AutoCloner

Multiple sequence alignment - TraesCS7D01G192800

Loading Multiple Alignment...

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	TraesCS7D01G192800	chr7D	100.000	3412	0	0	1	3412	148296056	148299467	0.000000e+00	6301.0
1	TraesCS7D01G192800	chr7D	89.263	1695	88	32	757	2426	149528673	149527048	0.000000e+00	2036.0
2	TraesCS7D01G192800	chr7D	98.915	737	6	2	1	735	101142442	101141706	0.000000e+00	1315.0
3	TraesCS7D01G192800	chr7D	98.650	741	8	2	1	740	89273000	89273739	0.000000e+00	1312.0
4	TraesCS7D01G192800	chr7D	98.650	741	8	2	1	740	169826538	169825799	0.000000e+00	1312.0
5	TraesCS7D01G192800	chr7D	88.073	545	62	3	2866	3410	149526339	149525798	0.000000e+00	643.0
6	TraesCS7D01G192800	chr7D	84.000	550	76	10	2867	3410	412972109	412971566	5.050000e-143	518.0
7	TraesCS7D01G192800	chr7D	83.122	551	85	8	2866	3410	580227845	580227297	2.360000e-136	496.0
8	TraesCS7D01G192800	chr7D	84.483	406	33	11	2462	2867	149527047	149526672	1.160000e-99	374.0
9	TraesCS7D01G192800	chr7A	94.112	2174	83	19	734	2870	149601189	149603354	0.000000e+00	3264.0
10	TraesCS7D01G192800	chr7B	91.325	1660	49	20	809	2432	111367508	111369108	0.000000e+00	2180.0
11	TraesCS7D01G192800	chr7B	88.427	337	36	3	2534	2870	111370772	111371105	1.470000e-108	403.0
12	TraesCS7D01G192800	chr7B	96.364	110	2	2	2428	2537	111369298	111369405	2.710000e-41	180.0
13	TraesCS7D01G192800	chr7B	76.263	198	45	2	2657	2853	441914667	441914471	1.670000e-18	104.0
14	TraesCS7D01G192800	chr1D	99.049	736	6	1	1	735	488830157	488830892	0.000000e+00	1319.0
15	TraesCS7D01G192800	chr1D	98.913	736	6	2	1	735	460320459	460321193	0.000000e+00	1314.0
16	TraesCS7D01G192800	chr6D	99.048	735	6	1	1	734	290842163	290842897	0.000000e+00	1317.0
17	TraesCS7D01G192800	chr3D	99.048	735	6	1	1	734	491628488	491627754	0.000000e+00	1317.0
18	TraesCS7D01G192800	chr5D	98.652	742	9	1	1	741	482673238	482672497	0.000000e+00	1314.0
19	TraesCS7D01G192800	chr5D	98.518	742	10	1	1	741	35127854	35127113	0.000000e+00	1308.0
20	TraesCS7D01G192800	chr6B	84.944	538	71	9	2867	3396	594544536	594544001	1.390000e-148	536.0
21	TraesCS7D01G192800	chr3A	84.715	543	72	10	2874	3410	491173592	491174129	1.800000e-147	532.0
22	TraesCS7D01G192800	chr3A	84.557	531	70	10	2874	3395	23235393	23234866	1.820000e-142	516.0
23	TraesCS7D01G192800	chr5B	84.690	516	73	6	2891	3403	282700607	282700095	8.450000e-141	510.0
24	TraesCS7D01G192800	chr5B	83.610	543	77	12	2874	3410	419406773	419407309	1.830000e-137	499.0
25	TraesCS7D01G192800	chr2B	84.310	529	74	9	2874	3396	641688471	641687946	3.040000e-140	508.0
26	TraesCS7D01G192800	chr2B	84.127	63	7	3	2681	2742	168538687	168538747	1.320000e-04	58.4
27	TraesCS7D01G192800	chr2B	94.595	37	1	1	2681	2717	168126697	168126732	4.760000e-04	56.5
28	TraesCS7D01G192800	chr4B	76.382	199	43	3	2657	2853	487881175	487881371	1.670000e-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	TraesCS7D01G192800	chr7D	148296056	148299467	3411	False	6301.000000	6301	100.000000	1	3412	1	chr7D.!!$F2	3411
1	TraesCS7D01G192800	chr7D	101141706	101142442	736	True	1315.000000	1315	98.915000	1	735	1	chr7D.!!$R1	734
2	TraesCS7D01G192800	chr7D	89273000	89273739	739	False	1312.000000	1312	98.650000	1	740	1	chr7D.!!$F1	739
3	TraesCS7D01G192800	chr7D	169825799	169826538	739	True	1312.000000	1312	98.650000	1	740	1	chr7D.!!$R2	739
4	TraesCS7D01G192800	chr7D	149525798	149528673	2875	True	1017.666667	2036	87.273000	757	3410	3	chr7D.!!$R5	2653
5	TraesCS7D01G192800	chr7D	412971566	412972109	543	True	518.000000	518	84.000000	2867	3410	1	chr7D.!!$R3	543
6	TraesCS7D01G192800	chr7D	580227297	580227845	548	True	496.000000	496	83.122000	2866	3410	1	chr7D.!!$R4	544
7	TraesCS7D01G192800	chr7A	149601189	149603354	2165	False	3264.000000	3264	94.112000	734	2870	1	chr7A.!!$F1	2136
8	TraesCS7D01G192800	chr7B	111367508	111371105	3597	False	921.000000	2180	92.038667	809	2870	3	chr7B.!!$F1	2061
9	TraesCS7D01G192800	chr1D	488830157	488830892	735	False	1319.000000	1319	99.049000	1	735	1	chr1D.!!$F2	734
10	TraesCS7D01G192800	chr1D	460320459	460321193	734	False	1314.000000	1314	98.913000	1	735	1	chr1D.!!$F1	734
11	TraesCS7D01G192800	chr6D	290842163	290842897	734	False	1317.000000	1317	99.048000	1	734	1	chr6D.!!$F1	733
12	TraesCS7D01G192800	chr3D	491627754	491628488	734	True	1317.000000	1317	99.048000	1	734	1	chr3D.!!$R1	733
13	TraesCS7D01G192800	chr5D	482672497	482673238	741	True	1314.000000	1314	98.652000	1	741	1	chr5D.!!$R2	740
14	TraesCS7D01G192800	chr5D	35127113	35127854	741	True	1308.000000	1308	98.518000	1	741	1	chr5D.!!$R1	740
15	TraesCS7D01G192800	chr6B	594544001	594544536	535	True	536.000000	536	84.944000	2867	3396	1	chr6B.!!$R1	529
16	TraesCS7D01G192800	chr3A	491173592	491174129	537	False	532.000000	532	84.715000	2874	3410	1	chr3A.!!$F1	536
17	TraesCS7D01G192800	chr3A	23234866	23235393	527	True	516.000000	516	84.557000	2874	3395	1	chr3A.!!$R1	521
18	TraesCS7D01G192800	chr5B	282700095	282700607	512	True	510.000000	510	84.690000	2891	3403	1	chr5B.!!$R1	512
19	TraesCS7D01G192800	chr5B	419406773	419407309	536	False	499.000000	499	83.610000	2874	3410	1	chr5B.!!$F1	536
20	TraesCS7D01G192800	chr2B	641687946	641688471	525	True	508.000000	508	84.310000	2874	3396	1	chr2B.!!$R1	522

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
930	936	0.106708	TGCATTCGCTCCATAGACCC	59.893	55.000	0.00	0.0	39.64	4.46	F
1724	1791	1.291272	GTACTGGTCGCCGTTCCTT	59.709	57.895	3.36	0.0	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2384	2460	0.245266	TTGCAGCCAGAATGTGCATG	59.755	50.0	0.00	0.0	46.18	4.06	R
2606	4246	0.535335	GGTTGGATGTAGAGCCGACA	59.465	55.0	15.85	0.0	43.14	4.35	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
333	334	1.528586	CGAGCTACACATGCCTATTGC	59.471	52.381	0.00	0.00	41.77	3.56
369	370	6.590234	TGTCTACTGTGACAACATATCAGT	57.410	37.500	9.56	0.00	43.08	3.41
482	484	1.523758	GTTCGGGTGCTTCATGTTCT	58.476	50.000	0.00	0.00	0.00	3.01
671	673	0.108963	CCCCAAGTCGGTTTGTACCA	59.891	55.000	0.00	0.00	45.31	3.25
764	767	7.011482	GGAAGTACTAACAGTCAATTGCATAGG	59.989	40.741	0.00	0.00	0.00	2.57
799	802	7.665559	TCAAGTAGTATTTCTTGGTTTCTGCAT	59.334	33.333	5.06	0.00	40.67	3.96
855	858	5.865085	TCTAACCATATAATTTGGCGCTCT	58.135	37.500	7.64	0.00	37.81	4.09
856	859	5.932303	TCTAACCATATAATTTGGCGCTCTC	59.068	40.000	7.64	0.00	37.81	3.20
857	860	3.067106	ACCATATAATTTGGCGCTCTCG	58.933	45.455	7.64	0.00	37.81	4.04
928	934	2.487934	ACATGCATTCGCTCCATAGAC	58.512	47.619	0.00	0.00	39.64	2.59
929	935	1.802960	CATGCATTCGCTCCATAGACC	59.197	52.381	0.00	0.00	39.64	3.85
930	936	0.106708	TGCATTCGCTCCATAGACCC	59.893	55.000	0.00	0.00	39.64	4.46
1098	1111	3.600388	CTTGCCTCTCGTTTACATCCTT	58.400	45.455	0.00	0.00	0.00	3.36
1109	1122	4.383118	CGTTTACATCCTTCTCCACTCCAT	60.383	45.833	0.00	0.00	0.00	3.41
1212	1234	6.143915	TCCTCCTCAAGGTATATAAGCAACT	58.856	40.000	0.00	0.00	46.32	3.16
1213	1235	6.267928	TCCTCCTCAAGGTATATAAGCAACTC	59.732	42.308	0.00	0.00	46.32	3.01
1214	1236	6.085555	TCCTCAAGGTATATAAGCAACTCG	57.914	41.667	0.00	0.00	36.34	4.18
1215	1237	5.831525	TCCTCAAGGTATATAAGCAACTCGA	59.168	40.000	0.00	0.00	36.34	4.04
1361	1428	2.434774	GGGAAGTGGGTGTGGGAC	59.565	66.667	0.00	0.00	0.00	4.46
1724	1791	1.291272	GTACTGGTCGCCGTTCCTT	59.709	57.895	3.36	0.00	0.00	3.36
2203	2279	3.050275	GGCGAAAAGGCAGCGACT	61.050	61.111	0.00	0.00	45.92	4.18
2384	2460	3.676172	TGGACACGTTCAACGACATATTC	59.324	43.478	18.84	3.10	46.05	1.75
2606	4246	5.238214	GCATCAGTCACTTCTTTTCTTGTCT	59.762	40.000	0.00	0.00	0.00	3.41
2612	4252	2.872858	ACTTCTTTTCTTGTCTGTCGGC	59.127	45.455	0.00	0.00	0.00	5.54
2655	4295	3.181485	CGTCATCTTCCTCCTACCAACTC	60.181	52.174	0.00	0.00	0.00	3.01
2676	4316	5.163426	ACTCTTGACATCAAATTTTGGCACA	60.163	36.000	9.18	3.10	35.15	4.57
2682	4322	5.613329	ACATCAAATTTTGGCACAGACAAT	58.387	33.333	9.18	0.00	42.39	2.71
2717	4357	8.877808	AAGATGACCTCAAATGAAAAAGTTTC	57.122	30.769	0.00	0.00	0.00	2.78
2719	4359	5.587289	TGACCTCAAATGAAAAAGTTTCCG	58.413	37.500	0.00	0.00	0.00	4.30
2720	4360	4.944048	ACCTCAAATGAAAAAGTTTCCGG	58.056	39.130	0.00	0.00	0.00	5.14
2726	4366	3.363341	TGAAAAAGTTTCCGGCATGAC	57.637	42.857	0.00	0.00	0.00	3.06
2798	4438	1.070758	GCGATCTCATCTAAAGGGCCA	59.929	52.381	6.18	0.00	0.00	5.36
2802	4442	4.823989	CGATCTCATCTAAAGGGCCAAAAT	59.176	41.667	6.18	0.00	0.00	1.82
2814	4454	2.262211	GGCCAAAATTGTGCTCGAATC	58.738	47.619	0.00	0.00	0.00	2.52
2826	4466	5.724328	TGTGCTCGAATCACTAAGATTTCT	58.276	37.500	15.64	0.00	46.76	2.52
2854	4494	4.693566	CAGAGTACTGTTCGGCCAATTAAA	59.306	41.667	0.00	0.00	39.11	1.52
2872	4846	2.867109	AACATCCAAGACAGACCCAG	57.133	50.000	0.00	0.00	0.00	4.45
2878	4852	1.421646	CCAAGACAGACCCAGAAACCT	59.578	52.381	0.00	0.00	0.00	3.50
2887	4861	2.552743	GACCCAGAAACCTAACTGTTGC	59.447	50.000	2.69	0.00	32.93	4.17
2911	4886	6.583562	CCTCAGACTTACCTAAATCCGATTT	58.416	40.000	11.09	11.09	36.29	2.17
2943	4918	6.745794	TTGGAAAGATTTGGACAGGATTTT	57.254	33.333	0.00	0.00	0.00	1.82
3044	5024	7.827819	TCGAACAATCATCTACCACTTTTAG	57.172	36.000	0.00	0.00	0.00	1.85
3088	5071	6.183360	CCTTGTTTTCTTCTTCCTCGTTCTTT	60.183	38.462	0.00	0.00	0.00	2.52
3255	5243	1.554042	CTTGCGTACCGTGCTTTCGT	61.554	55.000	0.00	0.00	0.00	3.85
3287	5275	3.808036	ACGTGAGTTGTGGTGCAC	58.192	55.556	8.80	8.80	46.40	4.57
3288	5276	1.220749	ACGTGAGTTGTGGTGCACT	59.779	52.632	17.98	0.00	46.40	4.40
3382	5370	0.759346	AGCTTTGAACGGTCTCCAGT	59.241	50.000	0.33	0.00	0.00	4.00
3397	5385	1.585006	CAGTCCGTTCCTGCTACGT	59.415	57.895	0.00	0.00	37.30	3.57
3410	5398	1.202452	TGCTACGTGGAGAGCATCATG	60.202	52.381	6.64	0.00	43.64	3.07
3411	5399	1.067669	GCTACGTGGAGAGCATCATGA	59.932	52.381	1.81	0.00	38.62	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
333	334	1.137086	AGTAGACAATAGTGGCCTGCG	59.863	52.381	3.32	0.00	30.22	5.18
369	370	4.030216	TGGATTGCTGGTCATGTAGACTA	58.970	43.478	0.00	0.00	46.72	2.59
482	484	1.257743	AGCAAACTGAGCCGTAGAGA	58.742	50.000	0.00	0.00	0.00	3.10
671	673	7.036220	GTGCGGCATACAAGAGTATATAAGAT	58.964	38.462	5.72	0.00	38.88	2.40
764	767	7.095607	CCAAGAAATACTACTTGATACCGATGC	60.096	40.741	0.00	0.00	43.98	3.91
799	802	0.035317	ACGCCAACAATCTGAGAGCA	59.965	50.000	0.00	0.00	0.00	4.26
856	859	4.675190	ACACCGTATATATCGGAGTTCG	57.325	45.455	22.37	4.92	46.34	3.95
857	860	7.185453	GTGATACACCGTATATATCGGAGTTC	58.815	42.308	22.37	18.92	46.34	3.01
876	879	6.715718	TGGAATCTAGCTAGTACTGGTGATAC	59.284	42.308	20.10	6.28	0.00	2.24
878	881	5.706447	TGGAATCTAGCTAGTACTGGTGAT	58.294	41.667	20.10	5.77	0.00	3.06
928	934	7.210174	CGGGATGTGTATGTATATAAGATGGG	58.790	42.308	0.00	0.00	0.00	4.00
929	935	7.210174	CCGGGATGTGTATGTATATAAGATGG	58.790	42.308	0.00	0.00	0.00	3.51
930	936	6.701841	GCCGGGATGTGTATGTATATAAGATG	59.298	42.308	2.18	0.00	0.00	2.90
1098	1111	3.729108	AGAAGATGGAATGGAGTGGAGA	58.271	45.455	0.00	0.00	0.00	3.71
1109	1122	7.568738	TGGTATATGAGAGGAAAGAAGATGGAA	59.431	37.037	0.00	0.00	0.00	3.53
1650	1717	2.275380	ACCGCCAGAATTTGTGGGC	61.275	57.895	13.93	5.96	42.98	5.36
1962	2029	3.095347	GCACCCTCCGGATCACCTC	62.095	68.421	3.57	0.00	0.00	3.85
2018	2085	0.751277	TTGACACCACCACCAGCTTG	60.751	55.000	0.00	0.00	0.00	4.01
2061	2128	2.090524	GGTTCGACGCGTACTTGGG	61.091	63.158	13.97	0.00	0.00	4.12
2105	2172	1.261480	CCTCTCCCTCATCATACGGG	58.739	60.000	0.00	0.00	39.41	5.28
2189	2265	2.335712	CCCCAGTCGCTGCCTTTTC	61.336	63.158	0.00	0.00	0.00	2.29
2384	2460	0.245266	TTGCAGCCAGAATGTGCATG	59.755	50.000	0.00	0.00	46.18	4.06
2606	4246	0.535335	GGTTGGATGTAGAGCCGACA	59.465	55.000	15.85	0.00	43.14	4.35
2612	4252	1.204704	TGTCAGCGGTTGGATGTAGAG	59.795	52.381	0.00	0.00	32.65	2.43
2655	4295	5.176223	GTCTGTGCCAAAATTTGATGTCAAG	59.824	40.000	7.37	0.00	37.15	3.02
2698	4338	4.739436	GCCGGAAACTTTTTCATTTGAGGT	60.739	41.667	5.05	0.00	0.00	3.85
2716	4356	0.953471	CGGAACTTTGTCATGCCGGA	60.953	55.000	5.05	0.00	35.42	5.14
2717	4357	1.234615	ACGGAACTTTGTCATGCCGG	61.235	55.000	0.00	0.00	42.76	6.13
2719	4359	3.190535	ACAATACGGAACTTTGTCATGCC	59.809	43.478	0.00	0.00	0.00	4.40
2720	4360	4.403453	GACAATACGGAACTTTGTCATGC	58.597	43.478	7.57	0.00	45.37	4.06
2726	4366	8.251750	TCTCATTTAGACAATACGGAACTTTG	57.748	34.615	0.00	0.00	0.00	2.77
2765	4405	2.431782	TGAGATCGCTTGGTGATGATCA	59.568	45.455	0.00	0.00	39.70	2.92
2777	4417	1.346068	GGCCCTTTAGATGAGATCGCT	59.654	52.381	0.00	0.00	0.00	4.93
2778	4418	1.070758	TGGCCCTTTAGATGAGATCGC	59.929	52.381	0.00	0.00	0.00	4.58
2798	4438	6.801539	TCTTAGTGATTCGAGCACAATTTT	57.198	33.333	18.72	4.55	38.70	1.82
2802	4442	6.166279	AGAAATCTTAGTGATTCGAGCACAA	58.834	36.000	18.72	11.56	43.99	3.33
2826	4466	3.512329	TGGCCGAACAGTACTCTGAATAA	59.488	43.478	0.00	0.00	43.76	1.40
2834	4474	4.391155	TGTTTAATTGGCCGAACAGTACT	58.609	39.130	0.00	0.00	0.00	2.73
2838	4478	3.192422	TGGATGTTTAATTGGCCGAACAG	59.808	43.478	0.00	0.00	35.69	3.16
2854	4494	2.030027	TCTGGGTCTGTCTTGGATGT	57.970	50.000	0.00	0.00	0.00	3.06
2872	4846	3.498777	GTCTGAGGCAACAGTTAGGTTTC	59.501	47.826	10.51	0.00	38.79	2.78
2878	4852	3.901844	AGGTAAGTCTGAGGCAACAGTTA	59.098	43.478	10.51	2.57	38.79	2.24
2887	4861	5.793030	ATCGGATTTAGGTAAGTCTGAGG	57.207	43.478	9.02	0.00	39.59	3.86
2911	4886	7.796054	TGTCCAAATCTTTCCAAAATTAACCA	58.204	30.769	0.00	0.00	0.00	3.67
2943	4918	7.176690	GGACTTTCCATACAAGAAAAGGATTCA	59.823	37.037	0.00	0.00	36.28	2.57
2996	4971	2.020720	TGTGTTGTTCAATCGGCTGTT	58.979	42.857	0.00	0.00	0.00	3.16
3044	5024	7.689446	ACAAGGGAGAAGATAAAAGTAAAGC	57.311	36.000	0.00	0.00	0.00	3.51
3088	5071	3.557054	CCCTCCAATCTTGAAGAACGACA	60.557	47.826	0.00	0.00	0.00	4.35
3255	5243	0.599558	CACGTTGAAGGAGACCCGTA	59.400	55.000	0.00	0.00	37.58	4.02
3287	5275	1.517832	CCTCCAACGCTGAGGGTAG	59.482	63.158	1.54	0.00	44.73	3.18
3288	5276	3.708210	CCTCCAACGCTGAGGGTA	58.292	61.111	1.54	0.00	44.73	3.69
3382	5370	1.592400	CTCCACGTAGCAGGAACGGA	61.592	60.000	0.00	0.00	44.48	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.