AutoCloner

Multiple sequence alignment - TraesCS6A01G362100

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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	TraesCS6A01G362100	chr6A	100.000	2105	0	0	296	2400	592204507	592206611	0.000000e+00	3888.0
1	TraesCS6A01G362100	chr6A	89.568	556	39	8	1033	1586	592212922	592213460	0.000000e+00	688.0
2	TraesCS6A01G362100	chr6A	100.000	162	0	0	1	162	592204212	592204373	1.390000e-77	300.0
3	TraesCS6A01G362100	chr6D	91.026	1326	83	13	399	1716	445613456	445614753	0.000000e+00	1757.0
4	TraesCS6A01G362100	chr6D	91.353	532	38	5	1051	1581	445656015	445656539	0.000000e+00	721.0
5	TraesCS6A01G362100	chr6D	96.212	132	3	2	28	158	445612997	445613127	5.200000e-52	215.0
6	TraesCS6A01G362100	chr6B	88.488	1329	109	23	399	1716	671883438	671884733	0.000000e+00	1567.0
7	TraesCS6A01G362100	chr6B	88.409	1320	104	21	402	1705	670904576	670903290	0.000000e+00	1544.0
8	TraesCS6A01G362100	chr6B	74.298	1175	218	48	420	1567	672059940	672061057	1.030000e-113	420.0
9	TraesCS6A01G362100	chr6B	87.302	126	12	3	28	153	671883122	671883243	8.940000e-30	141.0
10	TraesCS6A01G362100	chr1B	89.390	688	59	11	1717	2398	7051352	7052031	0.000000e+00	854.0
11	TraesCS6A01G362100	chr7B	95.154	454	17	3	1717	2167	709614190	709614641	0.000000e+00	712.0
12	TraesCS6A01G362100	chr7B	97.233	253	6	1	2148	2400	709614894	709615145	6.130000e-116	427.0
13	TraesCS6A01G362100	chr7B	80.526	190	20	11	2161	2349	643133752	643133579	1.940000e-26	130.0
14	TraesCS6A01G362100	chr4A	98.044	409	5	3	1992	2400	638673165	638673570	0.000000e+00	708.0
15	TraesCS6A01G362100	chr4A	97.276	257	7	0	1739	1995	638672807	638673063	1.020000e-118	436.0
16	TraesCS6A01G362100	chr4A	100.000	44	0	0	1717	1760	638672763	638672806	5.500000e-12	82.4
17	TraesCS6A01G362100	chr7D	88.000	400	27	10	1996	2390	5070114	5069731	1.010000e-123	453.0
18	TraesCS6A01G362100	chr2D	86.029	408	35	13	1988	2390	586463498	586463888	3.690000e-113	418.0
19	TraesCS6A01G362100	chr2D	88.189	127	14	1	28	154	646591569	646591444	1.490000e-32	150.0
20	TraesCS6A01G362100	chr2D	80.851	94	16	2	1717	1809	371151169	371151077	3.310000e-09	73.1
21	TraesCS6A01G362100	chr2A	88.000	125	12	3	31	154	773222152	773222274	6.910000e-31	145.0
22	TraesCS6A01G362100	chr4D	87.402	127	13	3	28	154	484705267	484705144	2.490000e-30	143.0
23	TraesCS6A01G362100	chr4B	86.719	128	14	2	28	154	530209379	530209504	3.220000e-29	139.0
24	TraesCS6A01G362100	chr3B	86.154	130	16	2	28	156	821686437	821686309	3.220000e-29	139.0
25	TraesCS6A01G362100	chr5A	86.047	129	16	2	28	156	343601266	343601392	1.160000e-28	137.0
26	TraesCS6A01G362100	chr2B	86.047	129	16	1	28	156	411972635	411972509	1.160000e-28	137.0

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	TraesCS6A01G362100	chr6A	592204212	592206611	2399	False	2094.0	3888	100.0000	1	2400	2	chr6A.!!$F2	2399
1	TraesCS6A01G362100	chr6A	592212922	592213460	538	False	688.0	688	89.5680	1033	1586	1	chr6A.!!$F1	553
2	TraesCS6A01G362100	chr6D	445612997	445614753	1756	False	986.0	1757	93.6190	28	1716	2	chr6D.!!$F2	1688
3	TraesCS6A01G362100	chr6D	445656015	445656539	524	False	721.0	721	91.3530	1051	1581	1	chr6D.!!$F1	530
4	TraesCS6A01G362100	chr6B	670903290	670904576	1286	True	1544.0	1544	88.4090	402	1705	1	chr6B.!!$R1	1303
5	TraesCS6A01G362100	chr6B	671883122	671884733	1611	False	854.0	1567	87.8950	28	1716	2	chr6B.!!$F2	1688
6	TraesCS6A01G362100	chr6B	672059940	672061057	1117	False	420.0	420	74.2980	420	1567	1	chr6B.!!$F1	1147
7	TraesCS6A01G362100	chr1B	7051352	7052031	679	False	854.0	854	89.3900	1717	2398	1	chr1B.!!$F1	681
8	TraesCS6A01G362100	chr7B	709614190	709615145	955	False	569.5	712	96.1935	1717	2400	2	chr7B.!!$F1	683
9	TraesCS6A01G362100	chr4A	638672763	638673570	807	False	408.8	708	98.4400	1717	2400	3	chr4A.!!$F1	683

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
635	731	0.316607	GCATCGTCAACACACGCAAA	60.317	50.0	0.0	0.0	39.74	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1597	1723	1.447945	CATATCCACGCAACACACCA	58.552	50.0	0.0	0.0	0.0	4.17	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
38	39	9.628746	TTTTAAGTTTGACTTTCAAAGTGGTAC	57.371	29.630	7.75	2.54	46.11	3.34
406	496	5.446143	TTTATGCCACGCCCTAAATAATG	57.554	39.130	0.00	0.00	0.00	1.90
407	497	1.686355	TGCCACGCCCTAAATAATGG	58.314	50.000	0.00	0.00	0.00	3.16
479	571	3.270027	TGCATTTCGATCCAACCTAGTG	58.730	45.455	0.00	0.00	0.00	2.74
499	593	1.339929	GGTGGGTTTGCGAGTTTGATT	59.660	47.619	0.00	0.00	0.00	2.57
568	662	3.374988	CGTGATAATTGGCAAAGAGAGCA	59.625	43.478	3.01	0.00	0.00	4.26
569	663	4.142622	CGTGATAATTGGCAAAGAGAGCAA	60.143	41.667	3.01	0.00	0.00	3.91
635	731	0.316607	GCATCGTCAACACACGCAAA	60.317	50.000	0.00	0.00	39.74	3.68
668	764	3.687698	CCGAAATCCAATCCACGTTAGTT	59.312	43.478	0.00	0.00	0.00	2.24
717	814	0.861837	CAGACAACGAACAGCTCACC	59.138	55.000	0.00	0.00	0.00	4.02
798	897	7.148722	CCGTTTTTCATTTTGTTTGTGTGTAGT	60.149	33.333	0.00	0.00	0.00	2.73
799	898	8.217778	CGTTTTTCATTTTGTTTGTGTGTAGTT	58.782	29.630	0.00	0.00	0.00	2.24
800	899	9.871299	GTTTTTCATTTTGTTTGTGTGTAGTTT	57.129	25.926	0.00	0.00	0.00	2.66
802	901	9.482627	TTTTCATTTTGTTTGTGTGTAGTTTCT	57.517	25.926	0.00	0.00	0.00	2.52
929	1028	2.575789	GCGTACGCAATTTGCCCG	60.576	61.111	33.90	15.00	41.12	6.13
933	1032	2.403378	TACGCAATTTGCCCGCTCC	61.403	57.895	15.45	0.00	41.12	4.70
937	1036	1.598701	GCAATTTGCCCGCTCCTTCT	61.599	55.000	10.34	0.00	37.42	2.85
951	1050	3.007398	GCTCCTTCTTCTTCACCTTCTCA	59.993	47.826	0.00	0.00	0.00	3.27
952	1051	4.819769	CTCCTTCTTCTTCACCTTCTCAG	58.180	47.826	0.00	0.00	0.00	3.35
971	1070	0.460987	GTCTCCCATCGAGCCAACTG	60.461	60.000	0.00	0.00	38.62	3.16
972	1071	1.817099	CTCCCATCGAGCCAACTGC	60.817	63.158	0.00	0.00	41.71	4.40
1005	1105	2.838202	ACCCCAAGACGACAAGATGTAT	59.162	45.455	0.00	0.00	0.00	2.29
1007	1107	3.116300	CCCAAGACGACAAGATGTATCG	58.884	50.000	0.00	0.00	41.60	2.92
1015	1115	3.242641	CGACAAGATGTATCGACGGAGAA	60.243	47.826	0.00	0.00	38.10	2.87
1019	1119	3.223435	AGATGTATCGACGGAGAACCAT	58.777	45.455	0.00	0.00	35.59	3.55
1044	1150	4.709886	TGTTTTCTCATCATCGTCCTCCTA	59.290	41.667	0.00	0.00	0.00	2.94
1108	1214	1.683365	GGCCCACCACATCATGCTT	60.683	57.895	0.00	0.00	35.26	3.91
1120	1239	5.766670	CCACATCATGCTTCAGGTACATATT	59.233	40.000	0.00	0.00	0.00	1.28
1173	1295	8.194769	TGCTTCGTTCTTTGTATGTATAGATGA	58.805	33.333	0.00	0.00	0.00	2.92
1209	1331	8.596293	TGTAATTATGATGATGATGCTAGGTGA	58.404	33.333	0.00	0.00	0.00	4.02
1287	1410	2.268920	GATGGGAGTTGCGAGGCA	59.731	61.111	0.00	0.00	36.47	4.75
1572	1698	6.877611	TCAATTTGGACTTCTGAGGTAAAC	57.122	37.500	0.00	0.00	0.00	2.01
1917	2073	4.664150	ATGTTCCGTTGGTGAAAACAAT	57.336	36.364	0.00	0.00	33.92	2.71
1953	2109	9.512588	CAAGATAAATATTAGCCATGTCTTCCT	57.487	33.333	0.00	0.00	0.00	3.36
1966	2122	3.347216	TGTCTTCCTTGCTAAATGCCTC	58.653	45.455	0.00	0.00	42.00	4.70
2078	2342	9.617523	AAAACAAAAATTCCTTCATGTGAGATT	57.382	25.926	0.00	0.00	0.00	2.40
2082	2348	9.865321	CAAAAATTCCTTCATGTGAGATTACAT	57.135	29.630	0.00	0.00	41.77	2.29
2288	2827	0.319083	TGCGAGTGGTATTTGACGGT	59.681	50.000	0.00	0.00	0.00	4.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	9.418045	TGAAAGTCAAACTTAAAAGAAGGTTTG	57.582	29.630	10.06	10.06	45.40	2.93
4	5	9.990360	TTGAAAGTCAAACTTAAAAGAAGGTTT	57.010	25.926	0.00	0.00	37.47	3.27
5	6	9.990360	TTTGAAAGTCAAACTTAAAAGAAGGTT	57.010	25.926	0.00	0.00	41.02	3.50
6	7	9.639601	CTTTGAAAGTCAAACTTAAAAGAAGGT	57.360	29.630	15.82	0.00	41.02	3.50
7	8	9.639601	ACTTTGAAAGTCAAACTTAAAAGAAGG	57.360	29.630	22.13	8.07	41.02	3.46
9	10	9.418045	CCACTTTGAAAGTCAAACTTAAAAGAA	57.582	29.630	22.13	5.24	41.02	2.52
10	11	8.581578	ACCACTTTGAAAGTCAAACTTAAAAGA	58.418	29.630	22.13	1.46	41.02	2.52
11	12	8.757164	ACCACTTTGAAAGTCAAACTTAAAAG	57.243	30.769	7.75	17.64	41.02	2.27
12	13	9.628746	GTACCACTTTGAAAGTCAAACTTAAAA	57.371	29.630	7.75	0.00	41.02	1.52
13	14	8.245491	GGTACCACTTTGAAAGTCAAACTTAAA	58.755	33.333	7.75	0.00	41.02	1.52
14	15	7.393796	TGGTACCACTTTGAAAGTCAAACTTAA	59.606	33.333	11.60	0.00	41.02	1.85
15	16	6.885376	TGGTACCACTTTGAAAGTCAAACTTA	59.115	34.615	11.60	0.00	41.02	2.24
16	17	5.712917	TGGTACCACTTTGAAAGTCAAACTT	59.287	36.000	11.60	0.00	41.02	2.66
17	18	5.258051	TGGTACCACTTTGAAAGTCAAACT	58.742	37.500	11.60	0.00	41.02	2.66
18	19	5.570234	TGGTACCACTTTGAAAGTCAAAC	57.430	39.130	11.60	6.18	41.02	2.93
19	20	6.406400	CCAATGGTACCACTTTGAAAGTCAAA	60.406	38.462	23.95	3.57	43.37	2.69
20	21	5.068460	CCAATGGTACCACTTTGAAAGTCAA	59.932	40.000	23.95	0.00	40.46	3.18
21	22	4.582656	CCAATGGTACCACTTTGAAAGTCA	59.417	41.667	23.95	3.28	40.46	3.41
22	23	4.825085	TCCAATGGTACCACTTTGAAAGTC	59.175	41.667	23.95	0.00	40.46	3.01
23	24	4.798882	TCCAATGGTACCACTTTGAAAGT	58.201	39.130	23.95	4.45	44.06	2.66
24	25	5.982890	ATCCAATGGTACCACTTTGAAAG	57.017	39.130	23.95	11.48	0.00	2.62
25	26	5.835819	TGAATCCAATGGTACCACTTTGAAA	59.164	36.000	23.95	14.53	0.00	2.69
26	27	5.389520	TGAATCCAATGGTACCACTTTGAA	58.610	37.500	23.95	9.36	0.00	2.69
387	443	2.238521	CCATTATTTAGGGCGTGGCAT	58.761	47.619	0.00	0.00	0.00	4.40
479	571	0.958822	ATCAAACTCGCAAACCCACC	59.041	50.000	0.00	0.00	0.00	4.61
519	613	1.806542	CACATTCCCTTCACCTTCACG	59.193	52.381	0.00	0.00	0.00	4.35
568	662	1.142060	TCCACCCTCGTGACACATTTT	59.858	47.619	6.37	0.00	43.14	1.82
569	663	0.762418	TCCACCCTCGTGACACATTT	59.238	50.000	6.37	0.00	43.14	2.32
635	731	1.298859	GGATTTCGGTGCTGCTCGTT	61.299	55.000	13.49	3.45	0.00	3.85
644	740	1.448985	ACGTGGATTGGATTTCGGTG	58.551	50.000	0.00	0.00	0.00	4.94
645	741	2.194201	AACGTGGATTGGATTTCGGT	57.806	45.000	0.00	0.00	0.00	4.69
668	764	1.980765	CTCTTATATCCCCAGCCAGCA	59.019	52.381	0.00	0.00	0.00	4.41
717	814	2.355009	GCTTGCTTTGTGCGTGGG	60.355	61.111	0.00	0.00	46.63	4.61
851	950	4.343239	GCTGAAAATCAAGGGGCAATATCT	59.657	41.667	0.00	0.00	0.00	1.98
925	1024	1.021920	GTGAAGAAGAAGGAGCGGGC	61.022	60.000	0.00	0.00	0.00	6.13
929	1028	3.007398	TGAGAAGGTGAAGAAGAAGGAGC	59.993	47.826	0.00	0.00	0.00	4.70
933	1032	5.467035	AGACTGAGAAGGTGAAGAAGAAG	57.533	43.478	0.00	0.00	0.00	2.85
937	1036	2.900546	GGGAGACTGAGAAGGTGAAGAA	59.099	50.000	0.00	0.00	0.00	2.52
979	1078	4.029809	GTCGTCTTGGGGTGGGGG	62.030	72.222	0.00	0.00	0.00	5.40
980	1079	2.748058	CTTGTCGTCTTGGGGTGGGG	62.748	65.000	0.00	0.00	0.00	4.96
981	1080	1.302511	CTTGTCGTCTTGGGGTGGG	60.303	63.158	0.00	0.00	0.00	4.61
982	1081	0.324943	ATCTTGTCGTCTTGGGGTGG	59.675	55.000	0.00	0.00	0.00	4.61
983	1082	1.270839	ACATCTTGTCGTCTTGGGGTG	60.271	52.381	0.00	0.00	0.00	4.61
984	1083	1.056660	ACATCTTGTCGTCTTGGGGT	58.943	50.000	0.00	0.00	0.00	4.95
995	1095	3.181489	GGTTCTCCGTCGATACATCTTGT	60.181	47.826	0.00	0.00	0.00	3.16
1007	1107	3.665190	AGAAAACAGATGGTTCTCCGTC	58.335	45.455	0.00	0.00	46.93	4.79
1015	1115	4.836825	ACGATGATGAGAAAACAGATGGT	58.163	39.130	0.00	0.00	0.00	3.55
1019	1119	4.382040	GGAGGACGATGATGAGAAAACAGA	60.382	45.833	0.00	0.00	0.00	3.41
1108	1214	5.251932	TCCAAAGGGAACAATATGTACCTGA	59.748	40.000	7.24	0.40	41.32	3.86
1173	1295	4.021456	TCATCATAATTACATCGACGGGCT	60.021	41.667	0.00	0.00	0.00	5.19
1225	1347	2.886913	TGAAGCCCATTCATTTGACCA	58.113	42.857	0.00	0.00	43.09	4.02
1247	1370	0.476771	GACACCTTTCCCCCTTGACA	59.523	55.000	0.00	0.00	0.00	3.58
1287	1410	2.188817	GTGGTATCCTCTGTCCCAAGT	58.811	52.381	0.00	0.00	0.00	3.16
1492	1617	7.218228	TGAAGCATGACAACTTATTTCACAT	57.782	32.000	0.00	0.00	0.00	3.21
1597	1723	1.447945	CATATCCACGCAACACACCA	58.552	50.000	0.00	0.00	0.00	4.17
1622	1748	2.035961	CAGCTAGCCGTTCCTTATGCTA	59.964	50.000	12.13	0.00	35.34	3.49
1810	1965	1.661112	GTTGCGCATCTGTTCTACTCC	59.339	52.381	12.75	0.00	0.00	3.85
1917	2073	7.715249	GGCTAATATTTATCTTGGTCAGTGTCA	59.285	37.037	0.00	0.00	0.00	3.58
1953	2109	8.999552	ATGGATTCCAATTGAGGCATTTAGCAA	62.000	37.037	9.98	0.00	40.73	3.91
1966	2122	6.620678	AGTTACAAACGATGGATTCCAATTG	58.379	36.000	9.98	14.06	34.84	2.32
2190	2728	6.500684	TGTGCACAGATTCTTTTATCTTCC	57.499	37.500	17.42	0.00	32.60	3.46
2239	2778	5.764131	TGAAAATAGCAACGGTCGATTTTT	58.236	33.333	0.00	0.00	31.59	1.94
2288	2827	9.442062	TCTCACTGATATGGTTAAGGGTAAATA	57.558	33.333	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.