AutoCloner

Multiple sequence alignment - TraesCS5D01G140500

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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	TraesCS5D01G140500	chr5D	100.000	2760	0	0	1	2760	223990780	223993539	0.000000e+00	5097.0
1	TraesCS5D01G140500	chr5D	97.210	466	13	0	2295	2760	111974573	111975038	0.000000e+00	789.0
2	TraesCS5D01G140500	chr5D	97.210	466	12	1	2295	2760	328932424	328931960	0.000000e+00	787.0
3	TraesCS5D01G140500	chr5D	90.393	458	39	4	1	458	540870331	540869879	5.090000e-167	597.0
4	TraesCS5D01G140500	chr5B	93.554	2777	125	19	1	2760	247244811	247242072	0.000000e+00	4087.0
5	TraesCS5D01G140500	chr5B	90.391	1280	99	16	1021	2293	316613549	316614811	0.000000e+00	1661.0
6	TraesCS5D01G140500	chr5B	90.125	1276	101	16	1026	2293	640440514	640441772	0.000000e+00	1635.0
7	TraesCS5D01G140500	chr5B	88.181	1413	69	28	781	2143	615378058	615376694	0.000000e+00	1594.0
8	TraesCS5D01G140500	chr4D	89.223	2329	138	33	1	2295	370058939	370056690	0.000000e+00	2806.0
9	TraesCS5D01G140500	chr4D	97.425	466	12	0	2295	2760	464790878	464790413	0.000000e+00	795.0
10	TraesCS5D01G140500	chr4D	90.455	440	34	3	1	440	506697861	506698292	8.570000e-160	573.0
11	TraesCS5D01G140500	chr3D	91.437	1705	79	20	610	2295	53984125	53985781	0.000000e+00	2278.0
12	TraesCS5D01G140500	chr3D	97.639	466	11	0	2295	2760	456902378	456902843	0.000000e+00	800.0
13	TraesCS5D01G140500	chr3D	97.634	465	10	1	2296	2760	410874856	410874393	0.000000e+00	797.0
14	TraesCS5D01G140500	chr3D	97.210	466	13	0	2295	2760	96658787	96658322	0.000000e+00	789.0
15	TraesCS5D01G140500	chr2A	90.219	1554	79	27	781	2295	497436222	497437741	0.000000e+00	1960.0
16	TraesCS5D01G140500	chr2A	84.625	839	53	26	775	1601	155627654	155626880	0.000000e+00	765.0
17	TraesCS5D01G140500	chr2A	92.585	472	33	2	1	471	497435422	497435892	0.000000e+00	676.0
18	TraesCS5D01G140500	chr2A	91.743	436	28	5	1	430	610160984	610160551	1.410000e-167	599.0
19	TraesCS5D01G140500	chr2A	88.750	160	4	8	655	814	524832936	524833081	1.690000e-42	183.0
20	TraesCS5D01G140500	chr2A	92.045	88	7	0	727	814	610160536	610160449	1.040000e-24	124.0
21	TraesCS5D01G140500	chr2A	94.030	67	4	0	747	813	155627648	155627582	4.860000e-18	102.0
22	TraesCS5D01G140500	chr2A	97.297	37	1	0	744	780	497436043	497436079	2.290000e-06	63.9
23	TraesCS5D01G140500	chr2B	89.391	1461	97	21	892	2295	644602598	644601139	0.000000e+00	1786.0
24	TraesCS5D01G140500	chr2B	88.142	506	38	9	9	508	113944715	113944226	1.420000e-162	582.0
25	TraesCS5D01G140500	chr2B	95.122	82	4	0	733	814	545002756	545002675	2.230000e-26	130.0
26	TraesCS5D01G140500	chr1B	87.964	1562	111	28	781	2295	29815900	29814369	0.000000e+00	1772.0
27	TraesCS5D01G140500	chr1B	85.682	447	41	17	1	444	643126632	643126206	1.510000e-122	449.0
28	TraesCS5D01G140500	chr6D	91.058	1286	86	19	1018	2293	381184715	381185981	0.000000e+00	1711.0
29	TraesCS5D01G140500	chr6B	88.873	1384	105	21	958	2295	633630162	633628782	0.000000e+00	1657.0
30	TraesCS5D01G140500	chr6B	87.174	881	46	21	781	1643	62825572	62824741	0.000000e+00	939.0
31	TraesCS5D01G140500	chr6B	89.247	372	26	5	93	458	633631132	633630769	1.170000e-123	453.0
32	TraesCS5D01G140500	chr6B	85.217	230	18	6	639	868	633630757	633630544	3.580000e-54	222.0
33	TraesCS5D01G140500	chr1A	92.745	1144	66	10	1154	2295	95534528	95533400	0.000000e+00	1637.0
34	TraesCS5D01G140500	chr7B	88.269	1398	77	34	781	2143	149634883	149633538	0.000000e+00	1592.0
35	TraesCS5D01G140500	chr7B	89.333	450	46	2	38	487	567025364	567024917	5.160000e-157	564.0
36	TraesCS5D01G140500	chr7B	91.599	369	29	2	1038	1405	567024004	567023637	2.450000e-140	508.0
37	TraesCS5D01G140500	chr7B	94.268	157	6	2	788	942	567024769	567024614	1.280000e-58	237.0
38	TraesCS5D01G140500	chrUn	88.880	1304	98	27	1018	2293	9915167	9916451	0.000000e+00	1561.0
39	TraesCS5D01G140500	chrUn	85.874	269	18	4	775	1043	101572994	101573242	4.530000e-68	268.0
40	TraesCS5D01G140500	chr3B	87.752	1192	103	25	958	2120	135536273	135537450	0.000000e+00	1352.0
41	TraesCS5D01G140500	chr1D	97.210	466	13	0	2295	2760	31477570	31477105	0.000000e+00	789.0
42	TraesCS5D01G140500	chr1D	97.436	78	2	0	737	814	209504044	209504121	1.720000e-27	134.0
43	TraesCS5D01G140500	chr2D	96.610	472	15	1	2289	2760	133650553	133650083	0.000000e+00	782.0
44	TraesCS5D01G140500	chr4B	89.562	479	35	7	1	473	577158412	577158881	6.580000e-166	593.0
45	TraesCS5D01G140500	chr4B	85.874	269	19	3	781	1049	655815320	655815569	4.530000e-68	268.0
46	TraesCS5D01G140500	chr4B	96.591	88	3	0	727	814	577159027	577159114	2.210000e-31	147.0

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	TraesCS5D01G140500	chr5D	223990780	223993539	2759	False	5097.000000	5097	100.000000	1	2760	1	chr5D.!!$F2	2759
1	TraesCS5D01G140500	chr5B	247242072	247244811	2739	True	4087.000000	4087	93.554000	1	2760	1	chr5B.!!$R1	2759
2	TraesCS5D01G140500	chr5B	316613549	316614811	1262	False	1661.000000	1661	90.391000	1021	2293	1	chr5B.!!$F1	1272
3	TraesCS5D01G140500	chr5B	640440514	640441772	1258	False	1635.000000	1635	90.125000	1026	2293	1	chr5B.!!$F2	1267
4	TraesCS5D01G140500	chr5B	615376694	615378058	1364	True	1594.000000	1594	88.181000	781	2143	1	chr5B.!!$R2	1362
5	TraesCS5D01G140500	chr4D	370056690	370058939	2249	True	2806.000000	2806	89.223000	1	2295	1	chr4D.!!$R1	2294
6	TraesCS5D01G140500	chr3D	53984125	53985781	1656	False	2278.000000	2278	91.437000	610	2295	1	chr3D.!!$F1	1685
7	TraesCS5D01G140500	chr2A	497435422	497437741	2319	False	899.966667	1960	93.367000	1	2295	3	chr2A.!!$F2	2294
8	TraesCS5D01G140500	chr2A	155626880	155627654	774	True	433.500000	765	89.327500	747	1601	2	chr2A.!!$R1	854
9	TraesCS5D01G140500	chr2A	610160449	610160984	535	True	361.500000	599	91.894000	1	814	2	chr2A.!!$R2	813
10	TraesCS5D01G140500	chr2B	644601139	644602598	1459	True	1786.000000	1786	89.391000	892	2295	1	chr2B.!!$R3	1403
11	TraesCS5D01G140500	chr1B	29814369	29815900	1531	True	1772.000000	1772	87.964000	781	2295	1	chr1B.!!$R1	1514
12	TraesCS5D01G140500	chr6D	381184715	381185981	1266	False	1711.000000	1711	91.058000	1018	2293	1	chr6D.!!$F1	1275
13	TraesCS5D01G140500	chr6B	62824741	62825572	831	True	939.000000	939	87.174000	781	1643	1	chr6B.!!$R1	862
14	TraesCS5D01G140500	chr6B	633628782	633631132	2350	True	777.333333	1657	87.779000	93	2295	3	chr6B.!!$R2	2202
15	TraesCS5D01G140500	chr1A	95533400	95534528	1128	True	1637.000000	1637	92.745000	1154	2295	1	chr1A.!!$R1	1141
16	TraesCS5D01G140500	chr7B	149633538	149634883	1345	True	1592.000000	1592	88.269000	781	2143	1	chr7B.!!$R1	1362
17	TraesCS5D01G140500	chr7B	567023637	567025364	1727	True	436.333333	564	91.733333	38	1405	3	chr7B.!!$R2	1367
18	TraesCS5D01G140500	chrUn	9915167	9916451	1284	False	1561.000000	1561	88.880000	1018	2293	1	chrUn.!!$F1	1275
19	TraesCS5D01G140500	chr3B	135536273	135537450	1177	False	1352.000000	1352	87.752000	958	2120	1	chr3B.!!$F1	1162
20	TraesCS5D01G140500	chr4B	577158412	577159114	702	False	370.000000	593	93.076500	1	814	2	chr4B.!!$F2	813

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
127	129	1.451927	TGACAAGCATCGCCCCATC	60.452	57.895	0.0	0.0	0.00	3.51	F
1332	2633	2.026262	TCTGTAAAGAATGGACTGGCCC	60.026	50.000	0.0	0.0	34.97	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1602	2971	0.639392	AGGCCACTCAGGGTCTATCT	59.361	55.0	5.01	0.0	42.28	1.98	R
2484	3860	0.666374	ACTTTTGCCACCGTTACTGC	59.334	50.0	0.00	0.0	0.00	4.40	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
118	119	1.687612	CAGGGAGGGTGACAAGCAT	59.312	57.895	0.00	0.00	0.00	3.79
127	129	1.451927	TGACAAGCATCGCCCCATC	60.452	57.895	0.00	0.00	0.00	3.51
491	521	2.351738	GGCTGGTTGTTGAACTATGTGC	60.352	50.000	0.00	0.00	32.15	4.57
507	537	3.275617	TGTGCTGTTGAACTAAGTGGT	57.724	42.857	0.00	0.00	0.00	4.16
511	541	4.448060	GTGCTGTTGAACTAAGTGGTAGTC	59.552	45.833	0.00	0.00	42.55	2.59
520	550	5.246145	ACTAAGTGGTAGTCGAACTATGC	57.754	43.478	0.00	0.00	38.84	3.14
529	559	2.932614	AGTCGAACTATGCTGTTGATGC	59.067	45.455	0.00	0.00	0.00	3.91
530	560	2.672874	GTCGAACTATGCTGTTGATGCA	59.327	45.455	0.00	0.00	44.95	3.96
543	573	4.005650	TGTTGATGCAGTTTGAGATCTCC	58.994	43.478	20.03	4.84	0.00	3.71
548	578	3.405831	TGCAGTTTGAGATCTCCTGTTG	58.594	45.455	20.03	13.58	0.00	3.33
549	579	3.181451	TGCAGTTTGAGATCTCCTGTTGT	60.181	43.478	20.03	0.00	0.00	3.32
550	580	3.817647	GCAGTTTGAGATCTCCTGTTGTT	59.182	43.478	20.03	0.00	0.00	2.83
551	581	4.276926	GCAGTTTGAGATCTCCTGTTGTTT	59.723	41.667	20.03	0.00	0.00	2.83
552	582	5.221126	GCAGTTTGAGATCTCCTGTTGTTTT	60.221	40.000	20.03	0.00	0.00	2.43
553	583	6.017109	GCAGTTTGAGATCTCCTGTTGTTTTA	60.017	38.462	20.03	0.00	0.00	1.52
585	615	6.232692	TGTTCTCTGTTGATGTTGATGATCA	58.767	36.000	0.00	0.00	0.00	2.92
989	2080	5.044712	AAGTTTGTACTTGCACACCCTGC	62.045	47.826	0.00	0.00	42.91	4.85
1112	2355	5.731187	TCCTCCATTTTCCTCCTCTATTTGA	59.269	40.000	0.00	0.00	0.00	2.69
1231	2490	2.696187	GTTAGTCATGTCCTCTCCTCCC	59.304	54.545	0.00	0.00	0.00	4.30
1332	2633	2.026262	TCTGTAAAGAATGGACTGGCCC	60.026	50.000	0.00	0.00	34.97	5.80
1775	3147	2.228343	AGCTGAGACATTTCAAGCTTGC	59.772	45.455	21.99	6.49	39.71	4.01
1884	3257	5.698545	GCTTGAGAAGAAGAAGAGCACTAAA	59.301	40.000	0.00	0.00	0.00	1.85
2057	3430	6.206042	AGGAGAAGATAAGGAAGCTTAAGGA	58.794	40.000	0.00	0.00	0.00	3.36
2069	3442	3.818180	AGCTTAAGGAGATGCTGAATGG	58.182	45.455	4.29	0.00	34.19	3.16
2085	3458	5.915196	GCTGAATGGTTTTGACTGAACTTAC	59.085	40.000	0.00	0.00	0.00	2.34
2170	3543	6.088824	GTCAACTGAATTTATCTTGCCTGTG	58.911	40.000	0.00	0.00	0.00	3.66
2179	3552	8.579850	AATTTATCTTGCCTGTGAACTGAATA	57.420	30.769	0.00	0.00	0.00	1.75
2189	3562	6.183360	GCCTGTGAACTGAATATTAAGTGCAT	60.183	38.462	15.73	0.00	34.46	3.96
2190	3563	7.412853	CCTGTGAACTGAATATTAAGTGCATC	58.587	38.462	15.73	10.47	34.46	3.91
2195	3568	8.147704	TGAACTGAATATTAAGTGCATCGGATA	58.852	33.333	9.40	0.00	26.36	2.59
2332	3708	1.202879	AGGGGATCGCAACAGTTTTCA	60.203	47.619	12.32	0.00	0.00	2.69
2346	3722	7.573283	GCAACAGTTTTCAAGGGTAGAGTATTC	60.573	40.741	0.00	0.00	0.00	1.75
2491	3867	7.010275	GCAAAGTAGTATGGAAGTAGCAGTAAC	59.990	40.741	0.00	0.00	0.00	2.50
2512	3888	2.095919	CGGTGGCAAAAGTAACAGTAGC	60.096	50.000	0.00	0.00	0.00	3.58
2533	3909	5.449304	AGCAGTTTTTGTAGCAATCGTAAC	58.551	37.500	0.00	0.00	0.00	2.50
2545	3921	0.319083	ATCGTAACAGTGGCAACGGA	59.681	50.000	8.60	0.00	42.51	4.69
2553	3929	2.356695	ACAGTGGCAACGGAAAAGTAAC	59.643	45.455	0.00	0.00	42.51	2.50
2582	3958	6.195983	GCAAAGATCAATATGTGAAAAGCTCG	59.804	38.462	0.00	0.00	40.50	5.03
2641	4017	4.455533	TGTGATTCCTCATGCAACAGTTAC	59.544	41.667	0.00	0.00	32.98	2.50
2656	4032	5.499004	ACAGTTACAACATAGGGTGACAT	57.501	39.130	0.00	0.00	0.00	3.06
2685	4061	8.023021	ACTAGCTCCAGTTCATCAATGTAATA	57.977	34.615	0.00	0.00	0.00	0.98
2739	4115	5.010922	TGCTTATGGAAAAGAACTTGCATGT	59.989	36.000	0.00	0.00	37.82	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	119	1.143838	CTCAACATCGATGGGGCGA	59.856	57.895	28.09	16.70	45.22	5.54
127	129	0.725686	CTGGAAGCAGCTCAACATCG	59.274	55.000	0.00	0.00	0.00	3.84
133	135	1.339438	GGAACATCTGGAAGCAGCTCA	60.339	52.381	0.00	0.00	0.00	4.26
491	521	5.117355	TCGACTACCACTTAGTTCAACAG	57.883	43.478	0.00	0.00	41.48	3.16
507	537	4.112634	GCATCAACAGCATAGTTCGACTA	58.887	43.478	0.00	0.00	34.82	2.59
511	541	2.674852	ACTGCATCAACAGCATAGTTCG	59.325	45.455	0.00	0.00	41.82	3.95
520	550	4.094590	GGAGATCTCAAACTGCATCAACAG	59.905	45.833	23.85	0.00	43.59	3.16
529	559	6.382869	AAAACAACAGGAGATCTCAAACTG	57.617	37.500	23.85	21.57	35.40	3.16
530	560	7.721399	ACATAAAACAACAGGAGATCTCAAACT	59.279	33.333	23.85	9.44	0.00	2.66
553	583	8.849168	TCAACATCAACAGAGAACATAAAACAT	58.151	29.630	0.00	0.00	0.00	2.71
585	615	5.073691	ACAGCCTTATATAGCAACTGGGATT	59.926	40.000	0.00	0.00	0.00	3.01
724	812	3.762288	AGCATCAACAAGACAGCATCAAT	59.238	39.130	0.00	0.00	34.14	2.57
1112	2355	2.403561	GGAATAGGAGCAGAGGAAGGT	58.596	52.381	0.00	0.00	0.00	3.50
1231	2490	1.369625	CTGTTTAACCCTAGCTGCGG	58.630	55.000	0.00	0.00	0.00	5.69
1552	2903	7.340487	ACTTCCTATCATCCAAACAAAGATTCC	59.660	37.037	0.00	0.00	0.00	3.01
1602	2971	0.639392	AGGCCACTCAGGGTCTATCT	59.361	55.000	5.01	0.00	42.28	1.98
2057	3430	4.401022	TCAGTCAAAACCATTCAGCATCT	58.599	39.130	0.00	0.00	0.00	2.90
2069	3442	7.085052	AGAACAAGGTAAGTTCAGTCAAAAC	57.915	36.000	8.54	0.00	45.93	2.43
2085	3458	2.348411	ACACAGGGACAAGAACAAGG	57.652	50.000	0.00	0.00	0.00	3.61
2170	3543	6.844696	TCCGATGCACTTAATATTCAGTTC	57.155	37.500	0.00	0.00	0.00	3.01
2179	3552	5.869579	AGAACCATATCCGATGCACTTAAT	58.130	37.500	0.00	0.00	0.00	1.40
2189	3562	8.593679	ACATATTACATTGAGAACCATATCCGA	58.406	33.333	0.00	0.00	0.00	4.55
2190	3563	8.777865	ACATATTACATTGAGAACCATATCCG	57.222	34.615	0.00	0.00	0.00	4.18
2195	3568	8.806429	TCACAACATATTACATTGAGAACCAT	57.194	30.769	0.00	0.00	0.00	3.55
2301	3677	1.002087	GCGATCCCCTATACTTGTGGG	59.998	57.143	0.00	0.00	40.59	4.61
2346	3722	7.312154	TGAGTCGAATCAATAAATTTGGGTTG	58.688	34.615	14.01	3.99	0.00	3.77
2484	3860	0.666374	ACTTTTGCCACCGTTACTGC	59.334	50.000	0.00	0.00	0.00	4.40
2491	3867	2.095919	GCTACTGTTACTTTTGCCACCG	60.096	50.000	0.00	0.00	0.00	4.94
2512	3888	6.356977	CACTGTTACGATTGCTACAAAAACTG	59.643	38.462	0.00	0.00	0.00	3.16
2533	3909	2.616842	AGTTACTTTTCCGTTGCCACTG	59.383	45.455	0.00	0.00	0.00	3.66
2553	3929	9.017669	GCTTTTCACATATTGATCTTTGCTTAG	57.982	33.333	0.00	0.00	32.84	2.18
2575	3951	2.092968	TGATCCATTGCCTACGAGCTTT	60.093	45.455	0.00	0.00	0.00	3.51
2582	3958	4.401022	TCCATCATTGATCCATTGCCTAC	58.599	43.478	0.00	0.00	0.00	3.18
2641	4017	5.986135	GCTAGTTCTATGTCACCCTATGTTG	59.014	44.000	0.00	0.00	0.00	3.33
2685	4061	8.306313	TGACTATATTCGGAATACATGCCTAT	57.694	34.615	12.39	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.