AutoCloner

Multiple sequence alignment - TraesCS7D01G105200

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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	TraesCS7D01G105200	chr7D	100.000	3574	0	0	1	3574	63920643	63924216	0.000000e+00	6601.0
1	TraesCS7D01G105200	chr7D	89.633	627	55	9	2664	3288	254339367	254338749	0.000000e+00	789.0
2	TraesCS7D01G105200	chr7A	95.527	1878	53	12	1716	3574	66922364	66920499	0.000000e+00	2974.0
3	TraesCS7D01G105200	chr7A	89.914	932	68	9	806	1725	66923473	66922556	0.000000e+00	1177.0
4	TraesCS7D01G105200	chr3D	97.395	806	19	1	1	806	481927819	481927016	0.000000e+00	1371.0
5	TraesCS7D01G105200	chr3D	95.609	797	33	2	9	805	126942901	126943695	0.000000e+00	1277.0
6	TraesCS7D01G105200	chr3D	87.706	911	73	10	2671	3574	69048807	69049685	0.000000e+00	1026.0
7	TraesCS7D01G105200	chr3D	90.620	629	46	4	2671	3299	585874833	585874218	0.000000e+00	822.0
8	TraesCS7D01G105200	chr3D	85.692	636	71	15	2667	3299	153588705	153589323	0.000000e+00	652.0
9	TraesCS7D01G105200	chr3D	89.407	236	18	4	3343	3574	585873941	585873709	1.260000e-74	291.0
10	TraesCS7D01G105200	chr7B	89.246	1088	69	11	860	1940	4595621	4596667	0.000000e+00	1317.0
11	TraesCS7D01G105200	chr7B	87.529	850	94	3	1802	2642	4651031	4651877	0.000000e+00	972.0
12	TraesCS7D01G105200	chr7B	89.718	710	65	5	1930	2633	4597044	4597751	0.000000e+00	900.0
13	TraesCS7D01G105200	chr7B	94.595	111	6	0	1477	1587	4635490	4635600	4.740000e-39	172.0
14	TraesCS7D01G105200	chr7B	100.000	59	0	0	805	863	4594683	4594741	3.770000e-20	110.0
15	TraesCS7D01G105200	chr5D	95.431	788	31	2	1	785	59243455	59242670	0.000000e+00	1251.0
16	TraesCS7D01G105200	chr5D	86.977	622	67	9	2670	3288	462838368	462838978	0.000000e+00	688.0
17	TraesCS7D01G105200	chr5D	88.462	416	35	7	3168	3574	563585804	563585393	1.150000e-134	490.0
18	TraesCS7D01G105200	chr5D	84.223	431	42	16	3160	3574	565354659	565355079	2.590000e-106	396.0
19	TraesCS7D01G105200	chr5D	80.654	367	35	20	3240	3574	462735149	462735511	5.920000e-63	252.0
20	TraesCS7D01G105200	chr6D	90.319	909	63	14	2670	3574	3645734	3646621	0.000000e+00	1168.0
21	TraesCS7D01G105200	chr6D	87.560	627	64	9	2674	3299	34924941	34924328	0.000000e+00	713.0
22	TraesCS7D01G105200	chr2D	87.582	910	94	15	2671	3574	237096465	237097361	0.000000e+00	1037.0
23	TraesCS7D01G105200	chr1D	86.123	908	73	25	2667	3574	449223984	449223130	0.000000e+00	929.0
24	TraesCS7D01G105200	chr2A	92.308	598	43	2	204	801	22189747	22190341	0.000000e+00	846.0
25	TraesCS7D01G105200	chr2A	90.909	209	19	0	1	209	22188727	22188935	7.550000e-72	281.0
26	TraesCS7D01G105200	chr2A	80.122	327	39	17	72	398	621485837	621485537	1.670000e-53	220.0
27	TraesCS7D01G105200	chr5A	85.546	678	83	12	2666	3340	72455367	72456032	0.000000e+00	695.0
28	TraesCS7D01G105200	chr5A	88.000	50	4	2	758	806	548715874	548715922	1.390000e-04	58.4
29	TraesCS7D01G105200	chr6A	82.653	392	56	11	1	390	62605888	62605507	1.590000e-88	337.0
30	TraesCS7D01G105200	chr6A	81.043	422	68	11	1	420	62638246	62637835	3.440000e-85	326.0
31	TraesCS7D01G105200	chr6B	82.090	402	54	15	1	398	118213609	118213222	9.570000e-86	327.0
32	TraesCS7D01G105200	chr6B	91.228	57	5	0	1158	1214	197767184	197767128	1.060000e-10	78.7
33	TraesCS7D01G105200	chr6B	100.000	35	0	0	389	423	6871340	6871374	8.280000e-07	65.8
34	TraesCS7D01G105200	chr5B	81.682	333	42	15	30	360	73092864	73092549	3.540000e-65	259.0
35	TraesCS7D01G105200	chr5B	89.583	48	3	2	758	804	51961839	51961885	3.850000e-05	60.2
36	TraesCS7D01G105200	chr1B	93.617	47	3	0	1155	1201	659549310	659549264	1.780000e-08	71.3
37	TraesCS7D01G105200	chr4D	96.875	32	1	0	755	786	482346309	482346340	2.000000e-03	54.7
38	TraesCS7D01G105200	chr3A	96.875	32	1	0	755	786	728543081	728543112	2.000000e-03	54.7
39	TraesCS7D01G105200	chr3A	96.875	32	1	0	755	786	728573542	728573573	2.000000e-03	54.7
40	TraesCS7D01G105200	chr3A	96.875	32	1	0	755	786	728593970	728594001	2.000000e-03	54.7

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	TraesCS7D01G105200	chr7D	63920643	63924216	3573	False	6601.000000	6601	100.0000	1	3574	1	chr7D.!!$F1	3573
1	TraesCS7D01G105200	chr7D	254338749	254339367	618	True	789.000000	789	89.6330	2664	3288	1	chr7D.!!$R1	624
2	TraesCS7D01G105200	chr7A	66920499	66923473	2974	True	2075.500000	2974	92.7205	806	3574	2	chr7A.!!$R1	2768
3	TraesCS7D01G105200	chr3D	481927016	481927819	803	True	1371.000000	1371	97.3950	1	806	1	chr3D.!!$R1	805
4	TraesCS7D01G105200	chr3D	126942901	126943695	794	False	1277.000000	1277	95.6090	9	805	1	chr3D.!!$F2	796
5	TraesCS7D01G105200	chr3D	69048807	69049685	878	False	1026.000000	1026	87.7060	2671	3574	1	chr3D.!!$F1	903
6	TraesCS7D01G105200	chr3D	153588705	153589323	618	False	652.000000	652	85.6920	2667	3299	1	chr3D.!!$F3	632
7	TraesCS7D01G105200	chr3D	585873709	585874833	1124	True	556.500000	822	90.0135	2671	3574	2	chr3D.!!$R2	903
8	TraesCS7D01G105200	chr7B	4651031	4651877	846	False	972.000000	972	87.5290	1802	2642	1	chr7B.!!$F2	840
9	TraesCS7D01G105200	chr7B	4594683	4597751	3068	False	775.666667	1317	92.9880	805	2633	3	chr7B.!!$F3	1828
10	TraesCS7D01G105200	chr5D	59242670	59243455	785	True	1251.000000	1251	95.4310	1	785	1	chr5D.!!$R1	784
11	TraesCS7D01G105200	chr5D	462838368	462838978	610	False	688.000000	688	86.9770	2670	3288	1	chr5D.!!$F2	618
12	TraesCS7D01G105200	chr6D	3645734	3646621	887	False	1168.000000	1168	90.3190	2670	3574	1	chr6D.!!$F1	904
13	TraesCS7D01G105200	chr6D	34924328	34924941	613	True	713.000000	713	87.5600	2674	3299	1	chr6D.!!$R1	625
14	TraesCS7D01G105200	chr2D	237096465	237097361	896	False	1037.000000	1037	87.5820	2671	3574	1	chr2D.!!$F1	903
15	TraesCS7D01G105200	chr1D	449223130	449223984	854	True	929.000000	929	86.1230	2667	3574	1	chr1D.!!$R1	907
16	TraesCS7D01G105200	chr2A	22188727	22190341	1614	False	563.500000	846	91.6085	1	801	2	chr2A.!!$F1	800
17	TraesCS7D01G105200	chr5A	72455367	72456032	665	False	695.000000	695	85.5460	2666	3340	1	chr5A.!!$F1	674

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
687	1506	0.89553	CGTAGGCTGAGGAGGTTGAA	59.104	55.0	0.0	0.0	0.00	2.69	F
1364	3073	0.82501	GCAGGATGGTAATGGCAGGG	60.825	60.0	0.0	0.0	35.86	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1561	3270	0.099968	CATGAAACCAGCGCTCCATG	59.900	55.000	7.13	12.34	0.0	3.66	R
2812	5131	7.282675	ACAGTGTGAGAATTATAGTAGTAGCGT	59.717	37.037	0.00	0.00	0.0	5.07	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
260	1079	9.687210	GCATAATCTTTCATGAATGATTTAGCA	57.313	29.630	35.48	25.19	41.95	3.49
297	1116	2.351726	GCCGGTAGTAGCAAATGAAGTG	59.648	50.000	1.90	0.00	0.00	3.16
565	1384	3.071479	CCGTGTAGTAGCAATGGTTGTT	58.929	45.455	0.00	0.00	0.00	2.83
687	1506	0.895530	CGTAGGCTGAGGAGGTTGAA	59.104	55.000	0.00	0.00	0.00	2.69
700	1519	3.165071	GAGGTTGAATGGGTGATTGGTT	58.835	45.455	0.00	0.00	0.00	3.67
904	2609	3.721087	AGGCAAGGTGTAATAAGCTGT	57.279	42.857	0.00	0.00	0.00	4.40
910	2615	2.829720	AGGTGTAATAAGCTGTGTCCGA	59.170	45.455	0.00	0.00	0.00	4.55
913	2618	4.634443	GGTGTAATAAGCTGTGTCCGATTT	59.366	41.667	0.00	0.00	0.00	2.17
927	2632	4.214986	TCCGATTTGGACTTGAAGCATA	57.785	40.909	0.00	0.00	43.74	3.14
928	2633	4.780815	TCCGATTTGGACTTGAAGCATAT	58.219	39.130	0.00	0.00	43.74	1.78
929	2634	5.924356	TCCGATTTGGACTTGAAGCATATA	58.076	37.500	0.00	0.00	43.74	0.86
930	2635	6.533730	TCCGATTTGGACTTGAAGCATATAT	58.466	36.000	0.00	0.00	43.74	0.86
931	2636	7.676004	TCCGATTTGGACTTGAAGCATATATA	58.324	34.615	0.00	0.00	43.74	0.86
1028	2733	3.766545	CTCCAAATCAAGGGAGGTTCAA	58.233	45.455	0.00	0.00	45.62	2.69
1029	2734	4.347607	CTCCAAATCAAGGGAGGTTCAAT	58.652	43.478	0.00	0.00	45.62	2.57
1030	2735	5.509498	CTCCAAATCAAGGGAGGTTCAATA	58.491	41.667	0.00	0.00	45.62	1.90
1044	2749	8.261522	GGGAGGTTCAATATATCTGAATAGACC	58.738	40.741	11.15	9.27	35.36	3.85
1054	2759	3.280295	TCTGAATAGACCTCCGTCTCAC	58.720	50.000	0.00	0.00	46.90	3.51
1055	2760	2.014857	TGAATAGACCTCCGTCTCACG	58.985	52.381	0.00	0.00	46.90	4.35
1077	2783	2.963782	ACCCTAATACGCCGAGAATTCT	59.036	45.455	7.95	7.95	0.00	2.40
1079	2785	4.586001	ACCCTAATACGCCGAGAATTCTTA	59.414	41.667	9.87	0.00	0.00	2.10
1084	2790	1.209128	CGCCGAGAATTCTTATGCGT	58.791	50.000	26.02	0.87	34.86	5.24
1254	2960	2.680352	TCAGTCCCTCACCTCCGC	60.680	66.667	0.00	0.00	0.00	5.54
1255	2961	2.681778	CAGTCCCTCACCTCCGCT	60.682	66.667	0.00	0.00	0.00	5.52
1277	2983	1.135774	GGAAAATCTTCAACGTCGCCC	60.136	52.381	0.00	0.00	32.75	6.13
1283	2989	3.876589	TTCAACGTCGCCCTGCTCC	62.877	63.158	0.00	0.00	0.00	4.70
1364	3073	0.825010	GCAGGATGGTAATGGCAGGG	60.825	60.000	0.00	0.00	35.86	4.45
1445	3154	1.230324	GCCTGGCGAGAATGATTACC	58.770	55.000	1.35	0.00	0.00	2.85
1475	3184	1.227704	TTCGTCTTCAAAGCCGCCA	60.228	52.632	0.00	0.00	0.00	5.69
1504	3213	2.464459	GGACAATTCGCGGCTCAGG	61.464	63.158	6.13	0.00	0.00	3.86
1561	3270	3.075641	GGGGAGTCGGAGGTGACC	61.076	72.222	0.00	0.00	39.77	4.02
1580	3289	0.099968	CATGGAGCGCTGGTTTCATG	59.900	55.000	18.48	16.04	0.00	3.07
1614	3323	3.541632	GTCTGGTTTCACTTTCTGGTGA	58.458	45.455	0.00	0.00	43.41	4.02
1615	3324	3.312697	GTCTGGTTTCACTTTCTGGTGAC	59.687	47.826	0.00	0.00	44.55	3.67
1618	3327	1.002792	GTTTCACTTTCTGGTGACGGC	60.003	52.381	0.00	0.00	44.55	5.68
1620	3329	2.030562	ACTTTCTGGTGACGGCGG	59.969	61.111	13.24	0.00	36.33	6.13
1671	3380	1.205417	GCTGGCCAAGTTTGTGCATAT	59.795	47.619	7.01	0.00	0.00	1.78
1715	3424	2.093764	GGAGCTGAGCTATGTGTGTTCT	60.094	50.000	7.08	0.00	39.88	3.01
1736	3646	1.229209	TCCCGTCTGCCCTCTTCTT	60.229	57.895	0.00	0.00	0.00	2.52
1737	3647	1.219393	CCCGTCTGCCCTCTTCTTC	59.781	63.158	0.00	0.00	0.00	2.87
1738	3648	1.261238	CCCGTCTGCCCTCTTCTTCT	61.261	60.000	0.00	0.00	0.00	2.85
1984	4296	0.608308	AAAGCAGCAGCAGCATCTCA	60.608	50.000	12.92	0.00	45.49	3.27
2000	4312	0.319040	CTCATACATCCGACTGCCCG	60.319	60.000	0.00	0.00	0.00	6.13
2028	4340	2.268298	CCGTCCCAAGACTTTATCACG	58.732	52.381	0.00	0.00	41.16	4.35
2048	4360	2.415090	CGAACCGACCAATTACTCGAGT	60.415	50.000	23.66	23.66	31.24	4.18
2137	4449	2.734591	GTCGGTGTCTGCTGTGGA	59.265	61.111	0.00	0.00	0.00	4.02
2261	4573	0.963962	TCTTAACGCCCGTCAGAAGT	59.036	50.000	0.00	0.00	0.00	3.01
2647	4966	3.346315	TGTTGGCATGGTTACTCATCAG	58.654	45.455	0.00	0.00	0.00	2.90
2656	4975	6.462500	CATGGTTACTCATCAGCTAGCTTAT	58.538	40.000	16.46	10.50	0.00	1.73
2664	4983	8.572855	ACTCATCAGCTAGCTTATTTTTCTTT	57.427	30.769	16.46	0.00	0.00	2.52
3209	5535	1.978454	ACTTCCTATAGCCGTAGCGT	58.022	50.000	0.00	0.00	46.67	5.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
297	1116	5.870978	TCGTTTGATTTTGCTACTACCTACC	59.129	40.000	0.00	0.00	0.00	3.18
565	1384	2.265367	TCCTACAGACAAGCATGGGAA	58.735	47.619	0.00	0.00	0.00	3.97
687	1506	3.900601	TGCAAGTTTAACCAATCACCCAT	59.099	39.130	0.00	0.00	0.00	4.00
700	1519	3.666638	CGCGTTGATCACATGCAAGTTTA	60.667	43.478	16.86	0.00	0.00	2.01
910	2615	9.950496	CCTAGTATATATGCTTCAAGTCCAAAT	57.050	33.333	8.72	0.00	0.00	2.32
913	2618	7.728532	TCACCTAGTATATATGCTTCAAGTCCA	59.271	37.037	8.72	0.00	0.00	4.02
919	2624	8.699130	CATGGATCACCTAGTATATATGCTTCA	58.301	37.037	8.72	0.00	37.04	3.02
927	2632	4.956700	CGACCCATGGATCACCTAGTATAT	59.043	45.833	15.22	0.00	37.04	0.86
928	2633	4.341487	CGACCCATGGATCACCTAGTATA	58.659	47.826	15.22	0.00	37.04	1.47
929	2634	3.165875	CGACCCATGGATCACCTAGTAT	58.834	50.000	15.22	0.00	37.04	2.12
930	2635	2.594131	CGACCCATGGATCACCTAGTA	58.406	52.381	15.22	0.00	37.04	1.82
931	2636	1.414158	CGACCCATGGATCACCTAGT	58.586	55.000	15.22	0.00	37.04	2.57
963	2668	5.163550	TGGTATCTGCCTCGTGTATATATGC	60.164	44.000	0.00	0.00	0.00	3.14
964	2669	6.095580	AGTGGTATCTGCCTCGTGTATATATG	59.904	42.308	0.00	0.00	0.00	1.78
966	2671	5.567430	AGTGGTATCTGCCTCGTGTATATA	58.433	41.667	0.00	0.00	0.00	0.86
1054	2759	0.664761	TTCTCGGCGTATTAGGGTCG	59.335	55.000	6.85	0.00	0.00	4.79
1055	2760	3.005578	AGAATTCTCGGCGTATTAGGGTC	59.994	47.826	6.85	0.00	0.00	4.46
1077	2783	1.488393	TGACCATGGATCCACGCATAA	59.512	47.619	21.47	0.00	0.00	1.90
1079	2785	0.475475	ATGACCATGGATCCACGCAT	59.525	50.000	21.47	14.70	0.00	4.73
1120	2826	2.358125	CCGTCATCGTGGTTGCCA	60.358	61.111	0.00	0.00	35.01	4.92
1153	2859	1.600663	CGATCTAGCATCACCCACGAC	60.601	57.143	0.00	0.00	0.00	4.34
1194	2900	2.048503	CCGGGAAAAGCTCGTCGT	60.049	61.111	0.00	0.00	39.40	4.34
1195	2901	2.092882	GTCCGGGAAAAGCTCGTCG	61.093	63.158	0.00	0.00	39.40	5.12
1196	2902	2.092882	CGTCCGGGAAAAGCTCGTC	61.093	63.158	0.00	0.00	39.40	4.20
1254	2960	2.412847	GCGACGTTGAAGATTTTCCCAG	60.413	50.000	7.08	0.00	32.09	4.45
1255	2961	1.533731	GCGACGTTGAAGATTTTCCCA	59.466	47.619	7.08	0.00	32.09	4.37
1259	2965	1.535462	CAGGGCGACGTTGAAGATTTT	59.465	47.619	7.08	0.00	0.00	1.82
1561	3270	0.099968	CATGAAACCAGCGCTCCATG	59.900	55.000	7.13	12.34	0.00	3.66
1580	3289	0.526662	ACCAGACCGATCGTGTTCTC	59.473	55.000	15.09	0.48	0.00	2.87
1618	3327	4.394078	TCGTCTTCGTCGCCACCG	62.394	66.667	0.00	0.00	38.33	4.94
1620	3329	0.938168	AAACTCGTCTTCGTCGCCAC	60.938	55.000	0.00	0.00	38.33	5.01
1632	3341	3.276846	GCACCACCGCAAACTCGT	61.277	61.111	0.00	0.00	0.00	4.18
1715	3424	4.704103	AGAGGGCAGACGGGAGCA	62.704	66.667	0.00	0.00	0.00	4.26
1736	3646	3.383185	GTGTTGGTGTTGGATTTGGAAGA	59.617	43.478	0.00	0.00	0.00	2.87
1737	3647	3.384467	AGTGTTGGTGTTGGATTTGGAAG	59.616	43.478	0.00	0.00	0.00	3.46
1738	3648	3.370104	AGTGTTGGTGTTGGATTTGGAA	58.630	40.909	0.00	0.00	0.00	3.53
1958	4270	1.380524	CTGCTGCTGCTTTCTGCTAT	58.619	50.000	17.00	0.00	43.37	2.97
1984	4296	1.740285	GACGGGCAGTCGGATGTAT	59.260	57.895	1.15	0.00	40.43	2.29
2000	4312	0.942884	GTCTTGGGACGGTTGTCGAC	60.943	60.000	9.11	9.11	46.49	4.20
2028	4340	3.227810	ACTCGAGTAATTGGTCGGTTC	57.772	47.619	18.46	0.00	36.81	3.62
2048	4360	1.183030	ACACACAGGCTGCGGTACTA	61.183	55.000	15.89	0.00	0.00	1.82
2119	4431	2.357517	CCACAGCAGACACCGACC	60.358	66.667	0.00	0.00	0.00	4.79
2137	4449	7.500992	TGTAAAAAGAACTGACTCTGATCTGT	58.499	34.615	0.00	0.00	32.66	3.41
2418	4730	7.798710	TCTTCTCCTCGGATATATGGAAAAT	57.201	36.000	0.00	0.00	0.00	1.82
2498	4810	7.554959	TTTAGTAGAAGTGACAAGGGAGAAT	57.445	36.000	0.00	0.00	0.00	2.40
2647	4966	7.335673	AGTGAGAGGAAAGAAAAATAAGCTAGC	59.664	37.037	6.62	6.62	0.00	3.42
2656	4975	7.850935	TCCTAGTAGTGAGAGGAAAGAAAAA	57.149	36.000	0.00	0.00	36.42	1.94
2811	5130	8.129840	CAGTGTGAGAATTATAGTAGTAGCGTT	58.870	37.037	0.00	0.00	0.00	4.84
2812	5131	7.282675	ACAGTGTGAGAATTATAGTAGTAGCGT	59.717	37.037	0.00	0.00	0.00	5.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.