AutoCloner

Multiple sequence alignment - TraesCS4B01G154800

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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	TraesCS4B01G154800	chr4B	100.000	2594	0	0	1	2594	273958918	273961511	0.000000e+00	4791
1	TraesCS4B01G154800	chr4B	92.284	1620	71	26	2	1567	167378792	167377173	0.000000e+00	2250
2	TraesCS4B01G154800	chr4B	96.120	1031	35	3	1569	2594	167375798	167374768	0.000000e+00	1677
3	TraesCS4B01G154800	chr7B	93.511	1572	91	9	1	1567	660101282	660102847	0.000000e+00	2327
4	TraesCS4B01G154800	chr3B	92.694	1574	84	16	1	1567	228014312	228015861	0.000000e+00	2241
5	TraesCS4B01G154800	chr3B	87.248	894	76	10	687	1567	821214090	821213222	0.000000e+00	985
6	TraesCS4B01G154800	chr6D	95.414	1330	54	5	241	1567	39065751	39064426	0.000000e+00	2111
7	TraesCS4B01G154800	chr6D	96.023	1031	36	3	1569	2594	39063334	39062304	0.000000e+00	1672
8	TraesCS4B01G154800	chr6D	87.943	141	7	4	1	132	39066295	39066156	9.610000e-35	158
9	TraesCS4B01G154800	chr2B	95.331	1328	61	1	241	1567	311925659	311924332	0.000000e+00	2108
10	TraesCS4B01G154800	chr2B	84.375	384	50	8	1	379	311925949	311925571	4.080000e-98	368
11	TraesCS4B01G154800	chr6A	95.131	1335	58	5	239	1567	603905460	603906793	0.000000e+00	2098
12	TraesCS4B01G154800	chr3A	94.327	1322	57	6	251	1567	144697447	144698755	0.000000e+00	2010
13	TraesCS4B01G154800	chr3A	96.132	1034	35	3	1566	2594	126054214	126055247	0.000000e+00	1683
14	TraesCS4B01G154800	chr3A	96.035	1034	36	3	1566	2594	144700616	144701649	0.000000e+00	1677
15	TraesCS4B01G154800	chr3A	82.967	364	26	15	1	330	144696819	144697180	1.950000e-76	296
16	TraesCS4B01G154800	chr4A	93.994	1332	50	5	241	1567	147536178	147534872	0.000000e+00	1989
17	TraesCS4B01G154800	chr4A	95.829	1031	38	3	1569	2594	147533035	147532005	0.000000e+00	1661
18	TraesCS4B01G154800	chr4A	93.333	1125	65	8	444	1567	410961461	410960346	0.000000e+00	1653
19	TraesCS4B01G154800	chr4A	82.082	413	37	16	1	379	147536550	147536141	4.170000e-83	318
20	TraesCS4B01G154800	chr7A	94.140	1314	57	10	260	1567	542714340	542715639	0.000000e+00	1982
21	TraesCS4B01G154800	chr7A	96.228	1034	34	3	1566	2594	542717501	542718534	0.000000e+00	1688
22	TraesCS4B01G154800	chr1A	94.910	1277	47	8	296	1567	564160204	564158941	0.000000e+00	1982
23	TraesCS4B01G154800	chr1A	96.411	1031	32	3	1569	2594	564157076	564156046	0.000000e+00	1694
24	TraesCS4B01G154800	chr1A	86.957	207	15	8	1	198	564160940	564160737	3.360000e-54	222
25	TraesCS4B01G154800	chr1A	89.231	130	10	2	151	276	564160760	564160631	2.670000e-35	159
26	TraesCS4B01G154800	chr2D	96.217	1031	33	4	1569	2594	618321854	618320825	0.000000e+00	1683
27	TraesCS4B01G154800	chr2D	84.024	338	39	11	1	330	618325368	618325038	6.970000e-81	311
28	TraesCS4B01G154800	chr6B	95.745	1034	39	3	1566	2594	18468429	18469462	0.000000e+00	1661
29	TraesCS4B01G154800	chr6B	96.076	892	31	3	680	1567	18463701	18462810	0.000000e+00	1450
30	TraesCS4B01G154800	chr6B	95.291	892	38	3	680	1567	18465676	18466567	0.000000e+00	1411
31	TraesCS4B01G154800	chr6B	84.715	386	47	9	1	379	18464357	18463977	2.440000e-100	375
32	TraesCS4B01G154800	chr6B	82.834	367	55	7	18	379	18465037	18465400	3.220000e-84	322

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	TraesCS4B01G154800	chr4B	273958918	273961511	2593	False	4791.000000	4791	100.000000	1	2594	1	chr4B.!!$F1	2593
1	TraesCS4B01G154800	chr4B	167374768	167378792	4024	True	1963.500000	2250	94.202000	2	2594	2	chr4B.!!$R1	2592
2	TraesCS4B01G154800	chr7B	660101282	660102847	1565	False	2327.000000	2327	93.511000	1	1567	1	chr7B.!!$F1	1566
3	TraesCS4B01G154800	chr3B	228014312	228015861	1549	False	2241.000000	2241	92.694000	1	1567	1	chr3B.!!$F1	1566
4	TraesCS4B01G154800	chr3B	821213222	821214090	868	True	985.000000	985	87.248000	687	1567	1	chr3B.!!$R1	880
5	TraesCS4B01G154800	chr6D	39062304	39066295	3991	True	1313.666667	2111	93.126667	1	2594	3	chr6D.!!$R1	2593
6	TraesCS4B01G154800	chr2B	311924332	311925949	1617	True	1238.000000	2108	89.853000	1	1567	2	chr2B.!!$R1	1566
7	TraesCS4B01G154800	chr6A	603905460	603906793	1333	False	2098.000000	2098	95.131000	239	1567	1	chr6A.!!$F1	1328
8	TraesCS4B01G154800	chr3A	126054214	126055247	1033	False	1683.000000	1683	96.132000	1566	2594	1	chr3A.!!$F1	1028
9	TraesCS4B01G154800	chr3A	144696819	144701649	4830	False	1327.666667	2010	91.109667	1	2594	3	chr3A.!!$F2	2593
10	TraesCS4B01G154800	chr4A	410960346	410961461	1115	True	1653.000000	1653	93.333000	444	1567	1	chr4A.!!$R1	1123
11	TraesCS4B01G154800	chr4A	147532005	147536550	4545	True	1322.666667	1989	90.635000	1	2594	3	chr4A.!!$R2	2593
12	TraesCS4B01G154800	chr7A	542714340	542718534	4194	False	1835.000000	1982	95.184000	260	2594	2	chr7A.!!$F1	2334
13	TraesCS4B01G154800	chr1A	564156046	564160940	4894	True	1014.250000	1982	91.877250	1	2594	4	chr1A.!!$R1	2593
14	TraesCS4B01G154800	chr2D	618320825	618325368	4543	True	997.000000	1683	90.120500	1	2594	2	chr2D.!!$R1	2593
15	TraesCS4B01G154800	chr6B	18465037	18469462	4425	False	1131.333333	1661	91.290000	18	2594	3	chr6B.!!$F1	2576
16	TraesCS4B01G154800	chr6B	18462810	18464357	1547	True	912.500000	1450	90.395500	1	1567	2	chr6B.!!$R1	1566

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
151	183	0.171903	GACCTAAACCTAGCGCGACA	59.828	55.0	12.1	0.00	0.0	4.35	F
152	184	0.172803	ACCTAAACCTAGCGCGACAG	59.827	55.0	12.1	5.16	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1285	2485	2.435069	CCTCTGACATGCTCTCATCCTT	59.565	50.000	0.0	0.0	0.00	3.36	R
2126	5693	3.261643	TGAGAATCACAAGCTAAGCCTCA	59.738	43.478	0.0	0.0	42.56	3.86	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
119	151	4.750695	TCTGCCCCCGATTCCCCA	62.751	66.667	0.00	0.00	0.00	4.96
149	181	0.737219	GAGACCTAAACCTAGCGCGA	59.263	55.000	12.10	0.00	0.00	5.87
150	182	0.455005	AGACCTAAACCTAGCGCGAC	59.545	55.000	12.10	0.04	0.00	5.19
151	183	0.171903	GACCTAAACCTAGCGCGACA	59.828	55.000	12.10	0.00	0.00	4.35
152	184	0.172803	ACCTAAACCTAGCGCGACAG	59.827	55.000	12.10	5.16	0.00	3.51
153	185	1.146358	CCTAAACCTAGCGCGACAGC	61.146	60.000	12.10	0.00	40.74	4.40
311	1317	2.763215	GAGGTGGCAATGGTGGGA	59.237	61.111	0.00	0.00	0.00	4.37
342	1348	1.593209	GCCAACCTGTTGACGACGA	60.593	57.895	11.47	0.00	42.93	4.20
351	1357	1.299544	TTGACGACGAGCAAAGCGA	60.300	52.632	0.00	0.00	0.00	4.93
425	1431	1.227883	TCGGCCTTGCGTGGTAAAA	60.228	52.632	0.00	0.00	0.00	1.52
482	1488	1.227147	GCGGCTACATCGGCTTGTA	60.227	57.895	0.00	0.00	0.00	2.41
541	1547	7.050377	CAGATTACTTAGAGATGGCCTTGAAA	58.950	38.462	3.32	0.00	0.00	2.69
604	1610	5.451242	GCACCTCTCTTCTAGATTTGTCGAT	60.451	44.000	0.00	0.00	32.41	3.59
611	1618	8.363390	TCTCTTCTAGATTTGTCGATATGCAAT	58.637	33.333	0.00	0.00	0.00	3.56
652	1678	7.991084	TCATTTAGAGATGGATATTTGCTGG	57.009	36.000	0.00	0.00	0.00	4.85
671	1697	7.383102	TGCTGGAAAATCTGAATTTAGAGAC	57.617	36.000	6.09	0.00	33.93	3.36
1273	2473	0.895559	TGAGAGCGAGGTTGAGAGCA	60.896	55.000	0.00	0.00	0.00	4.26
1285	2485	1.565067	TGAGAGCAAGGATGAGAGCA	58.435	50.000	0.00	0.00	0.00	4.26
1327	2527	5.584913	AGGTTGAAGTAGAGGAAGATGAGA	58.415	41.667	0.00	0.00	0.00	3.27
1414	2614	8.217799	ACGAAGGAAGAAAATATCCCAATATGA	58.782	33.333	0.00	0.00	36.31	2.15
1514	2715	7.665559	ACATAGGTTCAGAGCTTATTGTTCAAA	59.334	33.333	0.00	0.00	34.88	2.69
1542	2743	4.142609	TGAAGATAAGTGTCCATGGAGC	57.857	45.455	16.81	11.50	0.00	4.70
1654	5216	9.450807	CAACTACGAAAAAGAGAAAACATGATT	57.549	29.630	0.00	0.00	0.00	2.57
1971	5537	2.136298	TGTGTGGCCAACAAGAAAGA	57.864	45.000	7.24	0.00	41.57	2.52
2126	5693	3.311106	CAATGAGCACACGAAGCAAAAT	58.689	40.909	0.00	0.00	0.00	1.82
2192	5759	7.826252	TCATGGTTCATTTTGGAAACTTTTGAA	59.174	29.630	0.00	0.00	35.50	2.69
2289	5856	7.220030	ACATGATGTGAACCTGGACTATTATC	58.780	38.462	0.00	0.00	0.00	1.75
2341	5908	7.068348	TGTGTAGAGGACTAAATATGTGGACTC	59.932	40.741	0.00	0.00	0.00	3.36
2374	5941	3.288092	GTGAACCTGGACCAAGTTTCTT	58.712	45.455	9.86	0.00	0.00	2.52
2449	6016	3.679980	CGCATATATGAACTGTACAGGGC	59.320	47.826	26.12	17.22	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.003897	GGTGTTAACGGCAAAGAATGACA	59.996	43.478	0.26	0.00	36.57	3.58
119	151	1.232909	TTAGGTCTCGGGGAGGAGAT	58.767	55.000	0.00	0.00	44.34	2.75
162	194	2.580867	CTGCTACGTGCCTCGCTC	60.581	66.667	0.00	0.00	44.19	5.03
163	195	4.803426	GCTGCTACGTGCCTCGCT	62.803	66.667	0.00	0.00	44.19	4.93
222	305	2.610859	ATGGCCCTCGTCCACCTT	60.611	61.111	0.00	0.00	36.26	3.50
302	1308	4.060667	CCCCGCCTTCCCACCATT	62.061	66.667	0.00	0.00	0.00	3.16
342	1348	1.973281	CCACCATGGTCGCTTTGCT	60.973	57.895	16.53	0.00	31.35	3.91
409	1415	1.080772	GCTTTTACCACGCAAGGCC	60.081	57.895	0.00	0.00	46.39	5.19
425	1431	4.393155	TTGCTCCGGTGATGCGCT	62.393	61.111	9.73	0.00	0.00	5.92
431	1437	3.551496	CTTGGCCTTGCTCCGGTGA	62.551	63.158	7.92	0.00	0.00	4.02
541	1547	7.449704	GCATTTGGGATCCATCTCTAAGTAATT	59.550	37.037	15.23	0.00	31.53	1.40
652	1678	7.041712	GGGATCCGTCTCTAAATTCAGATTTTC	60.042	40.741	5.45	0.00	36.82	2.29
671	1697	1.462616	TGAGTTGCATTTGGGATCCG	58.537	50.000	5.45	0.00	0.00	4.18
841	1975	5.810587	GCTCTACGATTGATTCAACCAAGTA	59.189	40.000	0.15	3.70	0.00	2.24
965	2102	6.583912	TTGTCTTAGAGTGTTTCTCAAACG	57.416	37.500	0.00	0.00	44.98	3.60
1079	2216	7.797038	TCATCATCATCTTGTTCTATGTTGG	57.203	36.000	0.00	0.00	0.00	3.77
1273	2473	3.382278	TCTCATCCTTGCTCTCATCCTT	58.618	45.455	0.00	0.00	0.00	3.36
1285	2485	2.435069	CCTCTGACATGCTCTCATCCTT	59.565	50.000	0.00	0.00	0.00	3.36
1327	2527	3.750130	GCATGATCTGCCTCGTGATATTT	59.250	43.478	0.00	0.00	45.66	1.40
1414	2614	4.278419	AGAAAGCGCCAATTTAAACTCTGT	59.722	37.500	2.29	0.00	0.00	3.41
1514	2715	5.779241	TGGACACTTATCTTCATCCCTTT	57.221	39.130	0.00	0.00	0.00	3.11
1542	2743	9.662947	TGATCTTCCATTGTAGAAGCATATATG	57.337	33.333	8.45	8.45	40.48	1.78
1654	5216	5.248477	ACCTTTTTGATGCTCCAGTAGAGTA	59.752	40.000	0.00	0.00	45.21	2.59
1701	5266	7.631717	AAACCAAGCTTTCATCTAATCTACC	57.368	36.000	0.00	0.00	0.00	3.18
1873	5438	7.863722	TCACATATAGTAGCCCAGGTTAAAAA	58.136	34.615	0.00	0.00	0.00	1.94
1971	5537	6.369615	GGCATGTAATTTCAAAGCAACAGATT	59.630	34.615	12.53	0.00	0.00	2.40
2126	5693	3.261643	TGAGAATCACAAGCTAAGCCTCA	59.738	43.478	0.00	0.00	42.56	3.86
2289	5856	5.139435	TCAGGTTCACATAGAGTTCACAG	57.861	43.478	0.00	0.00	0.00	3.66
2341	5908	4.034048	GTCCAGGTTCACATATACGCAAAG	59.966	45.833	0.00	0.00	0.00	2.77
2374	5941	8.409371	TCACATGTATGCAAACTAAAAGTTCAA	58.591	29.630	0.00	0.00	37.47	2.69
2423	5990	5.409520	CCTGTACAGTTCATATATGCGCAAT	59.590	40.000	17.11	12.19	0.00	3.56
2427	5994	3.679980	GCCCTGTACAGTTCATATATGCG	59.320	47.826	21.18	1.61	0.00	4.73
2449	6016	9.745018	ACCTCCCTTGTATTTTGATGATATATG	57.255	33.333	0.00	0.00	0.00	1.78
2516	6083	4.686191	ACCAAATGAAACCAAATCTGCA	57.314	36.364	0.00	0.00	0.00	4.41
2557	6124	5.711506	AGTCAAAAGCAATGGTGATGTGATA	59.288	36.000	0.00	0.00	0.00	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.