AutoCloner

Multiple sequence alignment - TraesCS6B01G006700

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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	TraesCS6B01G006700	chr6B	100.000	2678	0	0	1	2678	4548699	4546022	0.000000e+00	4946
1	TraesCS6B01G006700	chr6B	92.520	2460	145	20	248	2678	4787235	4784786	0.000000e+00	3487
2	TraesCS6B01G006700	chr6B	91.304	115	9	1	684	797	5336522	5336408	3.570000e-34	156
3	TraesCS6B01G006700	chr6D	91.754	1807	115	19	880	2678	2080094	2081874	0.000000e+00	2481
4	TraesCS6B01G006700	chr6D	83.821	513	78	5	1	508	392580066	392580578	1.440000e-132	483
5	TraesCS6B01G006700	chr6D	90.090	111	8	3	684	792	46680846	46680955	1.000000e-29	141
6	TraesCS6B01G006700	chr5D	86.922	497	58	7	21	511	57825463	57824968	3.900000e-153	551
7	TraesCS6B01G006700	chr4A	86.160	513	64	7	1	509	571991378	571991887	5.040000e-152	547
8	TraesCS6B01G006700	chr3A	83.140	516	80	7	1	509	519747702	519747187	5.220000e-127	464
9	TraesCS6B01G006700	chr2D	83.107	515	79	8	1	508	194649193	194648680	1.880000e-126	462
10	TraesCS6B01G006700	chr1B	82.852	519	78	9	1	509	141720939	141721456	3.140000e-124	455
11	TraesCS6B01G006700	chr1B	90.000	110	9	2	684	792	684270225	684270117	1.000000e-29	141
12	TraesCS6B01G006700	chr7B	82.874	508	77	9	9	509	130477867	130477363	5.260000e-122	448
13	TraesCS6B01G006700	chr7D	82.432	518	75	11	1	509	222136557	222137067	3.170000e-119	438
14	TraesCS6B01G006700	chr7D	92.793	111	6	2	684	792	198028743	198028853	2.760000e-35	159
15	TraesCS6B01G006700	chr5A	91.597	119	8	2	684	800	1831733	1831615	2.130000e-36	163
16	TraesCS6B01G006700	chr4B	89.381	113	10	2	685	796	416621908	416622019	1.000000e-29	141
17	TraesCS6B01G006700	chr4B	89.091	110	11	1	684	792	63102725	63102834	4.650000e-28	135
18	TraesCS6B01G006700	chr1A	89.091	110	11	1	684	792	548518186	548518295	4.650000e-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	TraesCS6B01G006700	chr6B	4546022	4548699	2677	True	4946	4946	100.000	1	2678	1	chr6B.!!$R1	2677
1	TraesCS6B01G006700	chr6B	4784786	4787235	2449	True	3487	3487	92.520	248	2678	1	chr6B.!!$R2	2430
2	TraesCS6B01G006700	chr6D	2080094	2081874	1780	False	2481	2481	91.754	880	2678	1	chr6D.!!$F1	1798
3	TraesCS6B01G006700	chr6D	392580066	392580578	512	False	483	483	83.821	1	508	1	chr6D.!!$F3	507
4	TraesCS6B01G006700	chr4A	571991378	571991887	509	False	547	547	86.160	1	509	1	chr4A.!!$F1	508
5	TraesCS6B01G006700	chr3A	519747187	519747702	515	True	464	464	83.140	1	509	1	chr3A.!!$R1	508
6	TraesCS6B01G006700	chr2D	194648680	194649193	513	True	462	462	83.107	1	508	1	chr2D.!!$R1	507
7	TraesCS6B01G006700	chr1B	141720939	141721456	517	False	455	455	82.852	1	509	1	chr1B.!!$F1	508
8	TraesCS6B01G006700	chr7B	130477363	130477867	504	True	448	448	82.874	9	509	1	chr7B.!!$R1	500
9	TraesCS6B01G006700	chr7D	222136557	222137067	510	False	438	438	82.432	1	509	1	chr7D.!!$F2	508

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
446	461	0.100503	GGGCATCATTTTTAGCGCGT	59.899	50.0	8.43	0.0	0.0	6.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2348	2408	0.110486	ACGGGCTCAAGGTTGATGTT	59.89	50.0	0.0	0.0	36.46	2.71	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
60	65	0.319555	GCACAAGTACTCACTGGCGA	60.320	55.000	0.00	0.00	34.36	5.54
175	186	1.846124	GTGGAACAGGGTGAGGGGA	60.846	63.158	0.00	0.00	41.80	4.81
219	230	0.173255	CAAATTTGGCCGGAATCGCT	59.827	50.000	5.05	0.00	34.56	4.93
272	285	1.282653	TGTGGAAGGGGTGGTGAACA	61.283	55.000	0.00	0.00	0.00	3.18
288	301	0.604243	AACACGCGTGGGCTGAAATA	60.604	50.000	39.21	0.00	36.88	1.40
365	379	3.259930	CGTTTTCGCGGGTTGGAT	58.740	55.556	6.13	0.00	36.22	3.41
373	387	1.808531	CGCGGGTTGGATACGGGATA	61.809	60.000	0.00	0.00	42.18	2.59
432	447	2.124320	CGGGGTTTGATCGGGCAT	60.124	61.111	0.00	0.00	0.00	4.40
440	455	4.142049	GGGTTTGATCGGGCATCATTTTTA	60.142	41.667	0.00	0.00	41.42	1.52
446	461	0.100503	GGGCATCATTTTTAGCGCGT	59.899	50.000	8.43	0.00	0.00	6.01
513	534	4.280677	GGTCTGCTAGAGATGCTCTAATGT	59.719	45.833	5.75	0.00	41.74	2.71
523	544	4.469227	AGATGCTCTAATGTGGTCAGACTT	59.531	41.667	0.00	0.00	0.00	3.01
545	566	9.862371	GACTTGTTGATGACTCTTTCTATTCTA	57.138	33.333	0.00	0.00	0.00	2.10
572	593	9.621629	TCAAGTAAAAGTTCAGACAGGATTTAA	57.378	29.630	0.00	0.00	0.00	1.52
601	622	5.621193	AGTTGGTACAGAGTTTACTTGCAT	58.379	37.500	0.00	0.00	42.39	3.96
718	739	6.283161	ACTTTTACGACTTTGTGCTACTTC	57.717	37.500	0.00	0.00	0.00	3.01
720	741	2.503920	ACGACTTTGTGCTACTTCGT	57.496	45.000	0.00	0.00	35.00	3.85
721	742	2.124903	ACGACTTTGTGCTACTTCGTG	58.875	47.619	0.00	0.00	38.23	4.35
767	788	4.611310	CATCATTATTATGCAGAGGCCG	57.389	45.455	0.00	0.00	40.13	6.13
773	794	1.692173	TTATGCAGAGGCCGGGGTAC	61.692	60.000	2.18	0.00	40.13	3.34
872	897	6.327934	TCTAAACTATACAGCAACTCGTTCC	58.672	40.000	0.00	0.00	0.00	3.62
878	903	1.028905	CAGCAACTCGTTCCCCAAAA	58.971	50.000	0.00	0.00	0.00	2.44
933	976	1.390383	GCCTCCTAGTACCCCGTGTC	61.390	65.000	0.00	0.00	0.00	3.67
973	1016	2.512476	ACAGAAACCCTAACCACCAACT	59.488	45.455	0.00	0.00	0.00	3.16
1155	1198	3.222855	CTCCCGCTCTCGCTCCAT	61.223	66.667	0.00	0.00	0.00	3.41
1180	1223	3.687551	CGTCCTCTACCAGACCCAAGATA	60.688	52.174	0.00	0.00	0.00	1.98
1308	1351	2.630580	CCTCCTCCTATTCTGGCACTAC	59.369	54.545	0.00	0.00	0.00	2.73
1311	1354	2.223829	CCTCCTATTCTGGCACTACGTG	60.224	54.545	0.00	0.00	36.51	4.49
1417	1460	6.435591	GGATGATCACTACCTCATCTATGACA	59.564	42.308	0.00	0.00	44.62	3.58
1475	1524	2.225382	TACCCTCACCACGAGATTCA	57.775	50.000	0.00	0.00	45.45	2.57
1480	1529	3.914984	CACCACGAGATTCAGGTGT	57.085	52.632	0.00	0.00	44.95	4.16
1499	1548	4.310769	GTGTGTCATATCTCCAGGCATAC	58.689	47.826	0.00	0.00	0.00	2.39
1500	1549	4.039730	GTGTGTCATATCTCCAGGCATACT	59.960	45.833	0.00	0.00	0.00	2.12
1554	1603	0.331616	GGCCACCTTCACCCTACATT	59.668	55.000	0.00	0.00	0.00	2.71
1575	1624	6.660521	ACATTATGCATGTCTTCTCCTCAAAA	59.339	34.615	10.16	0.00	43.17	2.44
1663	1712	6.218746	GTCAAAATCAAACTGCCAAATCTCT	58.781	36.000	0.00	0.00	0.00	3.10
1785	1834	6.095720	GCTCATAGTAGGGACTATCATACACC	59.904	46.154	0.00	0.00	44.15	4.16
2089	2149	4.882671	AGATTTGCGGAATGACATGTAC	57.117	40.909	0.00	0.00	0.00	2.90
2167	2227	1.728068	ACGGTGTGTATTGCGCATTA	58.272	45.000	12.75	9.87	40.03	1.90
2203	2263	3.181466	GCACATTTGAGGTTTGGTTCCTT	60.181	43.478	0.00	0.00	35.20	3.36
2204	2264	4.038642	GCACATTTGAGGTTTGGTTCCTTA	59.961	41.667	0.00	0.00	35.20	2.69
2305	2365	2.739913	TCAAACCGACGAACAATGGATC	59.260	45.455	0.00	0.00	0.00	3.36
2319	2379	6.513806	ACAATGGATCGAAAAATCATGTGA	57.486	33.333	0.00	0.00	0.00	3.58
2331	2391	6.839124	AAAATCATGTGATCCACTAAAGCA	57.161	33.333	0.00	0.00	35.11	3.91
2348	2408	5.489792	AAAGCAGGATGAGTCAAAGACTA	57.510	39.130	0.00	0.00	43.53	2.59
2364	2424	3.944087	AGACTAACATCAACCTTGAGCC	58.056	45.455	0.00	0.00	41.08	4.70
2422	2482	4.384056	CTTATGATTGGAGCTCCGACAAT	58.616	43.478	25.63	19.68	39.43	2.71
2446	2506	6.112734	TGAAAATGCTATTGACACCGTAGAT	58.887	36.000	0.00	0.00	0.00	1.98
2463	2523	0.899717	GATTGGCCTGGAGGTTGCAA	60.900	55.000	3.32	0.00	37.57	4.08
2524	2584	6.081356	TGGATTTCACCCCTACAAAGAAATT	58.919	36.000	0.00	0.00	38.58	1.82
2542	2602	8.579682	AAGAAATTGTCTTGTTCAATAACAGC	57.420	30.769	0.00	0.00	45.29	4.40
2543	2603	7.715657	AGAAATTGTCTTGTTCAATAACAGCA	58.284	30.769	0.00	0.00	45.99	4.41
2554	2614	6.989759	TGTTCAATAACAGCAAGAGAACACTA	59.010	34.615	0.00	0.00	40.69	2.74
2566	2626	6.986817	GCAAGAGAACACTAGCCTATCATTTA	59.013	38.462	0.00	0.00	0.00	1.40
2601	2661	1.606885	CGGCATTTGGGCAAGATGGT	61.607	55.000	0.00	0.00	43.60	3.55
2609	2669	3.003394	TGGGCAAGATGGTAGTCAATG	57.997	47.619	0.00	0.00	0.00	2.82
2610	2670	2.301346	GGGCAAGATGGTAGTCAATGG	58.699	52.381	0.00	0.00	0.00	3.16
2616	2676	2.846206	AGATGGTAGTCAATGGCCTGAA	59.154	45.455	3.32	0.00	0.00	3.02
2622	2682	4.202461	GGTAGTCAATGGCCTGAATATGGA	60.202	45.833	3.32	0.00	29.48	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	3.364366	GCGCTATGCATAGTTGGTTCATC	60.364	47.826	29.62	12.39	45.45	2.92
35	40	3.457234	CAGTGAGTACTTGTGCTTGTGA	58.543	45.455	0.00	0.00	34.07	3.58
187	198	2.518949	CAAATTTGCGGACGGAATCAG	58.481	47.619	5.01	0.00	0.00	2.90
272	285	0.814010	GGATATTTCAGCCCACGCGT	60.814	55.000	5.58	5.58	41.18	6.01
432	447	1.816074	AAGGGACGCGCTAAAAATGA	58.184	45.000	5.73	0.00	0.00	2.57
440	455	2.616842	CCATTAAAATAAGGGACGCGCT	59.383	45.455	5.73	0.00	0.00	5.92
513	534	3.643320	AGAGTCATCAACAAGTCTGACCA	59.357	43.478	3.76	0.00	39.00	4.02
545	566	8.697507	AAATCCTGTCTGAACTTTTACTTGAT	57.302	30.769	0.00	0.00	0.00	2.57
574	595	8.537016	TGCAAGTAAACTCTGTACCAACTATAT	58.463	33.333	0.00	0.00	0.00	0.86
575	596	7.898918	TGCAAGTAAACTCTGTACCAACTATA	58.101	34.615	0.00	0.00	0.00	1.31
651	672	5.941948	AAAAAGTATTACAGCTCGCAAGT	57.058	34.783	0.00	0.00	39.48	3.16
676	697	2.158505	AGTATTACAGCTCGCTCCCCTA	60.159	50.000	0.00	0.00	0.00	3.53
688	709	7.793902	AGCACAAAGTCGTAAAAGTATTACAG	58.206	34.615	0.00	0.00	0.00	2.74
718	739	9.950680	ATGCAGTTATCTTATTAAAAATCCACG	57.049	29.630	0.00	0.00	0.00	4.94
720	741	9.748708	GCATGCAGTTATCTTATTAAAAATCCA	57.251	29.630	14.21	0.00	0.00	3.41
721	742	9.748708	TGCATGCAGTTATCTTATTAAAAATCC	57.251	29.630	18.46	0.00	0.00	3.01
755	776	2.138179	GTACCCCGGCCTCTGCATA	61.138	63.158	0.00	0.00	40.13	3.14
767	788	1.153025	GGAAATGGAGGCGTACCCC	60.153	63.158	0.00	0.00	36.11	4.95
860	885	1.029681	GTTTTGGGGAACGAGTTGCT	58.970	50.000	7.38	0.00	0.00	3.91
861	886	1.001706	GAGTTTTGGGGAACGAGTTGC	60.002	52.381	0.00	0.00	34.74	4.17
865	890	2.084546	GATGGAGTTTTGGGGAACGAG	58.915	52.381	0.00	0.00	34.74	4.18
872	897	2.158841	CGTAACGTGATGGAGTTTTGGG	59.841	50.000	0.00	0.00	0.00	4.12
878	903	1.403780	GCCTTCGTAACGTGATGGAGT	60.404	52.381	9.65	0.00	33.63	3.85
933	976	4.114073	CTGTCAAGCTAGCAATGAGAGAG	58.886	47.826	28.80	18.42	36.80	3.20
973	1016	1.471829	ATATCGATGGGCCTGCGACA	61.472	55.000	20.27	11.92	36.83	4.35
1030	1073	2.443952	ATGGCGGAGGATGTCGGA	60.444	61.111	0.00	0.00	0.00	4.55
1153	1196	0.103208	GTCTGGTAGAGGACGCCATG	59.897	60.000	0.00	0.00	0.00	3.66
1155	1198	1.681327	GGTCTGGTAGAGGACGCCA	60.681	63.158	0.00	0.00	33.70	5.69
1162	1205	3.288964	ACGTATCTTGGGTCTGGTAGAG	58.711	50.000	0.00	0.00	0.00	2.43
1180	1223	4.455877	GGAGAAGATTTTGGTGATGAACGT	59.544	41.667	0.00	0.00	0.00	3.99
1239	1282	1.300620	CTTGTCGTCAAGGCCACGA	60.301	57.895	12.38	12.38	45.02	4.35
1308	1351	3.428282	GTGGCGGGGTTTAGCACG	61.428	66.667	0.00	0.00	34.54	5.34
1358	1401	4.431131	CCATTGCCTCGCAGGGGT	62.431	66.667	4.65	0.00	40.61	4.95
1475	1524	1.765314	GCCTGGAGATATGACACACCT	59.235	52.381	0.00	0.00	0.00	4.00
1480	1529	5.219343	CAAGTATGCCTGGAGATATGACA	57.781	43.478	0.00	0.00	0.00	3.58
1499	1548	1.078759	GACTGATCCGTGACCGCAAG	61.079	60.000	0.00	0.00	0.00	4.01
1500	1549	1.080093	GACTGATCCGTGACCGCAA	60.080	57.895	0.00	0.00	0.00	4.85
1506	1555	1.668919	GCAGAAACGACTGATCCGTGA	60.669	52.381	11.57	0.00	40.44	4.35
1509	1558	1.428448	TTGCAGAAACGACTGATCCG	58.572	50.000	11.57	0.00	39.94	4.18
1554	1603	5.122239	CGTTTTTGAGGAGAAGACATGCATA	59.878	40.000	0.00	0.00	0.00	3.14
1575	1624	2.852075	TTCTCCCAGCACCCCGTT	60.852	61.111	0.00	0.00	0.00	4.44
1663	1712	5.352016	AGGCGACGTGTTATAAAAAGCATAA	59.648	36.000	0.00	0.00	0.00	1.90
1867	1923	4.686091	TGACACTCACGACTCAATTGAATC	59.314	41.667	9.88	8.30	0.00	2.52
1958	2014	4.045104	CAGTCTCTAAATAAGCGTGCGAT	58.955	43.478	0.00	0.00	0.00	4.58
1959	2015	3.119602	ACAGTCTCTAAATAAGCGTGCGA	60.120	43.478	0.00	0.00	0.00	5.10
1960	2016	3.179830	ACAGTCTCTAAATAAGCGTGCG	58.820	45.455	0.00	0.00	0.00	5.34
1961	2017	4.201724	CCAACAGTCTCTAAATAAGCGTGC	60.202	45.833	0.00	0.00	0.00	5.34
2055	2115	5.357257	TCCGCAAATCTATCCTGTAGAAAC	58.643	41.667	0.00	0.00	0.00	2.78
2089	2149	4.931002	CCATTTGCCAACTCAATAACTTGG	59.069	41.667	0.00	0.00	38.00	3.61
2105	2165	4.058124	GGTGTTCCTTCTTTTCCATTTGC	58.942	43.478	0.00	0.00	0.00	3.68
2203	2263	4.102367	TCCATCCGACCATGTGATTCATTA	59.898	41.667	0.00	0.00	34.09	1.90
2204	2264	3.117926	TCCATCCGACCATGTGATTCATT	60.118	43.478	0.00	0.00	34.09	2.57
2255	2315	4.688413	GCGAAAATCTCCTCTTATAGGCTG	59.312	45.833	0.00	0.00	46.10	4.85
2287	2347	1.067425	TCGATCCATTGTTCGTCGGTT	60.067	47.619	0.00	0.00	35.64	4.44
2305	2365	6.470235	GCTTTAGTGGATCACATGATTTTTCG	59.530	38.462	0.00	0.00	36.74	3.46
2319	2379	3.776969	TGACTCATCCTGCTTTAGTGGAT	59.223	43.478	0.00	0.00	40.85	3.41
2331	2391	6.611613	TGATGTTAGTCTTTGACTCATCCT	57.388	37.500	18.34	2.71	42.40	3.24
2348	2408	0.110486	ACGGGCTCAAGGTTGATGTT	59.890	50.000	0.00	0.00	36.46	2.71
2364	2424	2.159627	GCTTGGTTGTTGTCATCTACGG	59.840	50.000	0.00	0.00	0.00	4.02
2422	2482	5.483811	TCTACGGTGTCAATAGCATTTTCA	58.516	37.500	0.00	0.00	0.00	2.69
2446	2506	1.832167	GTTGCAACCTCCAGGCCAA	60.832	57.895	19.15	0.00	39.32	4.52
2486	2546	5.067805	GGTGAAATCCAAGACACTCAAAAGT	59.932	40.000	0.00	0.00	35.60	2.66
2524	2584	6.054941	TCTCTTGCTGTTATTGAACAAGACA	58.945	36.000	0.00	0.00	44.90	3.41
2542	2602	8.948631	TTAAATGATAGGCTAGTGTTCTCTTG	57.051	34.615	0.00	0.00	0.00	3.02
2543	2603	9.959721	TTTTAAATGATAGGCTAGTGTTCTCTT	57.040	29.630	0.00	0.00	0.00	2.85
2554	2614	7.179160	ACCTTTGAGCTTTTTAAATGATAGGCT	59.821	33.333	0.00	0.00	0.00	4.58
2566	2626	1.754226	TGCCGAACCTTTGAGCTTTTT	59.246	42.857	0.00	0.00	0.00	1.94
2601	2661	5.645056	TTCCATATTCAGGCCATTGACTA	57.355	39.130	5.01	0.00	0.00	2.59
2609	2669	4.473444	TCTTCCATTTCCATATTCAGGCC	58.527	43.478	0.00	0.00	0.00	5.19
2610	2670	5.136105	ACTCTTCCATTTCCATATTCAGGC	58.864	41.667	0.00	0.00	0.00	4.85
2616	2676	7.413446	TGGAAAAGACTCTTCCATTTCCATAT	58.587	34.615	14.77	0.00	45.88	1.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.