AutoCloner

Multiple sequence alignment - TraesCS6A01G193900

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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	TraesCS6A01G193900	chr6A	100.000	3167	0	0	1	3167	270787377	270790543	0.000000e+00	5849
1	TraesCS6A01G193900	chr6A	94.158	2636	119	10	1	2622	567088461	567085847	0.000000e+00	3982
2	TraesCS6A01G193900	chr6A	85.139	1043	116	19	1845	2861	270788188	270789217	0.000000e+00	1031
3	TraesCS6A01G193900	chr6A	85.139	1043	116	19	812	1841	270789221	270790237	0.000000e+00	1031
4	TraesCS6A01G193900	chr6A	84.990	1046	99	24	1845	2864	567087638	567086625	0.000000e+00	1009
5	TraesCS6A01G193900	chr6A	84.925	796	92	17	812	1594	567086624	567085844	0.000000e+00	780
6	TraesCS6A01G193900	chr3A	94.234	2636	116	10	1	2622	739817497	739820110	0.000000e+00	3993
7	TraesCS6A01G193900	chr3A	84.947	1043	99	24	1845	2861	739818319	739819329	0.000000e+00	1003
8	TraesCS6A01G193900	chr3A	85.120	793	90	17	812	1591	739819333	739820110	0.000000e+00	785
9	TraesCS6A01G193900	chr5B	94.144	2630	125	7	1	2622	42173975	42176583	0.000000e+00	3976
10	TraesCS6A01G193900	chr5B	85.043	1043	98	24	1845	2861	42174792	42175802	0.000000e+00	1009
11	TraesCS6A01G193900	chr5B	84.994	793	91	17	812	1591	42175806	42176583	0.000000e+00	780
12	TraesCS6A01G193900	chr4A	93.892	2636	125	11	1	2622	16840114	16837501	0.000000e+00	3943
13	TraesCS6A01G193900	chr4A	84.799	1046	101	24	1845	2864	16839291	16838278	0.000000e+00	998
14	TraesCS6A01G193900	chr4A	84.171	796	97	19	812	1594	16838277	16837498	0.000000e+00	745
15	TraesCS6A01G193900	chr7A	93.815	1924	82	13	1	1913	53221451	53219554	0.000000e+00	2859
16	TraesCS6A01G193900	chr7A	93.261	831	53	3	619	1449	48235776	48236603	0.000000e+00	1221
17	TraesCS6A01G193900	chr7A	84.608	1046	100	27	1845	2864	53220633	53219623	0.000000e+00	983
18	TraesCS6A01G193900	chr7A	94.475	362	19	1	2262	2622	53219490	53219129	9.920000e-155	556
19	TraesCS6A01G193900	chr7A	91.317	357	28	3	1238	1594	53219479	53219126	4.750000e-133	484
20	TraesCS6A01G193900	chr7A	93.684	95	6	0	1	95	1928054	1927960	3.290000e-30	143
21	TraesCS6A01G193900	chr3B	92.646	1591	99	8	1	1578	145705046	145703461	0.000000e+00	2274
22	TraesCS6A01G193900	chr3B	82.798	779	107	14	1845	2610	145704225	145703461	0.000000e+00	671
23	TraesCS6A01G193900	chr3D	95.213	1316	53	2	1	1306	321929139	321930454	0.000000e+00	2073
24	TraesCS6A01G193900	chr3D	96.160	1250	36	2	1217	2466	321930451	321931688	0.000000e+00	2032
25	TraesCS6A01G193900	chr3D	83.465	508	58	12	1845	2339	321929960	321930454	1.730000e-122	449
26	TraesCS6A01G193900	chr3D	96.970	264	4	3	2812	3072	321938017	321938279	1.040000e-119	440
27	TraesCS6A01G193900	chr3D	97.368	114	2	1	3054	3167	321939695	321939807	3.220000e-45	193
28	TraesCS6A01G193900	chr3D	85.165	182	23	4	2953	3133	497903161	497902983	1.940000e-42	183
29	TraesCS6A01G193900	chr3D	84.066	182	25	4	2953	3133	392968054	392967876	4.200000e-39	172
30	TraesCS6A01G193900	chr7B	94.615	1337	50	7	1851	3167	472508729	472507395	0.000000e+00	2050
31	TraesCS6A01G193900	chr7B	94.886	1271	51	5	594	1864	472510150	472508894	0.000000e+00	1975
32	TraesCS6A01G193900	chr7B	86.164	1048	107	19	817	1844	472508729	472507700	0.000000e+00	1098
33	TraesCS6A01G193900	chr7B	85.291	1047	100	26	1845	2864	472509933	472508914	0.000000e+00	1031
34	TraesCS6A01G193900	chr7B	94.323	229	10	1	302	527	472510371	472510143	6.500000e-92	348
35	TraesCS6A01G193900	chr5A	93.333	825	52	3	625	1449	472697515	472696694	0.000000e+00	1216
36	TraesCS6A01G193900	chr4B	89.464	522	41	5	1	510	397891612	397892131	0.000000e+00	647
37	TraesCS6A01G193900	chr1D	91.000	100	9	0	1	100	47848607	47848706	5.510000e-28	135

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	TraesCS6A01G193900	chr6A	270787377	270790543	3166	False	2637.000000	5849	90.092667	1	3167	3	chr6A.!!$F1	3166
1	TraesCS6A01G193900	chr6A	567085844	567088461	2617	True	1923.666667	3982	88.024333	1	2864	3	chr6A.!!$R1	2863
2	TraesCS6A01G193900	chr3A	739817497	739820110	2613	False	1927.000000	3993	88.100333	1	2861	3	chr3A.!!$F1	2860
3	TraesCS6A01G193900	chr5B	42173975	42176583	2608	False	1921.666667	3976	88.060333	1	2861	3	chr5B.!!$F1	2860
4	TraesCS6A01G193900	chr4A	16837498	16840114	2616	True	1895.333333	3943	87.620667	1	2864	3	chr4A.!!$R1	2863
5	TraesCS6A01G193900	chr7A	48235776	48236603	827	False	1221.000000	1221	93.261000	619	1449	1	chr7A.!!$F1	830
6	TraesCS6A01G193900	chr7A	53219126	53221451	2325	True	1220.500000	2859	91.053750	1	2864	4	chr7A.!!$R2	2863
7	TraesCS6A01G193900	chr3B	145703461	145705046	1585	True	1472.500000	2274	87.722000	1	2610	2	chr3B.!!$R1	2609
8	TraesCS6A01G193900	chr3D	321929139	321931688	2549	False	1518.000000	2073	91.612667	1	2466	3	chr3D.!!$F1	2465
9	TraesCS6A01G193900	chr3D	321938017	321939807	1790	False	316.500000	440	97.169000	2812	3167	2	chr3D.!!$F2	355
10	TraesCS6A01G193900	chr7B	472507395	472510371	2976	True	1300.400000	2050	91.055800	302	3167	5	chr7B.!!$R1	2865
11	TraesCS6A01G193900	chr5A	472696694	472697515	821	True	1216.000000	1216	93.333000	625	1449	1	chr5A.!!$R1	824
12	TraesCS6A01G193900	chr4B	397891612	397892131	519	False	647.000000	647	89.464000	1	510	1	chr4B.!!$F1	509

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
100	101	0.391228	TCTACCGCTTGCTCACAACA	59.609	50.0	0.0	0.00	0.00	3.33	F
1122	1154	0.106769	TGCAACACCTCAAGGAAGCA	60.107	50.0	2.3	4.48	38.94	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1996	2310	1.538512	CATGGACCTGCACAAGTCTTG	59.461	52.381	11.17	11.17	33.39	3.02	R
2368	2682	0.249031	GCACAATTAATCCAGCCGCC	60.249	55.000	0.00	0.00	0.00	6.13	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
84	85	1.918467	TTCTCCGCTCCCGTCCTCTA	61.918	60.000	0.00	0.00	0.00	2.43
100	101	0.391228	TCTACCGCTTGCTCACAACA	59.609	50.000	0.00	0.00	0.00	3.33
110	111	2.449518	TCACAACAGGAGCCCCCA	60.450	61.111	0.00	0.00	37.41	4.96
172	180	2.272146	GCCCAAGGATTCTCGCCA	59.728	61.111	0.00	0.00	0.00	5.69
476	508	1.374758	GGTTCGCCTCTGGTGTCTG	60.375	63.158	0.00	0.00	34.40	3.51
510	542	2.346541	CGCCAGAGTCAGAGCTCCA	61.347	63.158	10.93	0.00	36.20	3.86
527	559	1.564818	TCCACTATCGTCCAGTCCTCT	59.435	52.381	0.00	0.00	0.00	3.69
532	564	4.641094	CACTATCGTCCAGTCCTCTACTTT	59.359	45.833	0.00	0.00	35.76	2.66
553	585	1.139853	GGGCCGTCTCTCATCAATTCT	59.860	52.381	0.00	0.00	0.00	2.40
773	805	3.569194	TGTTGTCAAAAGTAGGCCTGA	57.431	42.857	17.99	0.00	0.00	3.86
786	818	3.947910	AGGCCTGACATTGTCAAAATG	57.052	42.857	19.44	8.56	42.26	2.32
793	825	6.222389	CCTGACATTGTCAAAATGGCTTTTA	58.778	36.000	19.44	0.00	42.26	1.52
796	828	7.495901	TGACATTGTCAAAATGGCTTTTAAGA	58.504	30.769	16.95	0.00	39.78	2.10
842	874	1.331756	CGAGGCACAACCATAATCTGC	59.668	52.381	0.00	0.00	43.14	4.26
897	929	5.965922	AGTATGCCCAATTTAAAACTGAGC	58.034	37.500	0.00	0.00	0.00	4.26
952	984	3.580458	ACTTGTGACTGAAGGACTATGCT	59.420	43.478	0.00	0.00	0.00	3.79
983	1015	2.977169	CCGTAAAAATTTGTGCAGGTCG	59.023	45.455	0.00	0.00	0.00	4.79
1122	1154	0.106769	TGCAACACCTCAAGGAAGCA	60.107	50.000	2.30	4.48	38.94	3.91
1223	1255	3.388024	GTGCTATCCTTGTCATCCTGGTA	59.612	47.826	0.00	0.00	0.00	3.25
1226	1258	4.101741	GCTATCCTTGTCATCCTGGTAAGT	59.898	45.833	0.00	0.00	0.00	2.24
1234	1266	6.222038	TGTCATCCTGGTAAGTCATACTTC	57.778	41.667	0.00	0.00	39.51	3.01
1240	1272	5.189145	TCCTGGTAAGTCATACTTCCCTTTC	59.811	44.000	3.50	0.00	39.51	2.62
1336	1454	4.535781	AGGCATGTTGGATGCAGTATTAA	58.464	39.130	8.78	0.00	46.21	1.40
1419	1537	8.846943	TGATTCTGTACAGTTAAATGATGTGT	57.153	30.769	21.99	0.00	0.00	3.72
1662	1790	6.274157	TCTGTTTTTGCAAGTAAACTGGAA	57.726	33.333	22.72	10.25	35.73	3.53
1806	1934	6.126652	ACCAGAGAAAGTATATCAACTGGCAT	60.127	38.462	0.00	0.00	42.19	4.40
2045	2359	2.742710	TTCGAAGTCTGCGTGGTCGG	62.743	60.000	0.00	0.00	37.56	4.79
2060	2374	2.070039	TCGGGGTCTATGGCAAGGG	61.070	63.158	0.00	0.00	0.00	3.95
2090	2404	1.828979	GGGGTATTCCGCAACTTCAA	58.171	50.000	0.17	0.00	44.68	2.69
2135	2449	3.393106	TGGAGATCCGCTGCTGCA	61.393	61.111	16.29	0.88	39.64	4.41
2223	2537	1.270907	CCTGCTCACCTAGACTTGGT	58.729	55.000	2.39	2.39	38.53	3.67
2260	2574	0.037790	GCTATCCTCGTCATCCTGGC	60.038	60.000	0.00	0.00	0.00	4.85
2322	2636	5.950965	AGCTGTATTACTTCGTTCATTCG	57.049	39.130	0.00	0.00	0.00	3.34
2368	2682	2.691526	AGGCATGTTGGATGCAGTATTG	59.308	45.455	8.78	0.00	46.21	1.90
2389	2703	1.534595	GCGGCTGGATTAATTGTGCTG	60.535	52.381	0.00	10.19	0.00	4.41
2501	2815	6.958192	ACTACCTTTCTGGGTGTTATCTAAGA	59.042	38.462	0.00	0.00	40.22	2.10
2502	2816	6.301169	ACCTTTCTGGGTGTTATCTAAGAG	57.699	41.667	0.00	0.00	41.11	2.85
2532	2846	1.559219	TCTCAAATTCAGGGGCGATCA	59.441	47.619	0.00	0.00	0.00	2.92
2603	2917	3.197766	TGACCTAGCAGGACCAATTAGTG	59.802	47.826	8.91	0.00	37.67	2.74
2606	2920	2.496899	AGCAGGACCAATTAGTGTGG	57.503	50.000	0.00	0.00	42.28	4.17
2622	2936	4.511527	AGTGTGGAGATGATGCTTGTTAG	58.488	43.478	0.00	0.00	0.00	2.34
2708	3022	5.763876	ACTGGAGCTGGTTCTTTATAGTT	57.236	39.130	0.00	0.00	0.00	2.24
2771	3085	8.315391	ACAAATTATCTGTATGTGATGGATCG	57.685	34.615	0.00	0.00	0.00	3.69
2773	3087	6.857437	ATTATCTGTATGTGATGGATCGGA	57.143	37.500	0.00	0.00	0.00	4.55
2792	3106	8.458843	GGATCGGAGAAAGTTTATCAATCAAAA	58.541	33.333	18.66	0.00	43.58	2.44
2793	3107	9.278734	GATCGGAGAAAGTTTATCAATCAAAAC	57.721	33.333	12.06	0.00	43.58	2.43
2794	3108	8.391075	TCGGAGAAAGTTTATCAATCAAAACT	57.609	30.769	12.06	0.00	45.44	2.66
2803	3127	6.839124	TTATCAATCAAAACTGCATGGACT	57.161	33.333	0.00	0.00	0.00	3.85
2880	3204	9.849166	TTGTATTAGTTTCCGGATTGAAAATTC	57.151	29.630	4.15	1.28	36.09	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	85	1.893808	CCTGTTGTGAGCAAGCGGT	60.894	57.895	0.00	0.00	34.94	5.68
100	101	4.115199	GTCGCATTGGGGGCTCCT	62.115	66.667	4.32	0.00	36.20	3.69
110	111	3.011517	AGCAGGGGAGGTCGCATT	61.012	61.111	0.00	0.00	0.00	3.56
211	221	2.575532	CCATAGAAACGATGGCATGGT	58.424	47.619	9.51	9.51	37.64	3.55
283	300	0.964358	CCGTCCCCTTCTCTGTACGT	60.964	60.000	0.00	0.00	0.00	3.57
341	373	2.102578	GAATTTGTCCCCATCCACCTG	58.897	52.381	0.00	0.00	0.00	4.00
476	508	2.776072	CGATTGGAACGTCGTGGC	59.224	61.111	0.00	0.00	35.04	5.01
527	559	1.480954	GATGAGAGACGGCCCAAAGTA	59.519	52.381	0.00	0.00	0.00	2.24
532	564	0.911769	AATTGATGAGAGACGGCCCA	59.088	50.000	0.00	0.00	0.00	5.36
553	585	1.134401	GGTGCAGTGCTCTAATGGCTA	60.134	52.381	17.60	0.00	0.00	3.93
683	715	0.894184	TCGGCGAGAAGGAACTCACT	60.894	55.000	4.99	0.00	38.49	3.41
747	779	4.038642	GGCCTACTTTTGACAACAATTGGA	59.961	41.667	10.83	0.00	35.85	3.53
773	805	7.725251	TCTCTTAAAAGCCATTTTGACAATGT	58.275	30.769	0.00	0.00	39.01	2.71
842	874	7.803189	ACATGAACAAAGCTTATTTCTAACACG	59.197	33.333	16.79	0.00	0.00	4.49
871	903	7.488150	GCTCAGTTTTAAATTGGGCATACTAAC	59.512	37.037	18.07	0.00	38.20	2.34
875	907	5.719173	TGCTCAGTTTTAAATTGGGCATAC	58.281	37.500	21.00	0.00	42.96	2.39
897	929	7.948357	ACCATAATGAAACCATTCTGATCATG	58.052	34.615	0.00	0.00	35.92	3.07
952	984	5.696724	CACAAATTTTTACGGGGCAACAATA	59.303	36.000	0.00	0.00	39.74	1.90
983	1015	8.250332	TGCAATACATTGGAAAAAGGAAGTATC	58.750	33.333	4.23	0.00	35.12	2.24
1223	1255	3.178865	TCGGGAAAGGGAAGTATGACTT	58.821	45.455	0.00	0.00	41.95	3.01
1226	1258	2.704065	GGATCGGGAAAGGGAAGTATGA	59.296	50.000	0.00	0.00	0.00	2.15
1234	1266	2.504519	GGACGGATCGGGAAAGGG	59.495	66.667	5.18	0.00	0.00	3.95
1240	1272	2.510064	TTCCAAACGGACGGATCGGG	62.510	60.000	5.18	0.00	30.04	5.14
1336	1454	1.743995	GCACCGTTAATCCAGCCGT	60.744	57.895	0.00	0.00	0.00	5.68
1396	1514	9.897744	CAAACACATCATTTAACTGTACAGAAT	57.102	29.630	29.30	18.49	0.00	2.40
1419	1537	9.026074	GCTAAAAACAACTATGTAACAAGCAAA	57.974	29.630	0.00	0.00	39.40	3.68
1662	1790	8.409358	AAAATCTGCAACTATAAAGAACCAGT	57.591	30.769	0.00	0.00	0.00	4.00
1806	1934	8.617809	GGTCGCCTATCTTTGATTAATTTGTTA	58.382	33.333	0.00	0.00	0.00	2.41
1996	2310	1.538512	CATGGACCTGCACAAGTCTTG	59.461	52.381	11.17	11.17	33.39	3.02
2039	2353	1.613928	TTGCCATAGACCCCGACCA	60.614	57.895	0.00	0.00	0.00	4.02
2045	2359	2.203209	CGCCCTTGCCATAGACCC	60.203	66.667	0.00	0.00	0.00	4.46
2090	2404	2.186384	GCGAGCAGATGCAGTCCT	59.814	61.111	7.68	0.00	45.16	3.85
2260	2574	2.222027	GGATGGGAAAAGTATGGCTCG	58.778	52.381	0.00	0.00	0.00	5.03
2322	2636	6.551601	TCAATTTCTAGGACCTCCAGATAGAC	59.448	42.308	0.00	0.00	38.89	2.59
2368	2682	0.249031	GCACAATTAATCCAGCCGCC	60.249	55.000	0.00	0.00	0.00	6.13
2389	2703	3.733443	AGAAAAACATTGGTGGTGCTC	57.267	42.857	0.00	0.00	0.00	4.26
2423	2737	6.182039	TCATTTAACTGTACAGAAGCATGC	57.818	37.500	29.30	10.51	0.00	4.06
2501	2815	6.717084	CCCCTGAATTTGAGAGAAAACTTACT	59.283	38.462	0.00	0.00	0.00	2.24
2502	2816	6.570571	GCCCCTGAATTTGAGAGAAAACTTAC	60.571	42.308	0.00	0.00	0.00	2.34
2532	2846	9.842775	TTCAAAGAATCATCTGTTGATATAGCT	57.157	29.630	1.87	0.00	44.51	3.32
2544	2858	5.302568	TGCAACAACCTTCAAAGAATCATCT	59.697	36.000	0.00	0.00	37.57	2.90
2603	2917	3.878778	ACCTAACAAGCATCATCTCCAC	58.121	45.455	0.00	0.00	0.00	4.02
2622	2936	4.491676	TCGACTATTTGTCAGCTTGTACC	58.508	43.478	0.00	0.00	45.60	3.34
2708	3022	3.569277	TCTTGCAAGCTACAAAATCTGCA	59.431	39.130	21.99	1.41	0.00	4.41
2771	3085	7.867403	TGCAGTTTTGATTGATAAACTTTCTCC	59.133	33.333	0.00	0.00	41.34	3.71
2773	3087	9.199982	CATGCAGTTTTGATTGATAAACTTTCT	57.800	29.630	0.00	0.00	41.34	2.52
2792	3106	1.701847	ACTTTCTCCAGTCCATGCAGT	59.298	47.619	0.00	0.00	0.00	4.40
2793	3107	2.486472	ACTTTCTCCAGTCCATGCAG	57.514	50.000	0.00	0.00	0.00	4.41
2794	3108	5.894298	ATATACTTTCTCCAGTCCATGCA	57.106	39.130	0.00	0.00	0.00	3.96
2880	3204	4.100653	TGCCTTGAATAGAGACCTCTGATG	59.899	45.833	9.65	0.00	40.71	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.