AutoCloner

Multiple sequence alignment - TraesCS1D01G406200

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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	TraesCS1D01G406200	chr1D	100.000	3254	0	0	1	3254	470083750	470087003	0.000000e+00	6010.0
1	TraesCS1D01G406200	chr1D	83.614	1544	232	16	751	2279	470180285	470181822	0.000000e+00	1430.0
2	TraesCS1D01G406200	chr1D	84.107	1378	178	21	913	2279	470135192	470136539	0.000000e+00	1293.0
3	TraesCS1D01G406200	chr1D	83.444	755	120	5	990	1742	470190101	470190852	0.000000e+00	697.0
4	TraesCS1D01G406200	chr1D	78.924	446	86	6	1825	2266	470524552	470524111	2.450000e-76	296.0
5	TraesCS1D01G406200	chr1D	79.070	430	89	1	1825	2254	470191557	470191985	8.830000e-76	294.0
6	TraesCS1D01G406200	chr1D	83.732	209	21	8	2289	2489	470136584	470136787	5.540000e-43	185.0
7	TraesCS1D01G406200	chr1A	91.735	1839	105	25	461	2278	563694834	563696646	0.000000e+00	2510.0
8	TraesCS1D01G406200	chr1A	81.908	1614	212	42	910	2489	563769605	563771172	0.000000e+00	1290.0
9	TraesCS1D01G406200	chr1A	82.908	784	126	6	964	1742	563783579	563784359	0.000000e+00	699.0
10	TraesCS1D01G406200	chr1A	82.891	754	122	6	991	1742	563774104	563774852	0.000000e+00	671.0
11	TraesCS1D01G406200	chr1A	82.143	784	133	6	964	1742	563765408	563766189	0.000000e+00	665.0
12	TraesCS1D01G406200	chr1A	92.172	396	22	6	2274	2661	563696696	563697090	4.750000e-153	551.0
13	TraesCS1D01G406200	chr1A	94.463	307	16	1	1	306	563692684	563692990	3.800000e-129	472.0
14	TraesCS1D01G406200	chr1A	95.053	283	10	2	2975	3254	563753279	563753560	2.980000e-120	442.0
15	TraesCS1D01G406200	chr1A	90.373	322	22	6	2662	2978	563697164	563697481	6.500000e-112	414.0
16	TraesCS1D01G406200	chr1A	80.410	439	78	7	1817	2251	563784398	563784832	8.710000e-86	327.0
17	TraesCS1D01G406200	chr1A	93.478	138	9	0	303	440	563694706	563694843	4.260000e-49	206.0
18	TraesCS1D01G406200	chr1A	80.952	147	17	5	2514	2653	563799794	563799936	4.440000e-19	106.0
19	TraesCS1D01G406200	chr1B	93.095	1593	97	11	696	2279	652467406	652468994	0.000000e+00	2320.0
20	TraesCS1D01G406200	chr1B	84.917	1379	166	19	913	2279	652518548	652519896	0.000000e+00	1356.0
21	TraesCS1D01G406200	chr1B	91.419	606	30	10	2662	3254	652469534	652470130	0.000000e+00	811.0
22	TraesCS1D01G406200	chr1B	89.753	527	48	6	1	525	652466489	652467011	0.000000e+00	669.0
23	TraesCS1D01G406200	chr1B	81.633	784	137	5	964	1742	652485884	652486665	0.000000e+00	643.0
24	TraesCS1D01G406200	chr1B	79.582	431	83	5	1825	2251	652565428	652565857	1.470000e-78	303.0
25	TraesCS1D01G406200	chr1B	91.441	222	13	4	2274	2490	652469043	652469263	1.900000e-77	300.0
26	TraesCS1D01G406200	chr1B	83.254	209	19	9	2289	2489	652519935	652520135	9.280000e-41	178.0
27	TraesCS1D01G406200	chr1B	81.395	129	18	4	2514	2641	652571225	652571348	2.070000e-17	100.0
28	TraesCS1D01G406200	chr1B	81.818	110	14	4	283	388	652488312	652488419	1.610000e-13	87.9

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	TraesCS1D01G406200	chr1D	470083750	470087003	3253	False	6010.000000	6010	100.0000	1	3254	1	chr1D.!!$F1	3253
1	TraesCS1D01G406200	chr1D	470180285	470181822	1537	False	1430.000000	1430	83.6140	751	2279	1	chr1D.!!$F2	1528
2	TraesCS1D01G406200	chr1D	470135192	470136787	1595	False	739.000000	1293	83.9195	913	2489	2	chr1D.!!$F3	1576
3	TraesCS1D01G406200	chr1D	470190101	470191985	1884	False	495.500000	697	81.2570	990	2254	2	chr1D.!!$F4	1264
4	TraesCS1D01G406200	chr1A	563765408	563774852	9444	False	875.333333	1290	82.3140	910	2489	3	chr1A.!!$F4	1579
5	TraesCS1D01G406200	chr1A	563692684	563697481	4797	False	830.600000	2510	92.4442	1	2978	5	chr1A.!!$F3	2977
6	TraesCS1D01G406200	chr1A	563783579	563784832	1253	False	513.000000	699	81.6590	964	2251	2	chr1A.!!$F5	1287
7	TraesCS1D01G406200	chr1B	652466489	652470130	3641	False	1025.000000	2320	91.4270	1	3254	4	chr1B.!!$F3	3253
8	TraesCS1D01G406200	chr1B	652518548	652520135	1587	False	767.000000	1356	84.0855	913	2489	2	chr1B.!!$F5	1576
9	TraesCS1D01G406200	chr1B	652485884	652488419	2535	False	365.450000	643	81.7255	283	1742	2	chr1B.!!$F4	1459

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
834	2863	0.8003	CTCCTTCTCTTCACGAGCGC	60.8	60.0	0.0	0.0	39.7	5.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2369	6422	1.539388	CTACAAAGGCATTTCACGGCA	59.461	47.619	0.0	0.0	0.0	5.69	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
117	119	7.284489	TGCTTTACAAAAGTTTCAGGTGATAGT	59.716	33.333	1.72	0.00	0.00	2.12
203	205	9.429359	CTTCTGATAGAAGTATGTGTTGTTTCT	57.571	33.333	9.80	0.00	45.03	2.52
380	2101	2.672961	TTTCCATAGACCGTCAGCAG	57.327	50.000	0.40	0.00	0.00	4.24
381	2102	0.824109	TTCCATAGACCGTCAGCAGG	59.176	55.000	0.40	0.00	0.00	4.85
431	2152	3.243068	ACATTTTCTTTCACGTGTCAGGC	60.243	43.478	16.51	0.00	0.00	4.85
435	2156	2.143122	TCTTTCACGTGTCAGGCATTC	58.857	47.619	16.51	0.00	0.00	2.67
437	2158	2.254546	TTCACGTGTCAGGCATTCTT	57.745	45.000	16.51	0.00	0.00	2.52
440	2161	2.548057	TCACGTGTCAGGCATTCTTTTC	59.452	45.455	16.51	0.00	0.00	2.29
441	2162	2.290367	CACGTGTCAGGCATTCTTTTCA	59.710	45.455	7.58	0.00	0.00	2.69
442	2163	2.948979	ACGTGTCAGGCATTCTTTTCAA	59.051	40.909	0.00	0.00	0.00	2.69
444	2165	4.037923	ACGTGTCAGGCATTCTTTTCAATT	59.962	37.500	0.00	0.00	0.00	2.32
445	2166	5.240623	ACGTGTCAGGCATTCTTTTCAATTA	59.759	36.000	0.00	0.00	0.00	1.40
446	2167	6.148948	CGTGTCAGGCATTCTTTTCAATTAA	58.851	36.000	0.00	0.00	0.00	1.40
447	2168	6.640499	CGTGTCAGGCATTCTTTTCAATTAAA	59.360	34.615	0.00	0.00	0.00	1.52
501	2256	1.534163	TCTCGAAGTATACATCGCCGG	59.466	52.381	22.21	15.16	37.05	6.13
531	2286	8.961294	AATCGAAATTGTTTCTCTCTCATTTG	57.039	30.769	0.00	0.00	37.52	2.32
546	2301	7.010160	TCTCTCATTTGTTTTGAGGGGTAATT	58.990	34.615	1.04	0.00	41.24	1.40
551	2306	8.705594	TCATTTGTTTTGAGGGGTAATTGTTTA	58.294	29.630	0.00	0.00	0.00	2.01
661	2416	1.476891	CTGTACGTATCCACAGCCAGT	59.523	52.381	0.00	0.00	36.09	4.00
709	2729	4.416738	GGGCAGCCACACTCCTCC	62.417	72.222	15.19	0.00	0.00	4.30
725	2745	0.820226	CTCCACTCGCTCCATTCTGA	59.180	55.000	0.00	0.00	0.00	3.27
728	2748	1.066573	CCACTCGCTCCATTCTGAACT	60.067	52.381	0.00	0.00	0.00	3.01
734	2754	1.339438	GCTCCATTCTGAACTCCAGCA	60.339	52.381	0.00	0.00	42.62	4.41
736	2756	3.008330	CTCCATTCTGAACTCCAGCAAG	58.992	50.000	0.00	0.00	42.62	4.01
737	2757	1.471684	CCATTCTGAACTCCAGCAAGC	59.528	52.381	0.00	0.00	42.62	4.01
739	2759	1.888215	TTCTGAACTCCAGCAAGCAG	58.112	50.000	0.00	0.00	42.62	4.24
834	2863	0.800300	CTCCTTCTCTTCACGAGCGC	60.800	60.000	0.00	0.00	39.70	5.92
843	2872	4.200283	CACGAGCGCTCCTCCTCC	62.200	72.222	30.66	5.85	37.27	4.30
871	2906	2.084546	CTCGGTGGGTTTTGAATCTCC	58.915	52.381	0.00	0.00	0.00	3.71
878	2913	2.043115	GGGTTTTGAATCTCCCTCCCTT	59.957	50.000	0.00	0.00	37.18	3.95
982	4277	3.925379	TCTTCGCTGATGCTGTTTCTTA	58.075	40.909	0.00	0.00	36.97	2.10
1006	4304	2.433888	TTGCAGGACCGATGGCAA	59.566	55.556	10.51	10.51	43.32	4.52
1020	4318	2.435372	TGGCAACAGAGAACAAACCT	57.565	45.000	0.00	0.00	46.17	3.50
1174	4475	2.692368	AGGTGATGCCCCCGACAT	60.692	61.111	0.00	0.00	38.26	3.06
1274	4576	1.956629	GCTGGGTACAAGAGCGCCTA	61.957	60.000	2.29	0.00	0.00	3.93
1389	4691	2.273449	CTCCGGCCTCCAAATGCT	59.727	61.111	0.00	0.00	0.00	3.79
1402	4704	2.076100	CAAATGCTGTCGCTAAGTGGA	58.924	47.619	0.00	0.00	36.97	4.02
1403	4705	2.679837	CAAATGCTGTCGCTAAGTGGAT	59.320	45.455	0.00	0.00	36.97	3.41
1408	4713	2.544069	GCTGTCGCTAAGTGGATACTCC	60.544	54.545	0.00	0.00	35.69	3.85
1491	4796	5.529060	GGAGCTGCACATAATTAAGCTACTT	59.471	40.000	10.03	0.00	44.00	2.24
1912	5223	1.286553	CTCCTAGACCTGGAGTGACCT	59.713	57.143	0.00	0.00	44.42	3.85
2365	6418	2.281276	GGTGTTCGGTGGTCCCAC	60.281	66.667	7.98	7.98	45.49	4.61
2387	6442	0.968405	ATGCCGTGAAATGCCTTTGT	59.032	45.000	0.00	0.00	0.00	2.83
2394	6449	4.092968	CCGTGAAATGCCTTTGTAGAGTAC	59.907	45.833	0.00	0.00	0.00	2.73
2423	6478	1.735571	CTTACGCCGTTAGTTGCCATT	59.264	47.619	0.00	0.00	0.00	3.16
2468	6528	3.433306	TGGTGGTTACTATGCAAGCTT	57.567	42.857	0.00	0.00	0.00	3.74
2491	6551	3.354089	AACTGCATCGGTTTTCAACTG	57.646	42.857	0.00	0.00	39.17	3.16
2548	6611	1.894881	TTGTGCAAGCTGCTCACATA	58.105	45.000	20.50	10.23	45.08	2.29
2556	6619	4.514441	GCAAGCTGCTCACATATGTTATCT	59.486	41.667	5.37	0.00	40.96	1.98
2588	6651	6.240031	CCATGGTATGTATGGTGGTTGGTATA	60.240	42.308	2.57	0.00	40.15	1.47
2692	6955	8.388103	CAATTAGTATACTGTGGTTGTTGCTAC	58.612	37.037	15.90	0.00	0.00	3.58
2722	6993	6.394809	TGAATGATCTTAAACTGCGTCACTA	58.605	36.000	0.00	0.00	0.00	2.74
2834	7120	7.119699	TCTCTTGTGATGGTATTTAACTTGCAG	59.880	37.037	0.00	0.00	0.00	4.41
2906	7366	7.234355	AGATTCACAGTTAATTTCTTGGTCCT	58.766	34.615	0.00	0.00	0.00	3.85
2972	7432	3.900601	TGGGAAGCCATTTGAAAAGCTAA	59.099	39.130	6.29	0.00	34.49	3.09
3006	7469	8.331730	TCTAATTAACCAGCTTACAAAGGAAC	57.668	34.615	0.00	0.00	0.00	3.62
3015	7478	3.852205	GCTTACAAAGGAACGAACAAGGC	60.852	47.826	0.00	0.00	0.00	4.35
3043	7724	5.104776	CCAGTTCTTCCATTCCATCTACTCA	60.105	44.000	0.00	0.00	0.00	3.41
3045	7726	6.482641	CAGTTCTTCCATTCCATCTACTCATG	59.517	42.308	0.00	0.00	0.00	3.07
3079	7888	4.099881	ACAGGTACTCCTAAAACACGTCAA	59.900	41.667	0.00	0.00	43.07	3.18
3087	7896	4.576873	TCCTAAAACACGTCAAGCAATTCA	59.423	37.500	0.00	0.00	0.00	2.57
3092	7901	7.763172	AAAACACGTCAAGCAATTCAAATAA	57.237	28.000	0.00	0.00	0.00	1.40
3103	7912	5.012975	AGCAATTCAAATAAAAAGGAGGGCA	59.987	36.000	0.00	0.00	0.00	5.36
3112	7921	2.568623	AAAGGAGGGCACACTAACAG	57.431	50.000	0.00	0.00	0.00	3.16
3150	9077	7.431960	GGTTTTGCCTTTTGATTGTGATTTTTC	59.568	33.333	0.00	0.00	0.00	2.29
3154	9081	8.592105	TGCCTTTTGATTGTGATTTTTCTTAG	57.408	30.769	0.00	0.00	0.00	2.18
3156	9083	9.260002	GCCTTTTGATTGTGATTTTTCTTAGAA	57.740	29.630	0.00	0.00	0.00	2.10
3217	9269	3.871594	ACCAGTTTTCGAAGTTGAGTGAG	59.128	43.478	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	54	5.626142	TGTATAGGCAAAGGACAAGAAACA	58.374	37.500	0.00	0.00	0.00	2.83
202	204	6.368791	TCGTGTTGATTTGACCTCTTATGAAG	59.631	38.462	0.00	0.00	0.00	3.02
203	205	6.227522	TCGTGTTGATTTGACCTCTTATGAA	58.772	36.000	0.00	0.00	0.00	2.57
423	2144	7.945033	TTTAATTGAAAAGAATGCCTGACAC	57.055	32.000	0.00	0.00	0.00	3.67
490	2240	1.512926	GATTTCAGCCGGCGATGTAT	58.487	50.000	23.20	12.23	0.00	2.29
501	2256	6.606768	AGAGAGAAACAATTTCGATTTCAGC	58.393	36.000	10.22	3.35	44.29	4.26
531	2286	8.349568	AGAGATAAACAATTACCCCTCAAAAC	57.650	34.615	0.00	0.00	0.00	2.43
546	2301	7.277981	GCCTTCTCGTTTTATGAGAGATAAACA	59.722	37.037	0.00	0.00	40.93	2.83
551	2306	4.363999	CGCCTTCTCGTTTTATGAGAGAT	58.636	43.478	0.00	0.00	40.93	2.75
587	2342	3.793492	GCTCTCTCACTGCAAAACAAAAC	59.207	43.478	0.00	0.00	0.00	2.43
661	2416	2.031012	CCAAGTGAGCGAGTGCCA	59.969	61.111	0.00	0.00	44.31	4.92
662	2417	3.426568	GCCAAGTGAGCGAGTGCC	61.427	66.667	0.00	0.00	44.31	5.01
699	2719	1.214062	GAGCGAGTGGAGGAGTGTG	59.786	63.158	0.00	0.00	0.00	3.82
709	2729	2.266554	GAGTTCAGAATGGAGCGAGTG	58.733	52.381	0.00	0.00	36.16	3.51
725	2745	2.670934	CGGCTGCTTGCTGGAGTT	60.671	61.111	0.00	0.00	44.06	3.01
834	2863	1.070758	CGAGAGAGAGAGGAGGAGGAG	59.929	61.905	0.00	0.00	0.00	3.69
843	2872	1.551452	AAACCCACCGAGAGAGAGAG	58.449	55.000	0.00	0.00	0.00	3.20
982	4277	1.135527	CATCGGTCCTGCAATGCAAAT	59.864	47.619	9.92	0.00	38.41	2.32
1006	4304	2.746472	GCCAGTGAGGTTTGTTCTCTGT	60.746	50.000	0.00	0.00	40.61	3.41
1020	4318	4.314440	GACGGTGGCTGCCAGTGA	62.314	66.667	24.10	0.00	32.34	3.41
1143	4444	3.573229	ACCTGCTTCCTGGCTGCA	61.573	61.111	0.50	11.68	33.65	4.41
1159	4460	2.774799	GCAATGTCGGGGGCATCAC	61.775	63.158	0.00	0.00	0.00	3.06
1274	4576	0.964358	GAAGACAAGCCAGCTGCCAT	60.964	55.000	8.66	0.00	42.71	4.40
1402	4704	3.852578	ACTTTTGACCCATCCTGGAGTAT	59.147	43.478	1.52	0.00	40.96	2.12
1403	4705	3.256704	ACTTTTGACCCATCCTGGAGTA	58.743	45.455	1.52	0.00	40.96	2.59
1408	4713	1.273327	GGCAACTTTTGACCCATCCTG	59.727	52.381	0.00	0.00	30.38	3.86
1491	4796	1.301716	GAGGTTTGGCGAGCACAGA	60.302	57.895	0.00	0.00	0.00	3.41
1912	5223	5.288804	GCTCTTTCCAGCAACAATTTTACA	58.711	37.500	0.00	0.00	39.43	2.41
2369	6422	1.539388	CTACAAAGGCATTTCACGGCA	59.461	47.619	0.00	0.00	0.00	5.69
2387	6442	6.149474	ACGGCGTAAGAAAGTTAAGTACTCTA	59.851	38.462	12.58	0.00	35.82	2.43
2394	6449	6.294363	CAACTAACGGCGTAAGAAAGTTAAG	58.706	40.000	15.20	4.41	43.02	1.85
2407	6462	2.598907	CGATAAATGGCAACTAACGGCG	60.599	50.000	4.80	4.80	37.61	6.46
2491	6551	4.314740	TGACAACAAAATAACCAGTGCC	57.685	40.909	0.00	0.00	0.00	5.01
2548	6611	8.441311	ACATACCATGGTCAGATAGATAACAT	57.559	34.615	23.76	0.76	33.60	2.71
2588	6651	2.900546	CCTAGGAGAACCACTGAACACT	59.099	50.000	1.05	0.00	38.94	3.55
2692	6955	4.260538	GCAGTTTAAGATCATTCAGAGGCG	60.261	45.833	0.00	0.00	0.00	5.52
2722	6993	9.783081	AAAAAGAAATCAACAAGCCAAAGATAT	57.217	25.926	0.00	0.00	0.00	1.63
2834	7120	2.358898	AGCACAACTGAACAATGTCCAC	59.641	45.455	0.00	0.00	0.00	4.02
2906	7366	1.974265	TTCATGTTGCCTTTGACCGA	58.026	45.000	0.00	0.00	0.00	4.69
2997	7460	0.661020	CGCCTTGTTCGTTCCTTTGT	59.339	50.000	0.00	0.00	0.00	2.83
3015	7478	2.778299	TGGAATGGAAGAACTGGAACG	58.222	47.619	0.00	0.00	0.00	3.95
3043	7724	7.312415	AGGAGTACCTGTAAAAGTGTTACAT	57.688	36.000	6.36	0.00	45.92	2.29
3079	7888	5.012975	TGCCCTCCTTTTTATTTGAATTGCT	59.987	36.000	0.00	0.00	0.00	3.91
3087	7896	5.836358	TGTTAGTGTGCCCTCCTTTTTATTT	59.164	36.000	0.00	0.00	0.00	1.40
3092	7901	2.489073	CCTGTTAGTGTGCCCTCCTTTT	60.489	50.000	0.00	0.00	0.00	2.27
3103	7912	6.374417	ACCAGATAAATGACCTGTTAGTGT	57.626	37.500	0.00	0.00	0.00	3.55
3112	7921	5.405935	AAGGCAAAACCAGATAAATGACC	57.594	39.130	0.00	0.00	43.14	4.02
3196	9248	3.303395	GCTCACTCAACTTCGAAAACTGG	60.303	47.826	0.00	0.00	0.00	4.00
3202	9254	6.801539	AATAAATGCTCACTCAACTTCGAA	57.198	33.333	0.00	0.00	0.00	3.71
3203	9255	6.801539	AAATAAATGCTCACTCAACTTCGA	57.198	33.333	0.00	0.00	0.00	3.71
3204	9256	8.015087	TGTTAAATAAATGCTCACTCAACTTCG	58.985	33.333	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.