.28
591	632	2.499289	TCCGGTTTACTTATAACCCGCA	59.501	45.455	0.00	0.00	43.16	5.69
592	633	3.055530	TCCGGTTTACTTATAACCCGCAA	60.056	43.478	0.00	0.00	43.16	4.85
648	689	2.427575	CGATGACGATCGCCGAGG	60.428	66.667	16.60	0.00	44.75	4.63
835	905	1.612739	ACTTCGTTCCCCTCCCCTC	60.613	63.158	0.00	0.00	0.00	4.30
923	996	2.904866	CGGGCGAGAGAGAGAGGG	60.905	72.222	0.00	0.00	0.00	4.30
924	997	3.223589	GGGCGAGAGAGAGAGGGC	61.224	72.222	0.00	0.00	0.00	5.19
1614	1717	2.126618	CGCTACTTCACCGACGCA	60.127	61.111	0.00	0.00	0.00	5.24
1917	2020	2.846532	CTCCACAAGGGCCCTGTT	59.153	61.111	29.50	13.21	36.21	3.16
1966	2069	2.502492	CCATGGGATCGCCTCGACT	61.502	63.158	2.85	0.00	39.18	4.18
2033	2136	0.248012	TACATTGGCGACGGTGATGT	59.752	50.000	0.00	2.53	35.36	3.06
2034	2137	1.298157	ACATTGGCGACGGTGATGTG	61.298	55.000	0.00	0.00	30.37	3.21
2043	2146	2.029288	CGGTGATGTGTCGCAAGCT	61.029	57.895	0.00	0.00	36.57	3.74
2179	2282	1.171308	GCCTTGCGATGCATATCCAT	58.829	50.000	0.00	0.00	38.76	3.41
2256	2359	3.379865	GAGGGGCGGTACATTGCGA	62.380	63.158	0.00	0.00	0.00	5.10
2301	2404	2.170166	CAGTGCATAGGGGAAGCAAAA	58.830	47.619	0.00	0.00	40.35	2.44
2531	2644	6.590234	GTTTCAATAAAACAGGGTGGATCT	57.410	37.500	0.00	0.00	45.49	2.75
2561	2674	3.045601	TGCTTCAGTGCTAAACTCTCC	57.954	47.619	0.00	0.00	36.83	3.71
2572	2688	4.096532	TGCTAAACTCTCCTGTATCTGTCG	59.903	45.833	0.00	0.00	0.00	4.35
2596	2712	2.431782	CCCTTGATGCGGAAATTCCATT	59.568	45.455	13.04	0.00	35.91	3.16
2621	2737	6.541278	TGAGAATGGCTTGATCTCTTGTTATG	59.459	38.462	0.00	0.00	40.18	1.90
2639	2755	7.189693	TGTTATGTCCATCTTTCGATAATGC	57.810	36.000	0.00	0.00	0.00	3.56
2658	2774	1.796459	GCTCAATTTTTGCTGTGGCTG	59.204	47.619	0.00	0.00	39.59	4.85
2797	2913	5.997746	TGGCCTCATATATTGCTGTTTCTAC	59.002	40.000	3.32	0.00	0.00	2.59
2798	2914	5.997746	GGCCTCATATATTGCTGTTTCTACA	59.002	40.000	0.00	0.00	0.00	2.74
2801	2917	7.361542	GCCTCATATATTGCTGTTTCTACATGG	60.362	40.741	0.00	0.00	32.86	3.66
2822	2938	3.377798	GGCCTACTATCTCCATACGCTAC	59.622	52.174	0.00	0.00	0.00	3.58
2823	2939	4.008330	GCCTACTATCTCCATACGCTACA	58.992	47.826	0.00	0.00	0.00	2.74
2844	2960	7.062255	GCTACAGTCCAAATTTATTGCTGTTTC	59.938	37.037	16.46	9.16	37.05	2.78
2859	2975	5.858381	TGCTGTTTCTCTACTTGTTCATCT	58.142	37.500	0.00	0.00	0.00	2.90
2955	3071	3.788227	TGCCTACTTGTTTCATCCAGT	57.212	42.857	0.00	0.00	0.00	4.00
2961	3077	5.647658	CCTACTTGTTTCATCCAGTATTGCA	59.352	40.000	0.00	0.00	0.00	4.08
2967	3083	5.355071	TGTTTCATCCAGTATTGCATGTCTC	59.645	40.000	0.00	0.00	0.00	3.36
3069	3188	6.870971	TTATTTAGTTTCAGCGGTTGTCTT	57.129	33.333	0.00	0.00	0.00	3.01
3070	3189	4.545823	TTTAGTTTCAGCGGTTGTCTTG	57.454	40.909	0.00	0.00	0.00	3.02
3072	3191	2.365582	AGTTTCAGCGGTTGTCTTGTT	58.634	42.857	0.00	0.00	0.00	2.83
3074	3193	2.325583	TTCAGCGGTTGTCTTGTTCT	57.674	45.000	0.00	0.00	0.00	3.01
3075	3194	3.462483	TTCAGCGGTTGTCTTGTTCTA	57.538	42.857	0.00	0.00	0.00	2.10
3076	3195	3.026630	TCAGCGGTTGTCTTGTTCTAG	57.973	47.619	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	6.811634	TTTTTAAGGGAATGCCATCATGAT	57.188	33.333	1.18	1.18	35.15	2.45
70	73	4.474226	AAAAGAACGACATCTCAAGCAC	57.526	40.909	0.00	0.00	0.00	4.40
97	101	9.458374	AAATAAATAAATTAATGAAGGACGCCG	57.542	29.630	0.00	0.00	0.00	6.46
121	125	8.881743	GCTGCCATTATTTGTGATGATTAAAAA	58.118	29.630	0.00	0.00	0.00	1.94
139	143	1.409251	TTGCAACCAAGGCTGCCATT	61.409	50.000	22.65	9.43	36.48	3.16
212	221	3.162068	CGCTTGTCACGTTACTCTACTC	58.838	50.000	1.01	0.00	0.00	2.59
214	223	2.907392	GACGCTTGTCACGTTACTCTAC	59.093	50.000	1.01	0.00	45.24	2.59
301	315	9.803315	GATGAGATACGACCAATTATGCTATAA	57.197	33.333	0.00	0.00	0.00	0.98
317	331	3.366883	GGAGGCAGCTAAGATGAGATACG	60.367	52.174	0.00	0.00	0.00	3.06
395	413	1.080569	GTGCAAGGGATTGGCAACG	60.081	57.895	0.00	0.00	39.57	4.10
423	441	4.215399	TGTGCCGATGAGAAAAGGTTTTAG	59.785	41.667	0.00	0.00	0.00	1.85
430	448	2.611292	GGATCTGTGCCGATGAGAAAAG	59.389	50.000	0.00	0.00	0.00	2.27
434	452	1.194218	TTGGATCTGTGCCGATGAGA	58.806	50.000	0.00	0.00	0.00	3.27
476	494	8.715998	AGTACAGTACGTATACTATACATGTGC	58.284	37.037	9.11	15.01	41.80	4.57
544	585	3.680642	AATTGCATCGGTCAATTCTCG	57.319	42.857	0.00	0.00	39.21	4.04
602	643	8.707449	TGATTAATCCGTGTTTAGTAGGGTTAT	58.293	33.333	12.90	0.00	30.39	1.89
603	644	8.076910	TGATTAATCCGTGTTTAGTAGGGTTA	57.923	34.615	12.90	0.00	0.00	2.85
604	645	6.949715	TGATTAATCCGTGTTTAGTAGGGTT	58.050	36.000	12.90	0.00	0.00	4.11
605	646	6.549433	TGATTAATCCGTGTTTAGTAGGGT	57.451	37.500	12.90	0.00	0.00	4.34
606	647	6.018180	GCTTGATTAATCCGTGTTTAGTAGGG	60.018	42.308	12.90	0.00	0.00	3.53
621	662	4.893036	CGATCGTCATCGCTTGATTAAT	57.107	40.909	7.03	0.00	45.28	1.40
671	734	0.037046	CCCCCGTGTTATATACCCGC	60.037	60.000	0.00	0.00	0.00	6.13
835	905	1.133809	TCTCTCTGGTTGGGTTGGGG	61.134	60.000	0.00	0.00	0.00	4.96
1020	1108	1.555477	CGGCCAACAACAACAAGAAC	58.445	50.000	2.24	0.00	0.00	3.01
1524	1627	4.200283	CGCGTCTCCCAGAGCCTC	62.200	72.222	0.00	0.00	0.00	4.70
1917	2020	0.538584	CTGACCAGTGCATCAGGCTA	59.461	55.000	12.62	0.00	45.15	3.93
2089	2192	3.385433	TCTGTCTACCAAGAAAACACCGA	59.615	43.478	0.00	0.00	32.16	4.69
2179	2282	3.057548	CGGCAGCTGTGATGGCAA	61.058	61.111	16.64	0.00	43.01	4.52
2301	2404	7.904977	CGAATTGTATCGTGAATGAACAAGAAT	59.095	33.333	0.00	0.00	38.01	2.40
2529	2642	5.555017	AGCACTGAAGCAAGAATAAGAAGA	58.445	37.500	0.00	0.00	36.85	2.87
2530	2643	5.876612	AGCACTGAAGCAAGAATAAGAAG	57.123	39.130	0.00	0.00	36.85	2.85
2531	2644	7.445402	AGTTTAGCACTGAAGCAAGAATAAGAA	59.555	33.333	0.00	0.00	32.83	2.52
2561	2674	1.751351	TCAAGGGAGCGACAGATACAG	59.249	52.381	0.00	0.00	0.00	2.74
2572	2688	1.066152	GAATTTCCGCATCAAGGGAGC	59.934	52.381	0.00	0.00	33.01	4.70
2596	2712	4.564782	ACAAGAGATCAAGCCATTCTCA	57.435	40.909	0.00	0.00	38.67	3.27
2608	2724	6.980978	TCGAAAGATGGACATAACAAGAGATC	59.019	38.462	0.00	0.00	33.31	2.75
2639	2755	2.224113	ACCAGCCACAGCAAAAATTGAG	60.224	45.455	0.00	0.00	43.56	3.02
2797	2913	3.429547	GCGTATGGAGATAGTAGGCCATG	60.430	52.174	5.01	0.00	41.05	3.66
2798	2914	2.761208	GCGTATGGAGATAGTAGGCCAT	59.239	50.000	5.01	0.00	43.22	4.40
2801	2917	4.008330	TGTAGCGTATGGAGATAGTAGGC	58.992	47.826	0.00	0.00	0.00	3.93
2822	2938	7.373493	AGAGAAACAGCAATAAATTTGGACTG	58.627	34.615	0.00	5.95	0.00	3.51
2823	2939	7.530426	AGAGAAACAGCAATAAATTTGGACT	57.470	32.000	0.00	0.00	0.00	3.85
2844	2960	7.271511	AGGCAATTCTAGATGAACAAGTAGAG	58.728	38.462	0.00	0.00	37.52	2.43
2859	2975	6.480763	TGGATGAACAAAGTAGGCAATTCTA	58.519	36.000	0.00	0.00	0.00	2.10
2891	3007	9.638239	GGCAAAATTGAAACAGACATAGATAAA	57.362	29.630	0.00	0.00	0.00	1.40
2955	3071	7.930325	CCTTCTTAGATGAAGAGACATGCAATA	59.070	37.037	5.90	0.00	45.05	1.90
2961	3077	4.968080	AGGCCTTCTTAGATGAAGAGACAT	59.032	41.667	0.00	0.00	45.05	3.06
2967	3083	5.700373	GCAGATTAGGCCTTCTTAGATGAAG	59.300	44.000	12.58	0.00	42.10	3.02
3074	3193	9.177304	CGACGAAACAGATAAGCAATTATACTA	57.823	33.333	0.00	0.00	0.00	1.82
3075	3194	7.919091	TCGACGAAACAGATAAGCAATTATACT	59.081	33.333	0.00	0.00	0.00	2.12
3076	3195	7.997104	GTCGACGAAACAGATAAGCAATTATAC	59.003	37.037	0.00	0.00	0.00	1.47

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.