AutoCloner

Multiple sequence alignment - TraesCS6B01G074900

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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	TraesCS6B01G074900	chr6B	100.000	3810	0	0	1	3810	51436775	51432966	0.000000e+00	7036.0
1	TraesCS6B01G074900	chr6B	93.570	762	39	5	1	753	499897298	499898058	0.000000e+00	1127.0
2	TraesCS6B01G074900	chr6B	85.382	773	101	7	998	1766	51537983	51538747	0.000000e+00	791.0
3	TraesCS6B01G074900	chr6B	77.265	1148	196	49	999	2103	51559011	51560136	7.000000e-172	614.0
4	TraesCS6B01G074900	chr6B	89.888	356	30	3	1919	2274	51553674	51554023	1.610000e-123	453.0
5	TraesCS6B01G074900	chr6B	80.427	562	101	6	998	1556	51732104	51732659	1.640000e-113	420.0
6	TraesCS6B01G074900	chr6B	81.818	154	24	4	1751	1902	49700664	49700513	4.000000e-25	126.0
7	TraesCS6B01G074900	chr6A	94.313	3095	139	10	753	3810	30422348	30425442	0.000000e+00	4706.0
8	TraesCS6B01G074900	chr6A	93.923	757	35	5	4	753	14220473	14219721	0.000000e+00	1133.0
9	TraesCS6B01G074900	chr6A	85.000	900	123	8	1056	1948	30283398	30282504	0.000000e+00	904.0
10	TraesCS6B01G074900	chr6A	84.579	642	74	9	1296	1929	30263664	30263040	7.000000e-172	614.0
11	TraesCS6B01G074900	chr6A	80.475	589	105	6	1011	1594	30036448	30035865	3.490000e-120	442.0
12	TraesCS6B01G074900	chr6A	88.163	245	23	3	2035	2279	30263030	30262792	1.730000e-73	287.0
13	TraesCS6B01G074900	chr6A	74.710	431	89	18	1682	2104	40529018	40528600	1.410000e-39	174.0
14	TraesCS6B01G074900	chr6A	74.663	371	70	22	1744	2104	40622737	40622381	3.970000e-30	143.0
15	TraesCS6B01G074900	chr6A	88.372	86	10	0	2004	2089	30282506	30282421	1.870000e-18	104.0
16	TraesCS6B01G074900	chr6D	95.000	3000	132	11	818	3808	27683908	27680918	0.000000e+00	4693.0
17	TraesCS6B01G074900	chr6D	84.808	1119	138	19	986	2094	27711096	27712192	0.000000e+00	1096.0
18	TraesCS6B01G074900	chr6D	80.331	605	106	8	998	1594	27845337	27845936	2.700000e-121	446.0
19	TraesCS6B01G074900	chr6D	75.472	371	67	19	1744	2104	36324680	36325036	3.940000e-35	159.0
20	TraesCS6B01G074900	chr6D	92.453	53	3	1	2049	2100	27760999	27761051	1.470000e-09	75.0
21	TraesCS6B01G074900	chr5B	98.670	752	8	2	4	755	680365232	680364483	0.000000e+00	1332.0
22	TraesCS6B01G074900	chr5B	93.307	762	41	6	1	754	436737723	436738482	0.000000e+00	1116.0
23	TraesCS6B01G074900	chr7B	98.400	750	12	0	4	753	605879359	605878610	0.000000e+00	1319.0
24	TraesCS6B01G074900	chr7B	93.307	762	36	7	1	753	125758763	125759518	0.000000e+00	1110.0
25	TraesCS6B01G074900	chr1B	98.141	753	13	1	1	753	661993429	661994180	0.000000e+00	1312.0
26	TraesCS6B01G074900	chr1B	93.377	770	35	11	4	763	668057964	668057201	0.000000e+00	1125.0
27	TraesCS6B01G074900	chr3D	93.083	665	35	5	5	662	98141604	98140944	0.000000e+00	963.0
28	TraesCS6B01G074900	chrUn	78.025	405	72	14	1629	2017	80234312	80233909	4.920000e-59	239.0
29	TraesCS6B01G074900	chrUn	78.025	405	72	14	1629	2017	327161051	327161454	4.920000e-59	239.0
30	TraesCS6B01G074900	chrUn	81.752	274	45	3	3017	3285	137673356	137673629	1.380000e-54	224.0
31	TraesCS6B01G074900	chr2B	83.696	184	16	6	576	757	129393874	129393703	1.100000e-35	161.0
32	TraesCS6B01G074900	chr2B	84.286	70	10	1	3665	3733	638635024	638635093	2.460000e-07	67.6

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	TraesCS6B01G074900	chr6B	51432966	51436775	3809	True	7036.0	7036	100.000	1	3810	1	chr6B.!!$R2	3809
1	TraesCS6B01G074900	chr6B	499897298	499898058	760	False	1127.0	1127	93.570	1	753	1	chr6B.!!$F5	752
2	TraesCS6B01G074900	chr6B	51537983	51538747	764	False	791.0	791	85.382	998	1766	1	chr6B.!!$F1	768
3	TraesCS6B01G074900	chr6B	51559011	51560136	1125	False	614.0	614	77.265	999	2103	1	chr6B.!!$F3	1104
4	TraesCS6B01G074900	chr6B	51732104	51732659	555	False	420.0	420	80.427	998	1556	1	chr6B.!!$F4	558
5	TraesCS6B01G074900	chr6A	30422348	30425442	3094	False	4706.0	4706	94.313	753	3810	1	chr6A.!!$F1	3057
6	TraesCS6B01G074900	chr6A	14219721	14220473	752	True	1133.0	1133	93.923	4	753	1	chr6A.!!$R1	749
7	TraesCS6B01G074900	chr6A	30282421	30283398	977	True	504.0	904	86.686	1056	2089	2	chr6A.!!$R6	1033
8	TraesCS6B01G074900	chr6A	30262792	30263664	872	True	450.5	614	86.371	1296	2279	2	chr6A.!!$R5	983
9	TraesCS6B01G074900	chr6A	30035865	30036448	583	True	442.0	442	80.475	1011	1594	1	chr6A.!!$R2	583
10	TraesCS6B01G074900	chr6D	27680918	27683908	2990	True	4693.0	4693	95.000	818	3808	1	chr6D.!!$R1	2990
11	TraesCS6B01G074900	chr6D	27711096	27712192	1096	False	1096.0	1096	84.808	986	2094	1	chr6D.!!$F1	1108
12	TraesCS6B01G074900	chr6D	27845337	27845936	599	False	446.0	446	80.331	998	1594	1	chr6D.!!$F3	596
13	TraesCS6B01G074900	chr5B	680364483	680365232	749	True	1332.0	1332	98.670	4	755	1	chr5B.!!$R1	751
14	TraesCS6B01G074900	chr5B	436737723	436738482	759	False	1116.0	1116	93.307	1	754	1	chr5B.!!$F1	753
15	TraesCS6B01G074900	chr7B	605878610	605879359	749	True	1319.0	1319	98.400	4	753	1	chr7B.!!$R1	749
16	TraesCS6B01G074900	chr7B	125758763	125759518	755	False	1110.0	1110	93.307	1	753	1	chr7B.!!$F1	752
17	TraesCS6B01G074900	chr1B	661993429	661994180	751	False	1312.0	1312	98.141	1	753	1	chr1B.!!$F1	752
18	TraesCS6B01G074900	chr1B	668057201	668057964	763	True	1125.0	1125	93.377	4	763	1	chr1B.!!$R1	759
19	TraesCS6B01G074900	chr3D	98140944	98141604	660	True	963.0	963	93.083	5	662	1	chr3D.!!$R1	657

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
920	984	0.036388	GGCACACTACCTGCTGCTTA	60.036	55.0	0.0	0.0	34.84	3.09	F
1725	1821	0.179121	TAGCGGTGATACAAGTGCCG	60.179	55.0	0.0	0.0	44.60	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2756	2873	0.392863	TCAGCCCCATCATGTTCACG	60.393	55.000	0.0	0.0	0.00	4.35	R
3189	3306	2.353208	CCAGGAGGAGAGAAACTGAACG	60.353	54.545	0.0	0.0	36.89	3.95	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
626	640	5.874810	GGCTCACATACAAATACAGAAGACA	59.125	40.000	0.00	0.00	0.00	3.41
641	655	1.366319	AGACAAGAGAATGGCACCCT	58.634	50.000	0.00	0.00	0.00	4.34
692	708	2.514458	AGAAAGCACGGATCCCAATT	57.486	45.000	6.06	0.00	0.00	2.32
765	781	3.084786	GCTCCACTCATTACAAAAGGCT	58.915	45.455	0.00	0.00	0.00	4.58
919	983	1.302832	GGCACACTACCTGCTGCTT	60.303	57.895	0.00	0.00	34.84	3.91
920	984	0.036388	GGCACACTACCTGCTGCTTA	60.036	55.000	0.00	0.00	34.84	3.09
1039	1107	1.004918	CCGCTGGAGGACGAAAACT	60.005	57.895	0.00	0.00	0.00	2.66
1343	1416	1.081892	CTTGTGCTCATCTCCAACGG	58.918	55.000	0.00	0.00	0.00	4.44
1345	1418	1.262417	TGTGCTCATCTCCAACGGTA	58.738	50.000	0.00	0.00	0.00	4.02
1561	1642	1.179152	TTATTCGTCAGAGACCGGCA	58.821	50.000	0.00	0.00	0.00	5.69
1621	1717	0.388907	TTACTGTACGGGCTTGTCGC	60.389	55.000	6.65	0.00	38.13	5.19
1680	1776	2.564947	TGGGTGTTTTTGTGCTGTTCTT	59.435	40.909	0.00	0.00	0.00	2.52
1710	1806	1.067250	GGAGAGGCAGAGCTTAGCG	59.933	63.158	0.00	0.00	0.00	4.26
1725	1821	0.179121	TAGCGGTGATACAAGTGCCG	60.179	55.000	0.00	0.00	44.60	5.69
1902	2010	7.856415	ACAAGCTACTTTCTCCTTATTCAGAT	58.144	34.615	0.00	0.00	0.00	2.90
1969	2080	1.301479	GTGTTCCTGACGGGTGGTC	60.301	63.158	0.00	0.00	46.27	4.02
2186	2302	8.890124	ATTGATTGTTTTGATGTTTGATGACA	57.110	26.923	0.00	0.00	0.00	3.58
2242	2358	1.086634	GTCCTGATCCTGACGCTTGC	61.087	60.000	0.00	0.00	0.00	4.01
2405	2521	9.317936	TCATTATCACTTCTGTTGCTATTAGTG	57.682	33.333	0.00	0.00	35.51	2.74
2443	2559	4.033472	CGTTTTGTTCAAATGTTGGGGAAC	59.967	41.667	0.00	0.00	39.93	3.62
2512	2629	2.358898	AGTTTGAGCGTGCATGTTCTTT	59.641	40.909	21.41	4.23	0.00	2.52
2621	2738	5.422666	TGTTGTATCAAAGCTGAGTTGTG	57.577	39.130	0.00	0.00	34.23	3.33
2676	2793	4.921470	ATATCGTGTTGGTGTTTTCTCG	57.079	40.909	0.00	0.00	0.00	4.04
2810	2927	2.095059	CCACAAGTGATTGCCTGTTAGC	60.095	50.000	0.94	0.00	0.00	3.09
2860	2977	6.122277	AGCAGGTAAGCTTATTTTCTGCATA	58.878	36.000	31.49	5.35	43.70	3.14
2893	3010	9.922305	GAGGTATATTGAAATGTTCTTTCGAAG	57.078	33.333	0.00	0.00	0.00	3.79
2948	3065	5.620206	TCAGTTACCAAATTGCAAGAGAGA	58.380	37.500	4.94	0.00	0.00	3.10
3189	3306	1.467920	CTTCCATCCAGTTCCCTTGC	58.532	55.000	0.00	0.00	0.00	4.01
3277	3394	0.460722	GCGGGTTCTTCTCCCTCTAC	59.539	60.000	0.00	0.00	42.56	2.59
3289	3406	3.529734	TCTCCCTCTACCTTCTCAGATGT	59.470	47.826	0.00	0.00	0.00	3.06
3290	3407	4.017037	TCTCCCTCTACCTTCTCAGATGTT	60.017	45.833	0.00	0.00	0.00	2.71
3402	3520	8.080417	GTGATTCGCTATTGGACACTAGTATAA	58.920	37.037	0.00	0.00	0.00	0.98
3563	3682	5.381757	TGGTAGTACAAGCCTTTCACAAAT	58.618	37.500	2.06	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
626	640	4.322057	AATACAAGGGTGCCATTCTCTT	57.678	40.909	0.00	0.00	0.00	2.85
677	693	0.181350	GAGGAATTGGGATCCGTGCT	59.819	55.000	5.45	1.26	42.03	4.40
809	838	1.705186	AGGAAGTTTCAGCCTTGCCTA	59.295	47.619	0.00	0.00	31.32	3.93
1176	1245	2.042230	TAACCGAGGAGGGGAGGC	60.042	66.667	0.00	0.00	46.96	4.70
1229	1298	0.108019	GTCGGGGGAATCCATGGTAC	59.892	60.000	12.58	4.41	37.22	3.34
1343	1416	1.429463	CAGGACTTGCTTCCGTGTAC	58.571	55.000	0.00	0.00	41.04	2.90
1345	1418	1.071471	CCAGGACTTGCTTCCGTGT	59.929	57.895	0.00	0.00	41.04	4.49
1561	1642	4.593206	TGTTAAGATAAGATCGCCCCATCT	59.407	41.667	0.00	0.00	34.34	2.90
1621	1717	1.173913	GAATTCCCAACCAAGACGGG	58.826	55.000	0.00	0.00	41.76	5.28
1626	1722	5.279456	CCAGTAAAAGGAATTCCCAACCAAG	60.279	44.000	21.22	6.91	37.41	3.61
1680	1776	3.072915	TCTGCCTCTCCAAATCAAACTCA	59.927	43.478	0.00	0.00	0.00	3.41
1710	1806	0.802494	CAACCGGCACTTGTATCACC	59.198	55.000	0.00	0.00	0.00	4.02
1725	1821	3.536570	GAAGCTATTCTCCTCACCAACC	58.463	50.000	0.00	0.00	32.33	3.77
1902	2010	0.975556	TGAATAGGGGCGCAGTCTCA	60.976	55.000	10.83	0.43	0.00	3.27
1969	2080	2.615447	GCTGTACCATGATGACACCATG	59.385	50.000	2.41	2.41	40.66	3.66
2242	2358	3.421741	CATTACATAAAACGGCACCACG	58.578	45.455	0.00	0.00	40.31	4.94
2376	2492	8.798859	AATAGCAACAGAAGTGATAATGACTT	57.201	30.769	0.00	0.00	36.33	3.01
2405	2521	7.739295	TGAACAAAACGAAGCTCATACTAATC	58.261	34.615	0.00	0.00	0.00	1.75
2443	2559	9.931210	AGTTGTCTAGAATTGTTTTTAAACTCG	57.069	29.630	0.00	0.00	39.59	4.18
2494	2611	4.764679	AATAAAGAACATGCACGCTCAA	57.235	36.364	0.00	0.00	0.00	3.02
2499	2616	7.719689	ATCGTAAAAATAAAGAACATGCACG	57.280	32.000	0.00	0.00	0.00	5.34
2594	2711	7.445402	ACAACTCAGCTTTGATACAACAATAGT	59.555	33.333	3.66	0.00	0.00	2.12
2621	2738	8.856490	AACTGACATGTGTAATTTGAGAAAAC	57.144	30.769	1.15	0.00	0.00	2.43
2660	2777	2.676342	AGACACGAGAAAACACCAACAC	59.324	45.455	0.00	0.00	0.00	3.32
2756	2873	0.392863	TCAGCCCCATCATGTTCACG	60.393	55.000	0.00	0.00	0.00	4.35
2802	2919	8.663025	CACATCATAATAAGCATAGCTAACAGG	58.337	37.037	0.00	0.00	38.25	4.00
2810	2927	7.173735	TCAACCAGCACATCATAATAAGCATAG	59.826	37.037	0.00	0.00	0.00	2.23
2919	3036	5.843673	TGCAATTTGGTAACTGAGAAACA	57.156	34.783	0.00	0.00	37.61	2.83
2924	3041	5.702670	TCTCTCTTGCAATTTGGTAACTGAG	59.297	40.000	0.00	0.00	37.61	3.35
2928	3045	6.319141	AGTTCTCTCTTGCAATTTGGTAAC	57.681	37.500	0.00	1.30	0.00	2.50
2964	3081	3.290710	ACAACTGAGCCAAGTGTCAAAT	58.709	40.909	0.00	0.00	0.00	2.32
2966	3083	2.418368	ACAACTGAGCCAAGTGTCAA	57.582	45.000	0.00	0.00	0.00	3.18
3189	3306	2.353208	CCAGGAGGAGAGAAACTGAACG	60.353	54.545	0.00	0.00	36.89	3.95
3277	3394	5.399858	CAAGCAATTGAACATCTGAGAAGG	58.600	41.667	10.34	0.00	0.00	3.46
3402	3520	8.268850	CTACATGTAGCTTAAACCAGACAAAT	57.731	34.615	19.55	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.