AutoCloner

Multiple sequence alignment - TraesCS6B01G261100

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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	TraesCS6B01G261100	chr6B	100.000	2305	0	0	458	2762	471157026	471159330	0.000000e+00	4257.0
1	TraesCS6B01G261100	chr6B	78.290	1497	255	49	831	2291	301573964	301572502	0.000000e+00	900.0
2	TraesCS6B01G261100	chr6B	100.000	346	0	0	2943	3288	471159511	471159856	9.950000e-180	640.0
3	TraesCS6B01G261100	chr6B	100.000	138	0	0	1	138	471156569	471156706	4.210000e-64	255.0
4	TraesCS6B01G261100	chr6A	95.524	2279	78	10	491	2759	100237346	100239610	0.000000e+00	3622.0
5	TraesCS6B01G261100	chr6A	83.686	331	14	5	2958	3288	100239901	100240191	3.230000e-70	276.0
6	TraesCS6B01G261100	chr6A	95.652	138	6	0	1	138	100236894	100237031	4.270000e-54	222.0
7	TraesCS6B01G261100	chr6A	100.000	28	0	0	109	136	465578167	465578194	6.000000e-03	52.8
8	TraesCS6B01G261100	chr1A	94.525	1315	63	7	1445	2754	530616560	530617870	0.000000e+00	2021.0
9	TraesCS6B01G261100	chr1A	96.360	989	35	1	458	1446	530606438	530607425	0.000000e+00	1626.0
10	TraesCS6B01G261100	chr1A	93.243	222	11	4	2958	3179	530618346	530618563	1.140000e-84	324.0
11	TraesCS6B01G261100	chr1A	94.891	137	6	1	1	137	530606224	530606359	2.570000e-51	213.0
12	TraesCS6B01G261100	chr1A	94.318	88	5	0	3201	3288	530618558	530618645	5.720000e-28	135.0
13	TraesCS6B01G261100	chr2B	83.780	1979	269	39	622	2560	793149778	793151744	0.000000e+00	1829.0
14	TraesCS6B01G261100	chr2B	78.357	1497	254	49	831	2291	66193825	66192363	0.000000e+00	905.0
15	TraesCS6B01G261100	chr2B	79.951	409	70	7	1567	1967	732061463	732061059	1.150000e-74	291.0
16	TraesCS6B01G261100	chr2B	92.424	132	10	0	5	136	793148978	793149109	4.330000e-44	189.0
17	TraesCS6B01G261100	chr2B	87.255	102	13	0	472	573	793149563	793149664	2.070000e-22	117.0
18	TraesCS6B01G261100	chr5A	83.665	1959	237	51	460	2352	603369282	603371223	0.000000e+00	1768.0
19	TraesCS6B01G261100	chr5A	92.537	134	10	0	3	136	603369065	603369198	3.350000e-45	193.0
20	TraesCS6B01G261100	chr4B	85.855	1216	156	14	1148	2352	127696382	127697592	0.000000e+00	1279.0
21	TraesCS6B01G261100	chr3B	79.529	1700	298	37	624	2291	88405178	88403497	0.000000e+00	1166.0
22	TraesCS6B01G261100	chr3B	78.490	1497	251	50	831	2291	556683103	556681642	0.000000e+00	915.0
23	TraesCS6B01G261100	chr1B	78.357	1497	253	50	831	2291	33820488	33819027	0.000000e+00	904.0
24	TraesCS6B01G261100	chr7B	79.167	1152	204	23	1154	2291	313189186	313188057	0.000000e+00	765.0
25	TraesCS6B01G261100	chr4D	78.814	1147	220	18	1155	2291	475029162	475030295	0.000000e+00	750.0
26	TraesCS6B01G261100	chr4D	87.768	466	57	0	621	1086	475028600	475029065	2.230000e-151	545.0
27	TraesCS6B01G261100	chr4D	83.990	381	45	10	2330	2697	102115590	102115213	5.220000e-93	351.0
28	TraesCS6B01G261100	chr3D	78.291	1147	227	17	1155	2291	597453544	597452410	0.000000e+00	719.0
29	TraesCS6B01G261100	chr2A	82.086	815	126	12	650	1446	705806543	705805731	0.000000e+00	678.0
30	TraesCS6B01G261100	chr2A	81.956	726	114	13	1576	2293	705805609	705804893	1.690000e-167	599.0
31	TraesCS6B01G261100	chr2A	89.362	94	10	0	458	551	705806776	705806683	5.760000e-23	119.0
32	TraesCS6B01G261100	chr4A	84.819	415	41	12	2330	2726	674746674	674746264	6.610000e-107	398.0
33	TraesCS6B01G261100	chr6D	86.851	289	24	9	2448	2726	414098284	414098000	8.860000e-81	311.0
34	TraesCS6B01G261100	chr6D	86.512	215	26	3	2240	2451	414099823	414099609	1.970000e-57	233.0

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	TraesCS6B01G261100	chr6B	471156569	471159856	3287	False	1717.333333	4257	100.000000	1	3288	3	chr6B.!!$F1	3287
1	TraesCS6B01G261100	chr6B	301572502	301573964	1462	True	900.000000	900	78.290000	831	2291	1	chr6B.!!$R1	1460
2	TraesCS6B01G261100	chr6A	100236894	100240191	3297	False	1373.333333	3622	91.620667	1	3288	3	chr6A.!!$F2	3287
3	TraesCS6B01G261100	chr1A	530606224	530607425	1201	False	919.500000	1626	95.625500	1	1446	2	chr1A.!!$F1	1445
4	TraesCS6B01G261100	chr1A	530616560	530618645	2085	False	826.666667	2021	94.028667	1445	3288	3	chr1A.!!$F2	1843
5	TraesCS6B01G261100	chr2B	66192363	66193825	1462	True	905.000000	905	78.357000	831	2291	1	chr2B.!!$R1	1460
6	TraesCS6B01G261100	chr2B	793148978	793151744	2766	False	711.666667	1829	87.819667	5	2560	3	chr2B.!!$F1	2555
7	TraesCS6B01G261100	chr5A	603369065	603371223	2158	False	980.500000	1768	88.101000	3	2352	2	chr5A.!!$F1	2349
8	TraesCS6B01G261100	chr4B	127696382	127697592	1210	False	1279.000000	1279	85.855000	1148	2352	1	chr4B.!!$F1	1204
9	TraesCS6B01G261100	chr3B	88403497	88405178	1681	True	1166.000000	1166	79.529000	624	2291	1	chr3B.!!$R1	1667
10	TraesCS6B01G261100	chr3B	556681642	556683103	1461	True	915.000000	915	78.490000	831	2291	1	chr3B.!!$R2	1460
11	TraesCS6B01G261100	chr1B	33819027	33820488	1461	True	904.000000	904	78.357000	831	2291	1	chr1B.!!$R1	1460
12	TraesCS6B01G261100	chr7B	313188057	313189186	1129	True	765.000000	765	79.167000	1154	2291	1	chr7B.!!$R1	1137
13	TraesCS6B01G261100	chr4D	475028600	475030295	1695	False	647.500000	750	83.291000	621	2291	2	chr4D.!!$F1	1670
14	TraesCS6B01G261100	chr3D	597452410	597453544	1134	True	719.000000	719	78.291000	1155	2291	1	chr3D.!!$R1	1136
15	TraesCS6B01G261100	chr2A	705804893	705806776	1883	True	465.333333	678	84.468000	458	2293	3	chr2A.!!$R1	1835
16	TraesCS6B01G261100	chr6D	414098000	414099823	1823	True	272.000000	311	86.681500	2240	2726	2	chr6D.!!$R1	486

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
727	937	0.320771	GAAGGCGAAAGAGCACCTCA	60.321	55.0	0.0	0.0	39.27	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2672	4283	0.331278	ATCAATTCTGGAACGGCCCA	59.669	50.0	0.0	0.0	34.97	5.36	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
25	26	4.382040	CCAGAGTTCTCGTATGTGGTTGAT	60.382	45.833	0.00	0.00	0.00	2.57
44	45	6.089954	GGTTGATGTTGATAAAGAAAGCAAGC	59.910	38.462	0.00	0.00	0.00	4.01
105	107	4.000325	CAGTACCACAATTTCGGTGATGA	59.000	43.478	5.90	0.00	38.54	2.92
106	108	4.454161	CAGTACCACAATTTCGGTGATGAA	59.546	41.667	5.90	0.00	38.54	2.57
544	665	4.456566	GCCTCCAAAAACAATACTAACCGA	59.543	41.667	0.00	0.00	0.00	4.69
707	917	1.879380	GTGTAAGTGGCATGTGCTTCA	59.121	47.619	4.84	0.00	41.70	3.02
727	937	0.320771	GAAGGCGAAAGAGCACCTCA	60.321	55.000	0.00	0.00	39.27	3.86
742	952	2.813179	CTCAGGCCGCATTACACGC	61.813	63.158	0.00	0.00	0.00	5.34
947	1157	2.350388	CGAAGCAAACCAGTACGCAAAT	60.350	45.455	0.00	0.00	0.00	2.32
1081	1301	4.445019	GGTTCCAAGAGAAGAGAACAAGGT	60.445	45.833	0.00	0.00	40.27	3.50
1110	1330	0.316204	CGACCAGACCTTAACCGTGT	59.684	55.000	0.00	0.00	0.00	4.49
1244	1493	4.163441	TGTTTGAGATGTTTGGTCAGGA	57.837	40.909	0.00	0.00	0.00	3.86
1471	1722	2.577700	CTGACTCTACCGCCTCTATGT	58.422	52.381	0.00	0.00	0.00	2.29
1487	1738	6.823689	GCCTCTATGTGAGTTCCTTCAATTAA	59.176	38.462	0.00	0.00	41.11	1.40
1612	1874	4.747108	CGGAAGATACCTAGCTTTCATGTG	59.253	45.833	0.00	0.00	31.17	3.21
1674	1936	4.446371	CTTCACCTCATCCATTACCAGAC	58.554	47.826	0.00	0.00	0.00	3.51
2024	2289	2.755952	ATCCACTTTATTGGCCCCTC	57.244	50.000	0.00	0.00	36.48	4.30
2031	2296	3.990245	ACTTTATTGGCCCCTCATAGGAT	59.010	43.478	0.00	0.00	37.67	3.24
2111	2376	3.166657	GTGCGATCAAGATTTTGCACTC	58.833	45.455	19.60	4.45	46.69	3.51
2144	2409	2.355837	GGCACAAGAGCACGACGA	60.356	61.111	0.00	0.00	35.83	4.20
2411	2683	1.809133	TGTCTTTGGGGTACTGGACA	58.191	50.000	0.00	0.00	0.00	4.02
2563	4165	5.979993	AGGTGGTTTGGTTTTAAAAACGAT	58.020	33.333	11.24	0.00	37.19	3.73
2651	4258	4.097286	TGTGCCTACCTTTTGAACAACTTC	59.903	41.667	0.00	0.00	0.00	3.01
2668	4279	1.351430	TTCTGCAGTCGTACGCATGC	61.351	55.000	27.29	27.29	37.54	4.06
2669	4280	1.807165	CTGCAGTCGTACGCATGCT	60.807	57.895	30.90	16.64	39.42	3.79
2670	4281	2.017458	CTGCAGTCGTACGCATGCTG	62.017	60.000	30.90	27.92	39.42	4.41
2671	4282	2.697425	CAGTCGTACGCATGCTGC	59.303	61.111	17.13	5.69	40.69	5.25
2672	4283	1.807165	CAGTCGTACGCATGCTGCT	60.807	57.895	17.13	0.07	42.25	4.24
2740	4351	0.028770	TCGTGCTTGCGGTTTTTCAG	59.971	50.000	0.00	0.00	0.00	3.02
2759	4370	5.212532	TCAGATTTTGAATTGTTGTGGGG	57.787	39.130	0.00	0.00	31.34	4.96
2760	4371	3.747529	CAGATTTTGAATTGTTGTGGGGC	59.252	43.478	0.00	0.00	0.00	5.80
2761	4372	3.647590	AGATTTTGAATTGTTGTGGGGCT	59.352	39.130	0.00	0.00	0.00	5.19
3009	4892	0.969894	CTTCTCCACTGGTCGACCTT	59.030	55.000	33.39	18.82	36.82	3.50
3023	4906	1.266989	CGACCTTTTCCTCACTTTGGC	59.733	52.381	0.00	0.00	0.00	4.52
3030	4913	1.270907	TCCTCACTTTGGCTCTCCTC	58.729	55.000	0.00	0.00	0.00	3.71
3032	4915	1.274712	CTCACTTTGGCTCTCCTCCT	58.725	55.000	0.00	0.00	0.00	3.69
3033	4916	1.627834	CTCACTTTGGCTCTCCTCCTT	59.372	52.381	0.00	0.00	0.00	3.36
3034	4917	2.039613	CTCACTTTGGCTCTCCTCCTTT	59.960	50.000	0.00	0.00	0.00	3.11
3038	4921	2.030027	TTGGCTCTCCTCCTTTCTCA	57.970	50.000	0.00	0.00	0.00	3.27
3088	4971	3.797353	CATGGCGCCCCCTGTAGT	61.797	66.667	26.77	0.00	0.00	2.73
3179	5062	4.626081	AGAGCACGCGGGCTGTTT	62.626	61.111	44.40	23.43	45.99	2.83
3180	5063	3.660111	GAGCACGCGGGCTGTTTT	61.660	61.111	44.40	18.40	45.99	2.43
3181	5064	3.194272	GAGCACGCGGGCTGTTTTT	62.194	57.895	44.40	17.42	45.99	1.94
3203	5086	1.941734	GCTAGTAGCACGCGAGCTG	60.942	63.158	35.97	22.32	46.11	4.24
3204	5087	1.429825	CTAGTAGCACGCGAGCTGT	59.570	57.895	35.97	25.72	46.11	4.40
3205	5088	0.179161	CTAGTAGCACGCGAGCTGTT	60.179	55.000	35.97	25.82	46.11	3.16
3279	5162	5.802465	AGGTGATATATTCATCCACTGCTG	58.198	41.667	0.00	0.00	35.96	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	9.030301	GTTTTTAGCTTGCTTTCTTTATCAACA	57.970	29.630	0.00	0.00	0.00	3.33
44	45	2.863809	AGTCCACAGCAGGGTTTTTAG	58.136	47.619	0.00	0.00	0.00	1.85
106	108	9.730420	GTCTTGTAAGTTGTGTCAAATGTTATT	57.270	29.630	0.00	0.00	0.00	1.40
588	729	9.487442	AAATCCTTATTAGGCTTCATACCAAAA	57.513	29.630	0.00	0.00	41.69	2.44
639	845	4.322080	TTGTTCTATAGCGACCTCCATG	57.678	45.455	0.00	0.00	0.00	3.66
707	917	0.036858	GAGGTGCTCTTTCGCCTTCT	60.037	55.000	0.00	0.00	46.22	2.85
742	952	1.396996	CGCCCTAAAATCACTCCGTTG	59.603	52.381	0.00	0.00	0.00	4.10
772	982	6.088824	CAGTTAGCATTTCATTGACAACCTC	58.911	40.000	0.00	0.00	0.00	3.85
812	1022	0.756442	AAGCAGTTCAGCCCAAGCAA	60.756	50.000	0.00	0.00	43.56	3.91
947	1157	0.602638	ATGGTTCGCACTTTCGCTCA	60.603	50.000	0.00	0.00	0.00	4.26
1081	1301	0.036765	GGTCTGGTCGCACATACCAA	60.037	55.000	8.25	0.00	46.14	3.67
1244	1493	0.322322	TCTTCCCGCACGGTACAAAT	59.678	50.000	8.49	0.00	0.00	2.32
1494	1745	5.308825	AGATGGTTAACTGAAGGTCACAAG	58.691	41.667	5.42	0.00	0.00	3.16
1612	1874	4.142945	GCATCTATTGTCCATCGCTTCATC	60.143	45.833	0.00	0.00	0.00	2.92
1674	1936	1.153289	CACGGAGGGCCTTGATCTG	60.153	63.158	7.89	2.03	35.54	2.90
1751	2013	2.232399	TGCATCAACATTGCTGTCACT	58.768	42.857	0.00	0.00	40.77	3.41
1905	2167	2.551097	TTCTTGATGCGCGCCGTCTA	62.551	55.000	30.77	21.01	0.00	2.59
1952	2214	0.743097	GATCCAAGGCCACATTCAGC	59.257	55.000	5.01	0.00	0.00	4.26
2024	2289	2.707791	TCCCCTTCTGCTTCATCCTATG	59.292	50.000	0.00	0.00	0.00	2.23
2031	2296	2.606587	GGCCTCCCCTTCTGCTTCA	61.607	63.158	0.00	0.00	0.00	3.02
2064	2329	3.413846	TGATCTCATATCCAGGCTTGC	57.586	47.619	0.00	0.00	0.00	4.01
2111	2376	4.008074	TGTGCCCTTTCTCTCTACAAAG	57.992	45.455	0.00	0.00	0.00	2.77
2383	2655	2.183679	ACCCCAAAGACAAGCAAAACA	58.816	42.857	0.00	0.00	0.00	2.83
2387	2659	2.582052	CAGTACCCCAAAGACAAGCAA	58.418	47.619	0.00	0.00	0.00	3.91
2391	2663	2.128535	TGTCCAGTACCCCAAAGACAA	58.871	47.619	0.00	0.00	31.70	3.18
2432	2704	5.561125	CCGAAACTAAAACACCGAAATAACG	59.439	40.000	0.00	0.00	0.00	3.18
2563	4165	1.032794	CCACACAGCGAGCTAGGATA	58.967	55.000	0.00	0.00	0.00	2.59
2651	4258	1.807165	AGCATGCGTACGACTGCAG	60.807	57.895	30.94	13.48	45.52	4.41
2672	4283	0.331278	ATCAATTCTGGAACGGCCCA	59.669	50.000	0.00	0.00	34.97	5.36
2740	4351	4.006780	AGCCCCACAACAATTCAAAATC	57.993	40.909	0.00	0.00	0.00	2.17
2943	4554	4.202010	CGATTGGTTTAAATAGCCCACAGG	60.202	45.833	0.00	0.00	0.00	4.00
2944	4555	4.733523	GCGATTGGTTTAAATAGCCCACAG	60.734	45.833	0.00	0.00	33.54	3.66
2945	4556	3.129638	GCGATTGGTTTAAATAGCCCACA	59.870	43.478	0.00	0.00	33.54	4.17
2946	4557	3.380320	AGCGATTGGTTTAAATAGCCCAC	59.620	43.478	0.00	0.00	38.49	4.61
2947	4558	3.380004	CAGCGATTGGTTTAAATAGCCCA	59.620	43.478	0.00	0.00	38.49	5.36
2948	4559	3.243401	CCAGCGATTGGTTTAAATAGCCC	60.243	47.826	0.00	0.00	42.41	5.19
2949	4560	3.243401	CCCAGCGATTGGTTTAAATAGCC	60.243	47.826	5.77	0.00	46.25	3.93
2950	4561	3.380320	ACCCAGCGATTGGTTTAAATAGC	59.620	43.478	0.00	0.00	46.25	2.97
2951	4562	4.638421	TCACCCAGCGATTGGTTTAAATAG	59.362	41.667	0.00	0.00	46.25	1.73
2952	4563	4.590918	TCACCCAGCGATTGGTTTAAATA	58.409	39.130	0.00	0.00	46.25	1.40
2953	4564	3.426615	TCACCCAGCGATTGGTTTAAAT	58.573	40.909	0.00	0.00	46.25	1.40
2954	4565	2.865079	TCACCCAGCGATTGGTTTAAA	58.135	42.857	0.00	0.00	46.25	1.52
2955	4566	2.570415	TCACCCAGCGATTGGTTTAA	57.430	45.000	0.00	0.00	46.25	1.52
2956	4567	2.364632	CATCACCCAGCGATTGGTTTA	58.635	47.619	0.00	0.00	46.25	2.01
3009	4892	2.039084	GAGGAGAGCCAAAGTGAGGAAA	59.961	50.000	0.00	0.00	36.29	3.13
3023	4906	4.465660	TGAATGACTGAGAAAGGAGGAGAG	59.534	45.833	0.00	0.00	0.00	3.20
3030	4913	2.005451	CGGCTGAATGACTGAGAAAGG	58.995	52.381	0.00	0.00	0.00	3.11
3032	4915	2.688507	GACGGCTGAATGACTGAGAAA	58.311	47.619	0.00	0.00	0.00	2.52
3033	4916	1.402852	CGACGGCTGAATGACTGAGAA	60.403	52.381	0.00	0.00	0.00	2.87
3034	4917	0.171231	CGACGGCTGAATGACTGAGA	59.829	55.000	0.00	0.00	0.00	3.27
3038	4921	1.460504	TCTACGACGGCTGAATGACT	58.539	50.000	0.00	0.00	0.00	3.41
3088	4971	5.996644	TGAAACCAACTACAGAGGAGAAAA	58.003	37.500	0.00	0.00	0.00	2.29
3185	5068	1.941734	CAGCTCGCGTGCTACTAGC	60.942	63.158	32.32	19.41	41.98	3.42
3186	5069	0.179161	AACAGCTCGCGTGCTACTAG	60.179	55.000	32.32	22.62	41.98	2.57
3187	5070	0.456142	CAACAGCTCGCGTGCTACTA	60.456	55.000	32.32	0.00	41.98	1.82
3188	5071	1.734477	CAACAGCTCGCGTGCTACT	60.734	57.895	32.32	20.30	41.98	2.57
3189	5072	1.678269	CTCAACAGCTCGCGTGCTAC	61.678	60.000	32.32	5.77	41.98	3.58
3190	5073	1.444383	CTCAACAGCTCGCGTGCTA	60.444	57.895	32.32	17.76	41.98	3.49
3191	5074	2.736236	CTCAACAGCTCGCGTGCT	60.736	61.111	28.37	28.37	45.18	4.40
3192	5075	3.782244	CCTCAACAGCTCGCGTGC	61.782	66.667	24.56	24.56	0.00	5.34
3193	5076	3.782244	GCCTCAACAGCTCGCGTG	61.782	66.667	5.77	4.44	0.00	5.34
3198	5081	2.669569	TTGGCGCCTCAACAGCTC	60.670	61.111	29.70	0.00	0.00	4.09
3199	5082	2.980233	GTTGGCGCCTCAACAGCT	60.980	61.111	29.70	0.00	44.51	4.24
3200	5083	4.389576	CGTTGGCGCCTCAACAGC	62.390	66.667	29.70	7.83	45.16	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.