AutoCloner

Multiple sequence alignment - TraesCS5D01G045900

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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	TraesCS5D01G045900	chr5D	100.000	3318	0	0	1	3318	45042691	45039374	0.000000e+00	6128.0
1	TraesCS5D01G045900	chr5D	95.918	49	1	1	2378	2425	388860955	388861003	9.870000e-11	78.7
2	TraesCS5D01G045900	chr2D	96.013	953	31	6	2369	3318	31013497	31012549	0.000000e+00	1543.0
3	TraesCS5D01G045900	chr5B	89.975	1197	85	13	1053	2244	45023899	45022733	0.000000e+00	1513.0
4	TraesCS5D01G045900	chr5B	86.439	1202	121	15	1113	2288	45026380	45025195	0.000000e+00	1279.0
5	TraesCS5D01G045900	chr5B	87.014	1055	107	12	1089	2128	44891116	44892155	0.000000e+00	1162.0
6	TraesCS5D01G045900	chr5B	97.426	272	6	1	366	637	271155268	271154998	2.330000e-126	462.0
7	TraesCS5D01G045900	chr5B	91.212	330	27	2	1767	2096	45002606	45002279	6.530000e-122	448.0
8	TraesCS5D01G045900	chr5B	88.199	161	12	5	804	963	45024095	45023941	5.650000e-43	185.0
9	TraesCS5D01G045900	chr5B	81.910	199	18	11	52	241	271155859	271155670	5.730000e-33	152.0
10	TraesCS5D01G045900	chr7D	91.860	946	67	10	2378	3318	147687444	147686504	0.000000e+00	1312.0
11	TraesCS5D01G045900	chr5A	96.159	807	23	2	1	799	439846333	439845527	0.000000e+00	1312.0
12	TraesCS5D01G045900	chr5A	86.535	557	41	9	1045	1580	35734292	35733749	1.720000e-162	582.0
13	TraesCS5D01G045900	chr5A	90.141	426	34	1	1742	2159	35700549	35700124	6.260000e-152	547.0
14	TraesCS5D01G045900	chr5A	85.714	182	15	6	623	795	345757590	345757411	7.310000e-42	182.0
15	TraesCS5D01G045900	chr5A	97.143	70	2	0	1582	1651	35700943	35700874	5.810000e-23	119.0
16	TraesCS5D01G045900	chr2A	95.931	811	24	3	1	803	43669478	43670287	0.000000e+00	1306.0
17	TraesCS5D01G045900	chr2A	91.099	955	53	18	2382	3318	47316062	47317002	0.000000e+00	1264.0
18	TraesCS5D01G045900	chr2A	91.573	178	7	4	626	795	43663208	43663385	4.280000e-59	239.0
19	TraesCS5D01G045900	chr2A	85.185	189	17	7	616	795	762400049	762400235	2.030000e-42	183.0
20	TraesCS5D01G045900	chr1B	95.037	806	30	5	1	798	623270208	623271011	0.000000e+00	1258.0
21	TraesCS5D01G045900	chr1B	90.055	181	10	2	623	795	623242671	623242851	9.260000e-56	228.0
22	TraesCS5D01G045900	chr1B	95.918	49	1	1	2378	2425	481324978	481325026	9.870000e-11	78.7
23	TraesCS5D01G045900	chr1B	92.157	51	2	2	2379	2427	32992227	32992177	1.650000e-08	71.3
24	TraesCS5D01G045900	chr4D	90.093	969	58	24	2378	3318	234705180	234706138	0.000000e+00	1223.0
25	TraesCS5D01G045900	chr6B	95.956	272	11	0	366	637	342808008	342808279	3.040000e-120	442.0
26	TraesCS5D01G045900	chr6B	91.071	56	3	2	2371	2425	162605372	162605318	1.280000e-09	75.0
27	TraesCS5D01G045900	chrUn	81.628	430	65	11	2814	3232	134381839	134382265	8.810000e-91	344.0
28	TraesCS5D01G045900	chr7A	80.886	429	64	12	2814	3232	470919701	470920121	4.130000e-84	322.0
29	TraesCS5D01G045900	chr7A	78.937	508	69	22	2733	3234	598329257	598329732	8.940000e-81	311.0
30	TraesCS5D01G045900	chr4A	78.917	517	74	21	2720	3232	532840228	532840713	5.340000e-83	318.0
31	TraesCS5D01G045900	chr4A	81.991	211	19	12	599	796	690237096	690237300	9.530000e-36	161.0
32	TraesCS5D01G045900	chr1D	78.351	485	77	21	2810	3274	192574202	192573726	4.190000e-74	289.0
33	TraesCS5D01G045900	chr2B	88.947	190	12	4	614	795	439913200	439913388	3.330000e-55	226.0
34	TraesCS5D01G045900	chr2B	89.326	178	10	5	626	795	439894513	439894689	7.210000e-52	215.0
35	TraesCS5D01G045900	chr2B	85.641	195	16	6	610	795	563618831	563618640	9.390000e-46	195.0
36	TraesCS5D01G045900	chr4B	87.179	156	11	5	649	795	86708806	86708961	5.690000e-38	169.0
37	TraesCS5D01G045900	chr3B	81.132	212	24	10	599	798	825991296	825991503	4.430000e-34	156.0

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	TraesCS5D01G045900	chr5D	45039374	45042691	3317	True	6128.000000	6128	100.000000	1	3318	1	chr5D.!!$R1	3317
1	TraesCS5D01G045900	chr2D	31012549	31013497	948	True	1543.000000	1543	96.013000	2369	3318	1	chr2D.!!$R1	949
2	TraesCS5D01G045900	chr5B	44891116	44892155	1039	False	1162.000000	1162	87.014000	1089	2128	1	chr5B.!!$F1	1039
3	TraesCS5D01G045900	chr5B	45022733	45026380	3647	True	992.333333	1513	88.204333	804	2288	3	chr5B.!!$R2	1484
4	TraesCS5D01G045900	chr5B	271154998	271155859	861	True	307.000000	462	89.668000	52	637	2	chr5B.!!$R3	585
5	TraesCS5D01G045900	chr7D	147686504	147687444	940	True	1312.000000	1312	91.860000	2378	3318	1	chr7D.!!$R1	940
6	TraesCS5D01G045900	chr5A	439845527	439846333	806	True	1312.000000	1312	96.159000	1	799	1	chr5A.!!$R3	798
7	TraesCS5D01G045900	chr5A	35733749	35734292	543	True	582.000000	582	86.535000	1045	1580	1	chr5A.!!$R1	535
8	TraesCS5D01G045900	chr5A	35700124	35700943	819	True	333.000000	547	93.642000	1582	2159	2	chr5A.!!$R4	577
9	TraesCS5D01G045900	chr2A	43669478	43670287	809	False	1306.000000	1306	95.931000	1	803	1	chr2A.!!$F2	802
10	TraesCS5D01G045900	chr2A	47316062	47317002	940	False	1264.000000	1264	91.099000	2382	3318	1	chr2A.!!$F3	936
11	TraesCS5D01G045900	chr1B	623270208	623271011	803	False	1258.000000	1258	95.037000	1	798	1	chr1B.!!$F3	797
12	TraesCS5D01G045900	chr4D	234705180	234706138	958	False	1223.000000	1223	90.093000	2378	3318	1	chr4D.!!$F1	940

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
969	1262	0.102481	CGTATGCCTCCTAACACGCT	59.898	55.0	0.00	0.00	0.00	5.07	F
1019	1312	0.104304	ACCTTCGAAGACGTGCTTGT	59.896	50.0	26.61	9.97	36.83	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2071	5154	0.253044	AGCATCCACACCGCATTACT	59.747	50.0	0.0	0.0	0.0	2.24	R
2594	5688	0.690762	ACCACCGTACAATGAAGCCT	59.309	50.0	0.0	0.0	0.0	4.58	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
243	251	2.202349	GTCGCGTTTGCTGCCATC	60.202	61.111	5.77	0.00	39.65	3.51
330	490	2.125753	GCTGTGTCGCCTGAGAGG	60.126	66.667	0.00	0.00	38.80	3.69
726	1011	5.418840	CCCTCATTACAAGGCAGTTACAAAT	59.581	40.000	0.00	0.00	32.15	2.32
727	1012	6.404734	CCCTCATTACAAGGCAGTTACAAATC	60.405	42.308	0.00	0.00	32.15	2.17
729	1014	6.908825	TCATTACAAGGCAGTTACAAATCAC	58.091	36.000	0.00	0.00	0.00	3.06
730	1015	6.714810	TCATTACAAGGCAGTTACAAATCACT	59.285	34.615	0.00	0.00	0.00	3.41
732	1017	4.718961	ACAAGGCAGTTACAAATCACTCT	58.281	39.130	0.00	0.00	0.00	3.24
733	1018	4.757149	ACAAGGCAGTTACAAATCACTCTC	59.243	41.667	0.00	0.00	0.00	3.20
735	1020	4.573900	AGGCAGTTACAAATCACTCTCTG	58.426	43.478	0.00	0.00	0.00	3.35
810	1103	9.603921	AATTCCTAACAATATTGATGCAAAAGG	57.396	29.630	22.16	12.69	0.00	3.11
811	1104	6.572519	TCCTAACAATATTGATGCAAAAGGC	58.427	36.000	22.16	0.00	45.13	4.35
823	1116	3.764885	GCAAAAGGCACACTACTATGG	57.235	47.619	0.00	0.00	43.97	2.74
824	1117	3.343617	GCAAAAGGCACACTACTATGGA	58.656	45.455	0.00	0.00	43.97	3.41
825	1118	3.756434	GCAAAAGGCACACTACTATGGAA	59.244	43.478	0.00	0.00	43.97	3.53
826	1119	4.217550	GCAAAAGGCACACTACTATGGAAA	59.782	41.667	0.00	0.00	43.97	3.13
827	1120	5.278758	GCAAAAGGCACACTACTATGGAAAA	60.279	40.000	0.00	0.00	43.97	2.29
828	1121	5.959618	AAAGGCACACTACTATGGAAAAC	57.040	39.130	0.00	0.00	0.00	2.43
829	1122	4.634012	AGGCACACTACTATGGAAAACA	57.366	40.909	0.00	0.00	0.00	2.83
830	1123	5.179452	AGGCACACTACTATGGAAAACAT	57.821	39.130	0.00	0.00	43.68	2.71
831	1124	4.943705	AGGCACACTACTATGGAAAACATG	59.056	41.667	0.00	0.00	40.82	3.21
832	1125	4.438744	GGCACACTACTATGGAAAACATGC	60.439	45.833	0.00	0.00	40.82	4.06
833	1126	4.396166	GCACACTACTATGGAAAACATGCT	59.604	41.667	0.00	0.00	40.82	3.79
834	1127	5.106157	GCACACTACTATGGAAAACATGCTT	60.106	40.000	0.00	0.00	40.82	3.91
835	1128	6.570378	GCACACTACTATGGAAAACATGCTTT	60.570	38.462	0.00	0.00	40.82	3.51
836	1129	7.370383	CACACTACTATGGAAAACATGCTTTT	58.630	34.615	0.00	1.12	40.82	2.27

Showing 1 to 25 of 290 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
268	350	3.642778	TTACTCCCAGCAGCGCGTC	62.643	63.158	8.43	0.00	0.00	5.19
330	490	1.520787	CAACCACCGGCCGAGTATC	60.521	63.158	30.73	0.00	0.00	2.24
726	1011	1.607801	CGGTGGCCATCAGAGAGTGA	61.608	60.000	18.15	0.00	40.38	3.41
727	1012	1.153489	CGGTGGCCATCAGAGAGTG	60.153	63.158	18.15	0.00	0.00	3.51
729	1014	1.142748	GTCGGTGGCCATCAGAGAG	59.857	63.158	18.15	0.00	0.00	3.20
730	1015	0.977627	ATGTCGGTGGCCATCAGAGA	60.978	55.000	18.15	13.07	0.00	3.10
732	1017	0.752658	CTATGTCGGTGGCCATCAGA	59.247	55.000	18.15	11.61	0.00	3.27
733	1018	0.882042	GCTATGTCGGTGGCCATCAG	60.882	60.000	18.15	9.21	0.00	2.90
735	1020	0.250467	ATGCTATGTCGGTGGCCATC	60.250	55.000	9.72	7.61	0.00	3.51
803	1096	3.343617	TCCATAGTAGTGTGCCTTTTGC	58.656	45.455	0.00	0.00	41.77	3.68
804	1097	5.957842	TTTCCATAGTAGTGTGCCTTTTG	57.042	39.130	0.00	0.00	0.00	2.44
805	1098	5.830991	TGTTTTCCATAGTAGTGTGCCTTTT	59.169	36.000	0.00	0.00	0.00	2.27
806	1099	5.381757	TGTTTTCCATAGTAGTGTGCCTTT	58.618	37.500	0.00	0.00	0.00	3.11
807	1100	4.980573	TGTTTTCCATAGTAGTGTGCCTT	58.019	39.130	0.00	0.00	0.00	4.35
808	1101	4.634012	TGTTTTCCATAGTAGTGTGCCT	57.366	40.909	0.00	0.00	0.00	4.75
809	1102	4.438744	GCATGTTTTCCATAGTAGTGTGCC	60.439	45.833	0.00	0.00	30.71	5.01
810	1103	4.396166	AGCATGTTTTCCATAGTAGTGTGC	59.604	41.667	0.00	0.00	30.71	4.57
811	1104	6.500684	AAGCATGTTTTCCATAGTAGTGTG	57.499	37.500	0.00	0.00	30.71	3.82
812	1105	7.230510	TCAAAAGCATGTTTTCCATAGTAGTGT	59.769	33.333	8.06	0.00	30.71	3.55
813	1106	7.592938	TCAAAAGCATGTTTTCCATAGTAGTG	58.407	34.615	8.06	0.25	30.71	2.74
814	1107	7.759489	TCAAAAGCATGTTTTCCATAGTAGT	57.241	32.000	8.06	0.00	30.71	2.73
815	1108	9.643693	ATTTCAAAAGCATGTTTTCCATAGTAG	57.356	29.630	8.06	0.00	30.71	2.57
816	1109	9.638239	GATTTCAAAAGCATGTTTTCCATAGTA	57.362	29.630	8.06	0.00	30.71	1.82
817	1110	7.603784	GGATTTCAAAAGCATGTTTTCCATAGT	59.396	33.333	8.06	0.00	30.71	2.12
818	1111	7.603404	TGGATTTCAAAAGCATGTTTTCCATAG	59.397	33.333	8.06	0.00	30.71	2.23

Showing 1 to 25 of 300 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.