AutoCloner

Multiple sequence alignment - TraesCS3A01G321500

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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	TraesCS3A01G321500	chr3A	100.000	3378	0	0	1	3378	565041086	565044463	0.000000e+00	6239.0
1	TraesCS3A01G321500	chr3A	84.058	138	12	6	81	209	128537246	128537382	1.270000e-24	124.0
2	TraesCS3A01G321500	chr3D	94.020	1020	20	13	759	1774	424002825	424001843	0.000000e+00	1507.0
3	TraesCS3A01G321500	chr3D	94.872	741	37	1	1	740	424004020	424003280	0.000000e+00	1157.0
4	TraesCS3A01G321500	chr3D	93.703	667	17	5	2332	2976	424001001	424000338	0.000000e+00	976.0
5	TraesCS3A01G321500	chr3D	97.933	387	8	0	1734	2120	424001843	424001457	0.000000e+00	671.0
6	TraesCS3A01G321500	chr3D	93.902	410	19	2	2969	3378	423999518	423999115	6.190000e-172	614.0
7	TraesCS3A01G321500	chr3D	97.289	332	7	1	2162	2491	424001339	424001008	2.280000e-156	562.0
8	TraesCS3A01G321500	chr3D	100.000	39	0	0	2121	2159	424001425	424001387	4.680000e-09	73.1
9	TraesCS3A01G321500	chr4A	93.977	880	23	12	898	1774	310239563	310240415	0.000000e+00	1304.0
10	TraesCS3A01G321500	chr4A	96.345	383	12	2	1739	2120	310240420	310240801	2.210000e-176	628.0
11	TraesCS3A01G321500	chr4A	97.568	329	7	1	2162	2489	310240919	310241247	2.280000e-156	562.0
12	TraesCS3A01G321500	chr3B	95.326	813	14	10	964	1774	552475664	552476454	0.000000e+00	1269.0
13	TraesCS3A01G321500	chr3B	96.180	445	17	0	1	445	552238503	552238947	0.000000e+00	728.0
14	TraesCS3A01G321500	chr3B	94.379	427	21	3	1734	2159	552476454	552476878	0.000000e+00	652.0
15	TraesCS3A01G321500	chr3B	96.144	389	15	0	2162	2550	552476926	552477314	1.320000e-178	636.0
16	TraesCS3A01G321500	chr3B	92.233	412	31	1	481	891	552238946	552239357	1.750000e-162	582.0
17	TraesCS3A01G321500	chr3B	91.624	394	27	2	2985	3378	552494360	552494747	1.070000e-149	540.0
18	TraesCS3A01G321500	chr3B	93.215	339	19	1	2577	2911	552491879	552492217	2.340000e-136	496.0
19	TraesCS3A01G321500	chr3B	94.521	73	4	0	2904	2976	552493856	552493928	2.750000e-21	113.0
20	TraesCS3A01G321500	chr4D	92.947	879	23	8	898	1774	183382876	183383717	0.000000e+00	1243.0
21	TraesCS3A01G321500	chr4D	98.172	383	6	1	1734	2116	183383717	183384098	0.000000e+00	667.0
22	TraesCS3A01G321500	chr4D	96.815	314	8	2	2178	2489	183384086	183384399	1.070000e-144	523.0
23	TraesCS3A01G321500	chr4D	91.089	202	16	2	3178	3378	143440419	143440619	4.290000e-69	272.0
24	TraesCS3A01G321500	chr4D	79.056	339	61	8	199	531	20896950	20896616	1.220000e-54	224.0
25	TraesCS3A01G321500	chr4D	85.246	183	26	1	558	740	197975623	197975442	1.600000e-43	187.0
26	TraesCS3A01G321500	chr4B	96.318	679	20	4	1097	1774	200657941	200657267	0.000000e+00	1110.0
27	TraesCS3A01G321500	chr4B	96.641	387	11	1	1734	2120	200657267	200656883	2.840000e-180	641.0
28	TraesCS3A01G321500	chr4B	95.137	329	15	1	2162	2489	200656765	200656437	5.000000e-143	518.0
29	TraesCS3A01G321500	chr4B	86.339	183	24	1	558	740	59479700	59479881	7.390000e-47	198.0
30	TraesCS3A01G321500	chr4B	100.000	43	0	0	1018	1060	200657993	200657951	2.790000e-11	80.5
31	TraesCS3A01G321500	chr4B	100.000	40	0	0	2120	2159	200656852	200656813	1.300000e-09	75.0
32	TraesCS3A01G321500	chr5D	82.892	567	77	13	1	554	222779965	222780524	3.030000e-135	492.0
33	TraesCS3A01G321500	chr5D	78.535	587	81	20	1	548	237624481	237625061	8.970000e-91	344.0
34	TraesCS3A01G321500	chr5D	97.143	35	1	0	2889	2923	205948956	205948990	3.640000e-05	60.2
35	TraesCS3A01G321500	chr1B	79.108	493	82	14	3	481	339721552	339721067	1.510000e-83	320.0
36	TraesCS3A01G321500	chr1B	85.792	183	25	1	558	740	341348631	341348812	3.440000e-45	193.0
37	TraesCS3A01G321500	chr5B	83.099	355	54	6	199	548	268078369	268078722	5.440000e-83	318.0
38	TraesCS3A01G321500	chr5B	91.542	201	17	0	3178	3378	438881208	438881008	9.230000e-71	278.0
39	TraesCS3A01G321500	chr6D	91.542	201	17	0	3178	3378	260017423	260017223	9.230000e-71	278.0
40	TraesCS3A01G321500	chr6D	91.045	201	18	0	3178	3378	154094308	154094508	4.290000e-69	272.0
41	TraesCS3A01G321500	chr6D	91.045	201	18	0	3178	3378	315778139	315778339	4.290000e-69	272.0
42	TraesCS3A01G321500	chr2D	91.542	201	17	0	3178	3378	162861196	162860996	9.230000e-71	278.0
43	TraesCS3A01G321500	chr2D	78.286	350	61	7	199	545	352033912	352034249	9.500000e-51	211.0
44	TraesCS3A01G321500	chr2D	95.238	42	2	0	2889	2930	104253616	104253657	2.180000e-07	67.6
45	TraesCS3A01G321500	chr1D	91.045	201	18	0	3178	3378	80529485	80529285	4.290000e-69	272.0
46	TraesCS3A01G321500	chr1D	85.246	183	26	1	558	740	436896211	436896030	1.600000e-43	187.0
47	TraesCS3A01G321500	chr1D	84.783	138	11	6	81	209	310133516	310133380	2.740000e-26	130.0
48	TraesCS3A01G321500	chr7A	85.792	183	25	1	558	740	604476924	604477105	3.440000e-45	193.0
49	TraesCS3A01G321500	chr6B	85.792	183	25	1	558	740	686072219	686072038	3.440000e-45	193.0
50	TraesCS3A01G321500	chr5A	85.792	183	25	1	558	740	79663289	79663470	3.440000e-45	193.0

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	TraesCS3A01G321500	chr3A	565041086	565044463	3377	False	6239.000000	6239	100.000000	1	3378	1	chr3A.!!$F2	3377
1	TraesCS3A01G321500	chr3D	423999115	424004020	4905	True	794.300000	1507	95.959857	1	3378	7	chr3D.!!$R1	3377
2	TraesCS3A01G321500	chr4A	310239563	310241247	1684	False	831.333333	1304	95.963333	898	2489	3	chr4A.!!$F1	1591
3	TraesCS3A01G321500	chr3B	552475664	552477314	1650	False	852.333333	1269	95.283000	964	2550	3	chr3B.!!$F2	1586
4	TraesCS3A01G321500	chr3B	552238503	552239357	854	False	655.000000	728	94.206500	1	891	2	chr3B.!!$F1	890
5	TraesCS3A01G321500	chr3B	552491879	552494747	2868	False	383.000000	540	93.120000	2577	3378	3	chr3B.!!$F3	801
6	TraesCS3A01G321500	chr4D	183382876	183384399	1523	False	811.000000	1243	95.978000	898	2489	3	chr4D.!!$F2	1591
7	TraesCS3A01G321500	chr4B	200656437	200657993	1556	True	484.900000	1110	97.619200	1018	2489	5	chr4B.!!$R1	1471
8	TraesCS3A01G321500	chr5D	222779965	222780524	559	False	492.000000	492	82.892000	1	554	1	chr5D.!!$F2	553
9	TraesCS3A01G321500	chr5D	237624481	237625061	580	False	344.000000	344	78.535000	1	548	1	chr5D.!!$F3	547

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
932	1416	0.03918	CCCTAACAAACCCCTCACCC	59.961	60.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2895	3849	1.672356	CACTGGTGCTTTCCCCGAG	60.672	63.158	0.0	0.0	0.0	4.63	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
264	302	7.502226	TCACCAACATACAATCTTCTTTCTGTT	59.498	33.333	0.00	0.00	0.00	3.16
334	374	2.710096	TTTTTCTCAGGCTATCCCCG	57.290	50.000	0.00	0.00	0.00	5.73
335	375	1.874129	TTTTCTCAGGCTATCCCCGA	58.126	50.000	0.00	0.00	0.00	5.14
519	560	2.629336	TGTGTACAACATGCACCTGA	57.371	45.000	0.00	0.00	42.88	3.86
571	612	5.816258	TGTGTGTTAAAAGTGATGTCGGTTA	59.184	36.000	0.00	0.00	0.00	2.85
576	617	8.497554	GTGTTAAAAGTGATGTCGGTTATGTAA	58.502	33.333	0.00	0.00	0.00	2.41
614	655	3.487376	CGTTTATTTGCACTGATGGCGAT	60.487	43.478	0.00	0.00	0.00	4.58
620	661	1.067706	TGCACTGATGGCGATTTTTGG	60.068	47.619	0.00	0.00	0.00	3.28
622	663	2.163412	GCACTGATGGCGATTTTTGGTA	59.837	45.455	0.00	0.00	0.00	3.25
651	692	7.903145	AGTGTATGTAATCTGTTGTCTGGTTA	58.097	34.615	0.00	0.00	0.00	2.85
680	721	0.322322	ATCACGGGTGGCGAACTTTA	59.678	50.000	0.00	0.00	0.00	1.85
690	731	2.361789	GGCGAACTTTAATGCCCAGTA	58.638	47.619	0.00	0.00	41.70	2.74
691	732	2.750712	GGCGAACTTTAATGCCCAGTAA	59.249	45.455	0.00	0.00	41.70	2.24
694	735	5.066764	GGCGAACTTTAATGCCCAGTAAATA	59.933	40.000	1.98	0.00	41.70	1.40
929	1413	3.691698	AAAACCCTAACAAACCCCTCA	57.308	42.857	0.00	0.00	0.00	3.86
930	1414	2.670019	AACCCTAACAAACCCCTCAC	57.330	50.000	0.00	0.00	0.00	3.51
931	1415	0.775542	ACCCTAACAAACCCCTCACC	59.224	55.000	0.00	0.00	0.00	4.02
932	1416	0.039180	CCCTAACAAACCCCTCACCC	59.961	60.000	0.00	0.00	0.00	4.61
933	1417	0.039180	CCTAACAAACCCCTCACCCC	59.961	60.000	0.00	0.00	0.00	4.95
934	1418	1.073098	CTAACAAACCCCTCACCCCT	58.927	55.000	0.00	0.00	0.00	4.79
935	1419	1.004394	CTAACAAACCCCTCACCCCTC	59.996	57.143	0.00	0.00	0.00	4.30
959	1443	2.356553	CGTCGCCGAAACCCTTCA	60.357	61.111	0.00	0.00	35.63	3.02
1283	1779	2.081212	GCAGAGGTGTCGACGTTCG	61.081	63.158	11.62	6.25	42.10	3.95
1330	1826	0.978385	CGAAGCTGACGAACGAGAAG	59.022	55.000	7.65	0.00	0.00	2.85
1422	1918	2.354821	GCCCCATCAACGAATCAGTAAC	59.645	50.000	0.00	0.00	0.00	2.50
1428	1924	4.177165	TCAACGAATCAGTAACCGCTTA	57.823	40.909	0.00	0.00	0.00	3.09
1442	1938	1.202580	CCGCTTACTTCCCCTCATCAG	60.203	57.143	0.00	0.00	0.00	2.90
1640	2137	1.065031	GCAATGCCGTAGCGTGTTTG	61.065	55.000	0.00	0.00	44.31	2.93
1736	2234	5.643777	TGCTCTAAATTTTAGGTCTGCTCAC	59.356	40.000	14.60	0.00	0.00	3.51
1878	2415	2.659016	CTCTCACGCTTCCTGCCA	59.341	61.111	0.00	0.00	38.78	4.92
2159	2878	4.202090	CGAAGGGAGTACCATTAGTGTACC	60.202	50.000	0.00	0.00	40.42	3.34
2160	2879	4.341863	AGGGAGTACCATTAGTGTACCA	57.658	45.455	0.00	0.00	43.89	3.25
2175	2939	4.021368	AGTGTACCACTAGTTACAGCTTGG	60.021	45.833	7.52	0.00	43.46	3.61
2398	3164	8.773404	TCTAGGATGTAGTTTTAAGTTTGCTC	57.227	34.615	0.00	0.00	0.00	4.26
2542	3474	7.173218	AGTGTTGAGTTAATGTTGGTGTATCAG	59.827	37.037	0.00	0.00	0.00	2.90
2554	3486	8.771920	TGTTGGTGTATCAGAATTACTTGTAG	57.228	34.615	0.00	0.00	0.00	2.74
2713	3662	2.605823	GGAGCCGTCGTCATCATCTAAG	60.606	54.545	0.00	0.00	0.00	2.18
2721	3670	2.735444	CGTCATCATCTAAGTGTGGCGT	60.735	50.000	0.00	0.00	33.66	5.68
2724	3673	2.078849	TCATCTAAGTGTGGCGTGTG	57.921	50.000	0.00	0.00	0.00	3.82
2786	3735	3.118075	TCTGTGATCCACCACAAAGACAA	60.118	43.478	0.00	0.00	45.27	3.18
2795	3744	4.142182	CCACCACAAAGACAACAACAATCT	60.142	41.667	0.00	0.00	0.00	2.40
2885	3839	0.465705	ATGGAGCCGTCGTCATCATT	59.534	50.000	0.00	0.00	0.00	2.57
2895	3849	5.229260	GCCGTCGTCATCATTTAATTTTTCC	59.771	40.000	0.00	0.00	0.00	3.13
2952	5552	1.417517	ACTGCCATCTTCAGTGTGTGA	59.582	47.619	0.00	0.00	42.63	3.58
3041	6767	8.607459	GCCTGATATCGACAAATATATTTCCAG	58.393	37.037	7.76	0.60	0.00	3.86
3042	6768	9.658799	CCTGATATCGACAAATATATTTCCAGT	57.341	33.333	7.76	3.79	0.00	4.00
3203	6929	5.645067	CACTTTGTCAGCATCTTTAGGATCA	59.355	40.000	0.00	0.00	31.27	2.92
3210	6936	7.177216	TGTCAGCATCTTTAGGATCAACAAAAT	59.823	33.333	0.00	0.00	31.27	1.82
3270	6996	7.910441	ACTCCATTAAAGAATGCATTTTTGG	57.090	32.000	14.33	12.13	41.09	3.28
3280	7006	2.843701	TGCATTTTTGGCGTCCATTTT	58.156	38.095	0.00	0.00	31.53	1.82
3292	7018	4.107622	GCGTCCATTTTCCAGATTTCATG	58.892	43.478	0.00	0.00	0.00	3.07
3326	7052	7.043961	TGTTGCAATTACTAACATGGTTCAA	57.956	32.000	0.59	0.00	30.06	2.69
3332	7058	8.028938	GCAATTACTAACATGGTTCAAACAGAT	58.971	33.333	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	111	6.622427	ACTTATGTATCCCTAGGTATTGGC	57.378	41.667	8.29	0.00	0.00	4.52
519	560	5.907662	TGAGGTCCATCTCCTTATGAAATCT	59.092	40.000	0.00	0.00	35.20	2.40
576	617	9.163903	GCAAATAAACGCACAAACAAAATAATT	57.836	25.926	0.00	0.00	0.00	1.40
614	655	9.661563	CAGATTACATACACTAGGTACCAAAAA	57.338	33.333	15.94	0.00	34.07	1.94
620	661	8.684520	AGACAACAGATTACATACACTAGGTAC	58.315	37.037	0.00	0.00	34.07	3.34
622	663	7.363880	CCAGACAACAGATTACATACACTAGGT	60.364	40.741	0.00	0.00	0.00	3.08
651	692	2.884639	GCCACCCGTGATAATAAAGCAT	59.115	45.455	0.00	0.00	0.00	3.79
680	721	7.676947	ACGTCATAGTATATTTACTGGGCATT	58.323	34.615	6.13	0.00	39.08	3.56
752	1229	1.072965	GACCCATTGGCCTCCATAGAG	59.927	57.143	3.32	0.00	35.93	2.43
755	1232	1.303898	TTGACCCATTGGCCTCCATA	58.696	50.000	3.32	0.00	31.53	2.74
757	1234	0.189574	TTTTGACCCATTGGCCTCCA	59.810	50.000	3.32	0.00	33.59	3.86
767	1244	4.202274	TGACAGAGATAACGTTTTGACCCA	60.202	41.667	5.91	0.00	0.00	4.51
805	1285	6.031471	GGTTGCTCGTTTTGTTTCTCTTAAA	58.969	36.000	0.00	0.00	0.00	1.52
806	1286	5.124138	TGGTTGCTCGTTTTGTTTCTCTTAA	59.876	36.000	0.00	0.00	0.00	1.85
807	1287	4.636648	TGGTTGCTCGTTTTGTTTCTCTTA	59.363	37.500	0.00	0.00	0.00	2.10
808	1288	3.442273	TGGTTGCTCGTTTTGTTTCTCTT	59.558	39.130	0.00	0.00	0.00	2.85
1422	1918	0.830648	TGATGAGGGGAAGTAAGCGG	59.169	55.000	0.00	0.00	0.00	5.52
1428	1924	4.910304	ACTATATTGCTGATGAGGGGAAGT	59.090	41.667	0.00	0.00	0.00	3.01
1442	1938	4.376340	AACTTTGCAGGCACTATATTGC	57.624	40.909	6.52	6.52	42.18	3.56
1512	2009	4.351874	TGAAGTGGTAAACTGCTAGCTT	57.648	40.909	17.23	4.51	39.81	3.74
1878	2415	6.942576	AGTAAACAGATCATTACTTTGGCTGT	59.057	34.615	10.89	0.00	38.81	4.40
2398	3164	6.671190	TGTAGAGCATCATGTTTCAACAAAG	58.329	36.000	0.00	0.00	43.03	2.77
2504	3436	9.086336	CATTAACTCAACACTTGACAACATTTT	57.914	29.630	0.00	0.00	35.46	1.82
2582	3531	3.951037	ACCAAATTGCGGCATACTAATCA	59.049	39.130	2.28	0.00	0.00	2.57
2713	3662	3.002862	TGTCTTAAAATCACACGCCACAC	59.997	43.478	0.00	0.00	0.00	3.82
2721	3670	8.715191	AAAATTGTTGCTGTCTTAAAATCACA	57.285	26.923	0.00	0.00	0.00	3.58
2786	3735	5.221925	ACAGAATACCAGTCCAGATTGTTGT	60.222	40.000	0.00	0.00	0.00	3.32
2795	3744	4.096681	AGATGTCACAGAATACCAGTCCA	58.903	43.478	0.00	0.00	0.00	4.02
2895	3849	1.672356	CACTGGTGCTTTCCCCGAG	60.672	63.158	0.00	0.00	0.00	4.63
3192	6918	7.944554	ACCAGAAGATTTTGTTGATCCTAAAGA	59.055	33.333	0.00	0.00	0.00	2.52
3203	6929	5.534207	TGATGCAACCAGAAGATTTTGTT	57.466	34.783	0.00	0.00	0.00	2.83
3210	6936	6.925610	GTTGTATATGATGCAACCAGAAGA	57.074	37.500	8.67	0.00	46.05	2.87
3247	6973	6.455913	CGCCAAAAATGCATTCTTTAATGGAG	60.456	38.462	13.38	12.06	45.22	3.86
3256	6982	1.617850	TGGACGCCAAAAATGCATTCT	59.382	42.857	13.38	0.00	0.00	2.40
3264	6990	2.695666	TCTGGAAAATGGACGCCAAAAA	59.304	40.909	2.68	0.00	36.95	1.94
3270	6996	3.848272	TGAAATCTGGAAAATGGACGC	57.152	42.857	0.00	0.00	0.00	5.19
3304	7030	7.492524	TGTTTGAACCATGTTAGTAATTGCAA	58.507	30.769	0.00	0.00	0.00	4.08
3312	7038	8.082242	GCTTAAATCTGTTTGAACCATGTTAGT	58.918	33.333	0.00	0.00	0.00	2.24
3321	7047	5.393962	AGCGATGCTTAAATCTGTTTGAAC	58.606	37.500	0.00	0.00	33.89	3.18
3326	7052	3.555956	CCGTAGCGATGCTTAAATCTGTT	59.444	43.478	0.00	0.00	40.44	3.16
3332	7058	1.205179	TCACCCGTAGCGATGCTTAAA	59.795	47.619	0.00	0.00	40.44	1.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.