AutoCloner

Multiple sequence alignment - TraesCS5A01G006800

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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	TraesCS5A01G006800	chr5A	100.000	2807	0	0	1	2807	4019545	4016739	0.000000e+00	5184.0
1	TraesCS5A01G006800	chr5A	91.667	204	17	0	843	1046	4711283	4711080	1.650000e-72	283.0
2	TraesCS5A01G006800	chr5A	93.846	65	4	0	843	907	4711424	4711360	6.400000e-17	99.0
3	TraesCS5A01G006800	chr5A	96.429	56	2	0	852	907	4711556	4711501	2.980000e-15	93.5
4	TraesCS5A01G006800	chr5B	92.173	1597	88	21	843	2434	24419224	24417660	0.000000e+00	2222.0
5	TraesCS5A01G006800	chr5B	94.059	1397	71	4	843	2233	30865206	30866596	0.000000e+00	2109.0
6	TraesCS5A01G006800	chr5B	93.656	1324	78	2	840	2163	48301691	48303008	0.000000e+00	1975.0
7	TraesCS5A01G006800	chr5B	92.465	1367	80	5	843	2209	6676620	6675277	0.000000e+00	1932.0
8	TraesCS5A01G006800	chr5B	99.645	846	3	0	1	846	48315425	48316270	0.000000e+00	1546.0
9	TraesCS5A01G006800	chr5B	91.398	372	30	1	2435	2806	48303098	48303467	2.490000e-140	508.0
10	TraesCS5A01G006800	chr5B	88.690	336	32	2	2435	2764	30866800	30867135	3.370000e-109	405.0
11	TraesCS5A01G006800	chr5B	88.131	337	32	3	2435	2765	24417697	24417363	7.290000e-106	394.0
12	TraesCS5A01G006800	chr5B	95.673	208	7	2	2229	2434	30866630	30866837	1.610000e-87	333.0
13	TraesCS5A01G006800	chr5B	94.574	129	5	2	2308	2434	48303007	48303135	6.130000e-47	198.0
14	TraesCS5A01G006800	chr2A	99.645	846	3	0	1	846	602798827	602799672	0.000000e+00	1546.0
15	TraesCS5A01G006800	chr1A	99.413	852	5	0	1	852	369458195	369457344	0.000000e+00	1546.0
16	TraesCS5A01G006800	chr3B	99.645	845	3	0	1	845	481625851	481626695	0.000000e+00	1544.0
17	TraesCS5A01G006800	chr3B	99.529	849	3	1	1	849	547671104	547671951	0.000000e+00	1544.0
18	TraesCS5A01G006800	chr3B	99.527	846	4	0	1	846	389958445	389957600	0.000000e+00	1541.0
19	TraesCS5A01G006800	chr7B	99.645	844	3	0	1	844	46025326	46024483	0.000000e+00	1543.0
20	TraesCS5A01G006800	chr4B	99.527	846	4	0	1	846	5373713	5372868	0.000000e+00	1541.0
21	TraesCS5A01G006800	chr1B	99.527	846	4	0	1	846	38490277	38489432	0.000000e+00	1541.0

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	TraesCS5A01G006800	chr5A	4016739	4019545	2806	True	5184.000000	5184	100.000000	1	2807	1	chr5A.!!$R1	2806
1	TraesCS5A01G006800	chr5B	6675277	6676620	1343	True	1932.000000	1932	92.465000	843	2209	1	chr5B.!!$R1	1366
2	TraesCS5A01G006800	chr5B	48315425	48316270	845	False	1546.000000	1546	99.645000	1	846	1	chr5B.!!$F1	845
3	TraesCS5A01G006800	chr5B	24417363	24419224	1861	True	1308.000000	2222	90.152000	843	2765	2	chr5B.!!$R2	1922
4	TraesCS5A01G006800	chr5B	30865206	30867135	1929	False	949.000000	2109	92.807333	843	2764	3	chr5B.!!$F2	1921
5	TraesCS5A01G006800	chr5B	48301691	48303467	1776	False	893.666667	1975	93.209333	840	2806	3	chr5B.!!$F3	1966
6	TraesCS5A01G006800	chr2A	602798827	602799672	845	False	1546.000000	1546	99.645000	1	846	1	chr2A.!!$F1	845
7	TraesCS5A01G006800	chr1A	369457344	369458195	851	True	1546.000000	1546	99.413000	1	852	1	chr1A.!!$R1	851
8	TraesCS5A01G006800	chr3B	481625851	481626695	844	False	1544.000000	1544	99.645000	1	845	1	chr3B.!!$F1	844
9	TraesCS5A01G006800	chr3B	547671104	547671951	847	False	1544.000000	1544	99.529000	1	849	1	chr3B.!!$F2	848
10	TraesCS5A01G006800	chr3B	389957600	389958445	845	True	1541.000000	1541	99.527000	1	846	1	chr3B.!!$R1	845
11	TraesCS5A01G006800	chr7B	46024483	46025326	843	True	1543.000000	1543	99.645000	1	844	1	chr7B.!!$R1	843
12	TraesCS5A01G006800	chr4B	5372868	5373713	845	True	1541.000000	1541	99.527000	1	846	1	chr4B.!!$R1	845
13	TraesCS5A01G006800	chr1B	38489432	38490277	845	True	1541.000000	1541	99.527000	1	846	1	chr1B.!!$R1	845

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
904	905	1.134371	GTTCCTAGGTCCATCACTGCC	60.134	57.143	9.08	0.0	0.0	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2039	2040	0.031994	GAACACATGCCTGCGGTTTT	59.968	50.0	0.0	0.0	0.0	2.43	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
420	421	3.674997	AGGCGACATGTTCAACAGTTAT	58.325	40.909	0.00	0.00	0.00	1.89
715	716	5.427036	AGTATCGACAAAGAGCTAGCTAC	57.573	43.478	19.38	11.48	0.00	3.58
904	905	1.134371	GTTCCTAGGTCCATCACTGCC	60.134	57.143	9.08	0.00	0.00	4.85
915	916	1.278985	CATCACTGCCTCCACCTTGTA	59.721	52.381	0.00	0.00	0.00	2.41
968	969	1.557371	TCGCTGGTTATTCATCACCCA	59.443	47.619	0.00	0.00	31.24	4.51
986	987	2.880890	CCCATTGATCCCAAATCGACTC	59.119	50.000	0.00	0.00	35.67	3.36
1001	1002	1.831580	GACTCTTTTCCCTGCAGCAT	58.168	50.000	8.66	0.00	0.00	3.79
1070	1071	5.837979	TCAAAGGTTCAATCTTTTCCATCCA	59.162	36.000	0.00	0.00	32.72	3.41
1095	1096	1.433534	CTCCGAAACAAGACCAGCTC	58.566	55.000	0.00	0.00	0.00	4.09
1173	1174	0.324943	ACGACAAGGTCAGGAATGGG	59.675	55.000	0.00	0.00	32.09	4.00
1254	1255	0.798776	CACACGGTTTGAGCCATCTC	59.201	55.000	0.00	0.00	39.78	2.75
1269	1270	2.480244	CCATCTCTTCAATGCGTCTCGA	60.480	50.000	0.00	0.00	0.00	4.04
1374	1375	4.575885	TGGTTAATGCTGTCAGGAAGTAC	58.424	43.478	0.00	0.00	0.00	2.73
1405	1406	2.026822	ACAGTAGCTGGGGTTGATTCAG	60.027	50.000	0.00	0.00	35.51	3.02
1489	1490	4.715523	GCGCCCAAGCACACCCTA	62.716	66.667	0.00	0.00	39.83	3.53
1509	1510	1.988107	ACCCTTGAGATCTCTGCCAAA	59.012	47.619	22.95	8.12	0.00	3.28
1763	1764	2.490217	CTCGATCTTCGTGGCGGT	59.510	61.111	0.00	0.00	41.35	5.68
1767	1768	1.080093	GATCTTCGTGGCGGTGTCA	60.080	57.895	0.00	0.00	0.00	3.58
1830	1831	0.602638	AAGCTGCAAATCGTCGACCA	60.603	50.000	10.58	0.00	0.00	4.02
2003	2004	8.511604	AGTAATATGTAGCATCCATAATTGCC	57.488	34.615	0.00	0.00	39.72	4.52
2024	2025	4.181578	CCAATGGTAAGTGTAAGTCTCGG	58.818	47.826	0.00	0.00	0.00	4.63
2039	2040	4.586884	AGTCTCGGAAGTACAGTATGACA	58.413	43.478	0.00	0.00	39.69	3.58
2077	2078	7.330262	TGTGTTCTTCAGATATGCTTATGTGA	58.670	34.615	13.50	13.50	36.59	3.58
2082	2083	8.969260	TCTTCAGATATGCTTATGTGATGTTT	57.031	30.769	21.33	0.00	37.78	2.83
2189	2192	1.068954	GGGCTGTGCTTCTTTTTCTCG	60.069	52.381	0.00	0.00	0.00	4.04
2297	2343	3.370840	TGGGTTCAGAATCAGGATTGG	57.629	47.619	0.00	0.00	0.00	3.16
2336	2382	6.611642	TCCTACCTGATTGCTATTAGAGTGTT	59.388	38.462	1.51	0.00	0.00	3.32
2392	2438	1.153086	CATCTAGTGGGGGCTGTGC	60.153	63.158	0.00	0.00	0.00	4.57
2411	2457	3.316308	GTGCTGTTTTCTGAATGTGAGGT	59.684	43.478	0.00	0.00	0.00	3.85
2412	2458	3.953612	TGCTGTTTTCTGAATGTGAGGTT	59.046	39.130	0.00	0.00	0.00	3.50
2413	2459	5.008613	GTGCTGTTTTCTGAATGTGAGGTTA	59.991	40.000	0.00	0.00	0.00	2.85
2414	2460	5.239306	TGCTGTTTTCTGAATGTGAGGTTAG	59.761	40.000	0.00	0.00	0.00	2.34
2415	2461	5.689383	TGTTTTCTGAATGTGAGGTTAGC	57.311	39.130	0.00	0.00	0.00	3.09
2416	2462	4.518970	TGTTTTCTGAATGTGAGGTTAGCC	59.481	41.667	0.00	0.00	0.00	3.93
2417	2463	4.365514	TTTCTGAATGTGAGGTTAGCCA	57.634	40.909	0.00	0.00	37.19	4.75
2418	2464	4.365514	TTCTGAATGTGAGGTTAGCCAA	57.634	40.909	0.00	0.00	37.19	4.52
2419	2465	3.942829	TCTGAATGTGAGGTTAGCCAAG	58.057	45.455	0.00	0.00	37.19	3.61
2420	2466	3.582647	TCTGAATGTGAGGTTAGCCAAGA	59.417	43.478	0.00	0.00	37.19	3.02
2421	2467	3.937706	CTGAATGTGAGGTTAGCCAAGAG	59.062	47.826	0.00	0.00	37.19	2.85
2422	2468	3.327757	TGAATGTGAGGTTAGCCAAGAGT	59.672	43.478	0.00	0.00	37.19	3.24
2423	2469	4.202461	TGAATGTGAGGTTAGCCAAGAGTT	60.202	41.667	0.00	0.00	37.19	3.01
2424	2470	3.857157	TGTGAGGTTAGCCAAGAGTTT	57.143	42.857	0.00	0.00	37.19	2.66
2425	2471	3.476552	TGTGAGGTTAGCCAAGAGTTTG	58.523	45.455	0.00	0.00	37.19	2.93
2438	2484	4.697514	CAAGAGTTTGGTTCAGAGTCTGA	58.302	43.478	19.10	19.10	38.87	3.27
2439	2485	5.118990	CAAGAGTTTGGTTCAGAGTCTGAA	58.881	41.667	27.96	27.96	46.50	3.02
2487	2533	5.261661	GTTCAGAGACATGATCGAAAATGC	58.738	41.667	0.00	4.55	0.00	3.56
2488	2534	3.553105	TCAGAGACATGATCGAAAATGCG	59.447	43.478	0.00	0.00	0.00	4.73
2502	2548	1.971505	AATGCGGGTAGCTGCTAGCA	61.972	55.000	32.27	26.12	45.56	3.49
2520	2566	4.795970	AGCACAGTTCGTAGAACTTTTG	57.204	40.909	12.19	12.75	45.90	2.44
2539	2585	2.468831	TGATTCTTGTGCCGTTTTTGC	58.531	42.857	0.00	0.00	0.00	3.68
2553	2599	5.605327	CCGTTTTTGCTATATTATCCGTCG	58.395	41.667	0.00	0.00	0.00	5.12
2565	2611	0.881118	ATCCGTCGTGCAGCAATTTT	59.119	45.000	0.00	0.00	0.00	1.82
2622	2672	1.201998	CGCACTGCTATGTTGCTTCAG	60.202	52.381	0.00	0.00	0.00	3.02
2705	2755	7.237255	AGGTGTACAGGTCCTATATACCTTAC	58.763	42.308	17.65	5.80	45.26	2.34
2766	2818	7.608153	TGTAACTCCTTTCGTGATCTCATTTA	58.392	34.615	0.00	0.00	0.00	1.40
2767	2819	7.759886	TGTAACTCCTTTCGTGATCTCATTTAG	59.240	37.037	0.00	0.00	0.00	1.85
2784	2836	8.201464	TCTCATTTAGTGTCTCACTGTTTTGTA	58.799	33.333	11.92	0.00	45.01	2.41
2785	2837	8.138365	TCATTTAGTGTCTCACTGTTTTGTAC	57.862	34.615	11.92	0.00	45.01	2.90
2800	2852	4.764679	TTTGTACATGCATGGTTGAGAC	57.235	40.909	29.41	16.54	0.00	3.36
2806	2858	1.511850	TGCATGGTTGAGACGTTCAG	58.488	50.000	0.00	0.00	37.07	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
420	421	1.955495	ATACGCATCTCCGCCACACA	61.955	55.000	0.00	0.00	0.00	3.72
904	905	1.004394	GGGGGAAAGTACAAGGTGGAG	59.996	57.143	0.00	0.00	0.00	3.86
915	916	0.710588	GGAGGGAATTGGGGGAAAGT	59.289	55.000	0.00	0.00	0.00	2.66
968	969	5.358160	GGAAAAGAGTCGATTTGGGATCAAT	59.642	40.000	0.00	0.00	32.28	2.57
986	987	1.136305	CCATCATGCTGCAGGGAAAAG	59.864	52.381	17.12	6.14	0.00	2.27
1001	1002	1.541310	AACGTCCTCTTCCGCCATCA	61.541	55.000	0.00	0.00	0.00	3.07
1070	1071	1.947456	GGTCTTGTTTCGGAGCAAACT	59.053	47.619	0.00	0.00	37.20	2.66
1095	1096	3.077359	AGCCAGGATTTTGAGTTCTTCG	58.923	45.455	0.00	0.00	0.00	3.79
1173	1174	3.507622	AGGCAAAACCAGTAGAAGAATGC	59.492	43.478	0.00	0.00	43.14	3.56
1254	1255	1.714794	AAGGTCGAGACGCATTGAAG	58.285	50.000	0.00	0.00	0.00	3.02
1269	1270	2.032620	AGTGTCTCTCGTGTCAAAGGT	58.967	47.619	0.00	0.00	0.00	3.50
1374	1375	1.669115	AGCTACTGTTGCAGTGCCG	60.669	57.895	13.72	0.85	45.01	5.69
1405	1406	6.428159	ACACTCAGAACAATTGTATCTTCACC	59.572	38.462	12.39	0.00	0.00	4.02
1489	1490	1.661463	TTGGCAGAGATCTCAAGGGT	58.339	50.000	24.39	0.16	0.00	4.34
1509	1510	5.300286	GCACTGCCTATGATTTATTGGAGTT	59.700	40.000	0.00	0.00	34.04	3.01
1686	1687	0.657368	CGCCGTTTGAGTTGAACAGC	60.657	55.000	0.00	0.00	0.00	4.40
1763	1764	1.409101	CCCATCCATGCAGATGTGACA	60.409	52.381	13.23	0.00	41.79	3.58
1767	1768	0.184451	GGACCCATCCATGCAGATGT	59.816	55.000	13.23	0.00	45.47	3.06
1982	1983	7.147794	CCATTGGCAATTATGGATGCTACATAT	60.148	37.037	10.65	0.00	43.25	1.78
2003	2004	5.068234	TCCGAGACTTACACTTACCATTG	57.932	43.478	0.00	0.00	0.00	2.82
2024	2025	4.449743	TGCGGTTTTGTCATACTGTACTTC	59.550	41.667	0.00	0.00	0.00	3.01
2039	2040	0.031994	GAACACATGCCTGCGGTTTT	59.968	50.000	0.00	0.00	0.00	2.43
2077	2078	5.638133	CATGGATGAGGGAGGAATAAACAT	58.362	41.667	0.00	0.00	0.00	2.71
2082	2083	1.625315	CGCATGGATGAGGGAGGAATA	59.375	52.381	0.00	0.00	0.00	1.75
2088	2089	1.281867	AGAAAACGCATGGATGAGGGA	59.718	47.619	0.00	0.00	31.50	4.20
2189	2192	6.279513	ACTAATATACAGCTGAGGCATCTC	57.720	41.667	23.35	0.00	41.70	2.75
2297	2343	1.095807	GTAGGAGCGGCCAACATTCC	61.096	60.000	2.24	1.43	40.02	3.01
2336	2382	6.129179	AGACCAAACCAGAAGAAGAATGAAA	58.871	36.000	0.00	0.00	0.00	2.69
2392	2438	5.335191	GGCTAACCTCACATTCAGAAAACAG	60.335	44.000	0.00	0.00	0.00	3.16
2411	2457	9.990885	CAGACTCTGAACCAAACTCTTGGCTAA	62.991	44.444	0.00	0.00	44.07	3.09
2412	2458	8.633522	CAGACTCTGAACCAAACTCTTGGCTA	62.634	46.154	0.00	0.00	44.07	3.93
2413	2459	7.938231	CAGACTCTGAACCAAACTCTTGGCT	62.938	48.000	0.00	0.00	44.07	4.75
2414	2460	5.803738	CAGACTCTGAACCAAACTCTTGGC	61.804	50.000	0.00	0.00	44.07	4.52
2415	2461	3.812053	CAGACTCTGAACCAAACTCTTGG	59.188	47.826	0.00	2.31	44.94	3.61
2416	2462	4.697514	TCAGACTCTGAACCAAACTCTTG	58.302	43.478	6.26	0.00	37.57	3.02
2417	2463	5.359194	TTCAGACTCTGAACCAAACTCTT	57.641	39.130	16.22	0.00	44.27	2.85
2428	2474	4.081972	GCTAACCTCACATTCAGACTCTGA	60.082	45.833	4.50	4.50	38.87	3.27
2429	2475	4.180057	GCTAACCTCACATTCAGACTCTG	58.820	47.826	0.00	0.00	0.00	3.35
2430	2476	3.196685	GGCTAACCTCACATTCAGACTCT	59.803	47.826	0.00	0.00	0.00	3.24
2431	2477	3.055819	TGGCTAACCTCACATTCAGACTC	60.056	47.826	0.00	0.00	36.63	3.36
2432	2478	2.906389	TGGCTAACCTCACATTCAGACT	59.094	45.455	0.00	0.00	36.63	3.24
2433	2479	3.334583	TGGCTAACCTCACATTCAGAC	57.665	47.619	0.00	0.00	36.63	3.51
2434	2480	3.582647	TCTTGGCTAACCTCACATTCAGA	59.417	43.478	0.00	0.00	36.63	3.27
2435	2481	3.937706	CTCTTGGCTAACCTCACATTCAG	59.062	47.826	0.00	0.00	36.63	3.02
2436	2482	3.327757	ACTCTTGGCTAACCTCACATTCA	59.672	43.478	0.00	0.00	36.63	2.57
2437	2483	3.686726	CACTCTTGGCTAACCTCACATTC	59.313	47.826	0.00	0.00	36.63	2.67
2438	2484	3.073062	ACACTCTTGGCTAACCTCACATT	59.927	43.478	0.00	0.00	36.63	2.71
2439	2485	2.639839	ACACTCTTGGCTAACCTCACAT	59.360	45.455	0.00	0.00	36.63	3.21
2440	2486	2.047061	ACACTCTTGGCTAACCTCACA	58.953	47.619	0.00	0.00	36.63	3.58
2441	2487	2.841442	ACACTCTTGGCTAACCTCAC	57.159	50.000	0.00	0.00	36.63	3.51
2442	2488	3.476552	CAAACACTCTTGGCTAACCTCA	58.523	45.455	0.00	0.00	36.63	3.86
2443	2489	2.814336	CCAAACACTCTTGGCTAACCTC	59.186	50.000	0.00	0.00	39.55	3.85
2444	2490	2.863809	CCAAACACTCTTGGCTAACCT	58.136	47.619	0.00	0.00	39.55	3.50
2487	2533	1.227089	CTGTGCTAGCAGCTACCCG	60.227	63.158	20.03	0.00	42.97	5.28
2488	2534	0.250513	AACTGTGCTAGCAGCTACCC	59.749	55.000	20.03	5.66	42.97	3.69
2502	2548	7.280205	ACAAGAATCAAAAGTTCTACGAACTGT	59.720	33.333	9.74	2.01	34.97	3.55
2520	2566	2.742774	AGCAAAAACGGCACAAGAATC	58.257	42.857	0.00	0.00	0.00	2.52
2539	2585	3.833442	TGCTGCACGACGGATAATATAG	58.167	45.455	0.00	0.00	0.00	1.31
2553	2599	4.687018	TGATGATCACAAAAATTGCTGCAC	59.313	37.500	0.00	0.00	0.00	4.57
2565	2611	5.422145	ACGACAGATGAATGATGATCACAA	58.578	37.500	0.00	0.00	0.00	3.33
2622	2672	0.607489	ACTGCAGTGAAGACCATGCC	60.607	55.000	20.97	0.00	37.89	4.40
2680	2730	5.944809	AGGTATATAGGACCTGTACACCT	57.055	43.478	19.71	19.71	45.90	4.00
2705	2755	6.201044	CACCTACGCTGAAATTTATAGACAGG	59.799	42.308	6.20	9.31	0.00	4.00
2756	2808	7.897575	AAACAGTGAGACACTAAATGAGATC	57.102	36.000	0.00	0.00	43.43	2.75
2758	2810	7.047891	ACAAAACAGTGAGACACTAAATGAGA	58.952	34.615	0.00	0.00	43.43	3.27
2766	2818	4.273480	GCATGTACAAAACAGTGAGACACT	59.727	41.667	0.00	0.00	46.51	3.55
2767	2819	4.035091	TGCATGTACAAAACAGTGAGACAC	59.965	41.667	0.00	0.00	42.70	3.67
2784	2836	1.806542	GAACGTCTCAACCATGCATGT	59.193	47.619	24.58	10.59	0.00	3.21
2785	2837	1.805943	TGAACGTCTCAACCATGCATG	59.194	47.619	20.19	20.19	0.00	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.