AutoCloner

Multiple sequence alignment - TraesCS7A01G275600

Loading Multiple Alignment...

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	TraesCS7A01G275600	chr7A	100.000	2708	0	0	1	2708	287889090	287891797	0.000000e+00	5001
1	TraesCS7A01G275600	chr7A	94.620	855	42	3	1192	2045	287862649	287863500	0.000000e+00	1321
2	TraesCS7A01G275600	chr7A	79.648	398	29	21	1	385	287862158	287862516	3.480000e-59	239
3	TraesCS7A01G275600	chr7D	90.312	2787	161	51	1	2708	264338247	264341003	0.000000e+00	3550
4	TraesCS7A01G275600	chr7D	95.290	1656	58	7	391	2045	264325930	264327566	0.000000e+00	2608
5	TraesCS7A01G275600	chr7D	91.717	1666	103	28	390	2045	264360765	264362405	0.000000e+00	2279
6	TraesCS7A01G275600	chr7D	91.744	1502	97	24	390	1886	264370638	264372117	0.000000e+00	2061
7	TraesCS7A01G275600	chr7D	87.692	455	45	6	2044	2497	264362445	264362889	1.110000e-143	520
8	TraesCS7A01G275600	chr7D	84.382	429	22	4	1	384	264360279	264360707	1.970000e-101	379
9	TraesCS7A01G275600	chr7D	83.180	434	20	11	1	384	264370150	264370580	5.550000e-92	348
10	TraesCS7A01G275600	chr7D	83.333	402	27	11	1	385	264325374	264325752	4.320000e-88	335
11	TraesCS7A01G275600	chr7B	96.490	2023	66	4	688	2708	244651643	244653662	0.000000e+00	3338
12	TraesCS7A01G275600	chr7B	89.608	2117	160	39	390	2497	244692775	244694840	0.000000e+00	2636
13	TraesCS7A01G275600	chr7B	91.647	1664	105	29	390	2045	244644973	244646610	0.000000e+00	2272
14	TraesCS7A01G275600	chr7B	92.077	1502	91	25	390	1886	244716249	244717727	0.000000e+00	2089
15	TraesCS7A01G275600	chr7B	90.796	402	19	9	1	384	244650968	244651369	3.090000e-144	521
16	TraesCS7A01G275600	chr7B	83.077	455	50	13	2044	2497	244646650	244647078	3.270000e-104	388
17	TraesCS7A01G275600	chr7B	96.364	220	7	1	390	609	244651426	244651644	7.130000e-96	361
18	TraesCS7A01G275600	chr7B	82.488	434	26	10	1	384	244692284	244692717	4.320000e-88	335
19	TraesCS7A01G275600	chr7B	81.327	407	44	15	1	384	244715794	244716191	4.380000e-78	302
20	TraesCS7A01G275600	chr7B	81.446	415	25	9	1	369	244644199	244644607	2.640000e-75	292

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	TraesCS7A01G275600	chr7A	287889090	287891797	2707	False	5001.000000	5001	100.000000	1	2708	1	chr7A.!!$F1	2707
1	TraesCS7A01G275600	chr7A	287862158	287863500	1342	False	780.000000	1321	87.134000	1	2045	2	chr7A.!!$F2	2044
2	TraesCS7A01G275600	chr7D	264338247	264341003	2756	False	3550.000000	3550	90.312000	1	2708	1	chr7D.!!$F1	2707
3	TraesCS7A01G275600	chr7D	264325374	264327566	2192	False	1471.500000	2608	89.311500	1	2045	2	chr7D.!!$F2	2044
4	TraesCS7A01G275600	chr7D	264370150	264372117	1967	False	1204.500000	2061	87.462000	1	1886	2	chr7D.!!$F4	1885
5	TraesCS7A01G275600	chr7D	264360279	264362889	2610	False	1059.333333	2279	87.930333	1	2497	3	chr7D.!!$F3	2496
6	TraesCS7A01G275600	chr7B	244692284	244694840	2556	False	1485.500000	2636	86.048000	1	2497	2	chr7B.!!$F2	2496
7	TraesCS7A01G275600	chr7B	244715794	244717727	1933	False	1195.500000	2089	86.702000	1	1886	2	chr7B.!!$F3	1885
8	TraesCS7A01G275600	chr7B	244644199	244653662	9463	False	1195.333333	3338	89.970000	1	2708	6	chr7B.!!$F1	2707

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
276	318	0.321298	TCGCACCCACCTTTTAGAGC	60.321	55.0	0.0	0.0	0.0	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1737	2282	0.323725	AAGGTGGAAGCCAATCGCAT	60.324	50.0	0.0	0.0	41.38	4.73	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
53	62	0.745845	ATGCTTCAGTCATCCACGCC	60.746	55.000	0.00	0.00	0.00	5.68
54	63	1.078848	GCTTCAGTCATCCACGCCT	60.079	57.895	0.00	0.00	0.00	5.52
56	65	1.363744	CTTCAGTCATCCACGCCTTC	58.636	55.000	0.00	0.00	0.00	3.46
75	84	4.156739	CCTTCCCTACTGAAGCAAATTGTC	59.843	45.833	0.00	0.00	40.34	3.18
196	217	3.608008	GCAGTGCTTAGACTTTGTTGAGC	60.608	47.826	8.18	0.00	0.00	4.26
207	228	3.760684	ACTTTGTTGAGCAGATTGATCCC	59.239	43.478	0.00	0.00	30.48	3.85
257	299	3.719268	TGCCTATGGTTCACTGTGATT	57.281	42.857	11.86	0.31	0.00	2.57
258	300	3.609853	TGCCTATGGTTCACTGTGATTC	58.390	45.455	11.86	7.98	0.00	2.52
276	318	0.321298	TCGCACCCACCTTTTAGAGC	60.321	55.000	0.00	0.00	0.00	4.09
277	319	1.635663	CGCACCCACCTTTTAGAGCG	61.636	60.000	0.00	0.00	37.91	5.03
347	409	3.953712	TGGAGCATTTAACTCAGACGA	57.046	42.857	0.00	0.00	35.79	4.20
385	746	6.233434	ACAGTTACTCAGAAATGCTCATCAA	58.767	36.000	0.00	0.00	0.00	2.57
386	747	6.148480	ACAGTTACTCAGAAATGCTCATCAAC	59.852	38.462	0.00	0.00	0.00	3.18
387	748	6.148315	CAGTTACTCAGAAATGCTCATCAACA	59.852	38.462	0.00	0.00	0.00	3.33
388	749	6.712095	AGTTACTCAGAAATGCTCATCAACAA	59.288	34.615	0.00	0.00	0.00	2.83
435	970	1.003928	AGATGCCATGTGTTGCTCAGA	59.996	47.619	0.00	0.00	0.00	3.27
457	992	2.949447	ACAAGCAAAGGATCCTTGTGT	58.051	42.857	27.71	22.96	45.22	3.72
560	1098	4.761739	ACACACCACACCTATTCAATTCAG	59.238	41.667	0.00	0.00	0.00	3.02
566	1104	7.970061	CACCACACCTATTCAATTCAGTAAATG	59.030	37.037	0.00	0.00	0.00	2.32
612	1153	2.235402	CACCAACCCATACTCGGTTAGT	59.765	50.000	0.00	0.00	41.78	2.24
620	1161	4.828939	CCCATACTCGGTTAGTACACCATA	59.171	45.833	3.50	0.00	43.47	2.74
621	1162	5.278660	CCCATACTCGGTTAGTACACCATAC	60.279	48.000	3.50	0.00	43.47	2.39
622	1163	5.300034	CCATACTCGGTTAGTACACCATACA	59.700	44.000	3.50	0.00	43.47	2.29
623	1164	6.183360	CCATACTCGGTTAGTACACCATACAA	60.183	42.308	3.50	0.00	43.47	2.41
624	1165	5.726980	ACTCGGTTAGTACACCATACAAA	57.273	39.130	3.50	0.00	36.36	2.83
625	1166	6.100404	ACTCGGTTAGTACACCATACAAAA	57.900	37.500	3.50	0.00	36.36	2.44
626	1167	6.704310	ACTCGGTTAGTACACCATACAAAAT	58.296	36.000	3.50	0.00	36.36	1.82
666	1209	5.762179	TTGTCAAGATCCACCAATAGAGT	57.238	39.130	0.00	0.00	0.00	3.24
672	1215	6.443849	TCAAGATCCACCAATAGAGTAAACCT	59.556	38.462	0.00	0.00	0.00	3.50
858	1402	4.503910	TGATTCCTTGTGTCTACCATTCG	58.496	43.478	0.00	0.00	0.00	3.34
1119	1663	3.192422	CCATGACCATCGAGACTATCTCC	59.808	52.174	0.00	0.00	40.34	3.71
1270	1814	5.804944	ACTAGATCTCTGCAATGCTATGT	57.195	39.130	6.82	0.00	0.00	2.29
1312	1856	4.166725	TGAAGGCCATTATCCAAGATCTGT	59.833	41.667	5.01	0.00	0.00	3.41
1343	1887	2.289694	CCAGAAAAGGAGATGACACCGT	60.290	50.000	0.00	0.00	32.13	4.83
1350	1894	2.069273	GGAGATGACACCGTTGTTCAG	58.931	52.381	0.00	0.00	35.47	3.02
1557	2101	4.065088	CAAAATGGTCTCTCGTCTCCAAA	58.935	43.478	0.00	0.00	33.55	3.28
1695	2239	6.096282	AGAGCAGAGTTACTCTCCTAAACATC	59.904	42.308	12.49	0.00	43.71	3.06
1712	2256	8.807118	CCTAAACATCCTTAGCTCATAGATACA	58.193	37.037	0.00	0.00	0.00	2.29
1722	2267	6.721704	AGCTCATAGATACACTCAACATCA	57.278	37.500	0.00	0.00	0.00	3.07
1736	2281	3.007290	TCAACATCAGCTACTCTTGCACT	59.993	43.478	0.00	0.00	0.00	4.40
1737	2282	4.220602	TCAACATCAGCTACTCTTGCACTA	59.779	41.667	0.00	0.00	0.00	2.74
1789	2336	2.810274	CTGATCTTTCCCAGTGTGTGTG	59.190	50.000	0.00	0.00	0.00	3.82
1801	2348	6.382859	TCCCAGTGTGTGTGTATATGTAGAAT	59.617	38.462	0.00	0.00	0.00	2.40
1847	2394	8.197439	AGAAAGGAAACAAAAGTTTTGATCGAT	58.803	29.630	30.20	17.19	0.00	3.59
1930	2478	6.946009	ACCTGCTTGTTTGTACCTTGTATATT	59.054	34.615	0.00	0.00	0.00	1.28
1931	2479	8.104566	ACCTGCTTGTTTGTACCTTGTATATTA	58.895	33.333	0.00	0.00	0.00	0.98
2096	9075	9.638239	AAAAACACAATTACAATGATAGCGATT	57.362	25.926	0.00	0.00	0.00	3.34
2112	9091	8.087750	TGATAGCGATTCCAACTTCAAATTTTT	58.912	29.630	0.00	0.00	0.00	1.94
2206	9185	4.039730	ACTCAGTACTGGCATCCATATCAC	59.960	45.833	22.48	0.00	30.82	3.06
2269	9248	5.171476	CACTACCTTCATTACTGACACCAG	58.829	45.833	0.00	0.00	45.76	4.00
2283	9262	6.010219	ACTGACACCAGCCAAATAAGTTAAT	58.990	36.000	0.00	0.00	44.16	1.40
2359	9338	8.579006	GGATTTGGAATAACATGATAAGATGCA	58.421	33.333	0.00	0.00	0.00	3.96
2389	9368	6.500910	TGATGACTCAATAATTCTGCATTGC	58.499	36.000	0.46	0.46	33.14	3.56
2461	9440	1.812235	CATGGCAGCAGACACTACAA	58.188	50.000	0.00	0.00	33.89	2.41
2505	9484	4.087892	CCACGGTGGGAGCTCTGG	62.088	72.222	19.63	8.40	32.67	3.86
2524	9503	3.224324	GGCGGACGAGGCATCCTA	61.224	66.667	0.00	0.00	31.76	2.94
2562	9541	4.572571	GCCGGTGGTGGTTGGTGA	62.573	66.667	1.90	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	62	4.761739	TGACAATTTGCTTCAGTAGGGAAG	59.238	41.667	0.00	0.00	45.58	3.46
54	63	4.724399	TGACAATTTGCTTCAGTAGGGAA	58.276	39.130	0.00	0.00	0.00	3.97
56	65	4.676196	GCATGACAATTTGCTTCAGTAGGG	60.676	45.833	0.00	0.00	35.95	3.53
75	84	3.938963	ACCACTTGTTATAACTCGGCATG	59.061	43.478	16.33	6.55	0.00	4.06
119	128	4.202141	TGTTGCATGGAAGTCTTTTCTTGG	60.202	41.667	0.00	0.00	0.00	3.61
196	217	1.411977	ACTCTGCTCGGGATCAATCTG	59.588	52.381	0.00	0.00	0.00	2.90
207	228	5.178252	TCATTCAGAAAAGAAACTCTGCTCG	59.822	40.000	0.00	0.00	39.17	5.03
257	299	0.321298	GCTCTAAAAGGTGGGTGCGA	60.321	55.000	0.00	0.00	0.00	5.10
258	300	1.635663	CGCTCTAAAAGGTGGGTGCG	61.636	60.000	0.00	0.00	35.90	5.34
276	318	4.152402	AGCAGCATAAACAGTAAACTGACG	59.848	41.667	16.74	1.86	46.59	4.35
277	319	5.179368	TCAGCAGCATAAACAGTAAACTGAC	59.821	40.000	16.74	0.00	46.59	3.51
385	746	2.906389	TGGCCATCTTGTAGAGACTTGT	59.094	45.455	0.00	0.00	37.17	3.16
386	747	3.616956	TGGCCATCTTGTAGAGACTTG	57.383	47.619	0.00	0.00	37.17	3.16
387	748	3.521126	ACATGGCCATCTTGTAGAGACTT	59.479	43.478	17.61	0.00	37.17	3.01
388	749	3.110705	ACATGGCCATCTTGTAGAGACT	58.889	45.455	17.61	0.00	37.17	3.24
542	1077	8.055279	ACATTTACTGAATTGAATAGGTGTGG	57.945	34.615	0.00	0.00	0.00	4.17
631	1174	6.096705	TGGATCTTGACAAAATTGTGTGTTCT	59.903	34.615	5.84	0.00	42.43	3.01
632	1175	6.198966	GTGGATCTTGACAAAATTGTGTGTTC	59.801	38.462	5.84	0.00	42.43	3.18
634	1177	5.451798	GGTGGATCTTGACAAAATTGTGTGT	60.452	40.000	5.84	0.00	42.43	3.72
644	1187	5.762179	ACTCTATTGGTGGATCTTGACAA	57.238	39.130	0.00	0.00	0.00	3.18
672	1215	1.153353	GCGACAAGAATCAACCGGAA	58.847	50.000	9.46	0.00	0.00	4.30
695	1238	9.060347	AGATATCACATTGTCATGTTCCATTAC	57.940	33.333	5.32	0.00	41.16	1.89
1119	1663	1.089920	CAAGCCTCCTCAAACCATCG	58.910	55.000	0.00	0.00	0.00	3.84
1270	1814	3.427573	TCAACTCGGTGAAGTCCTCATA	58.572	45.455	0.00	0.00	36.14	2.15
1312	1856	1.695242	TCCTTTTCTGGTCGCCACTTA	59.305	47.619	0.00	0.00	0.00	2.24
1343	1887	3.648067	AGACTGGATCTTGACCTGAACAA	59.352	43.478	0.00	0.00	31.62	2.83
1557	2101	3.594134	CGAGTTCTTCTTCTGGAATGCT	58.406	45.455	0.00	0.00	33.01	3.79
1695	2239	7.043961	TGTTGAGTGTATCTATGAGCTAAGG	57.956	40.000	0.00	0.00	0.00	2.69
1712	2256	3.007290	TGCAAGAGTAGCTGATGTTGAGT	59.993	43.478	12.30	0.00	0.00	3.41
1722	2267	1.751351	TCGCATAGTGCAAGAGTAGCT	59.249	47.619	2.63	0.00	45.36	3.32
1736	2281	0.546122	AGGTGGAAGCCAATCGCATA	59.454	50.000	0.00	0.00	41.38	3.14
1737	2282	0.323725	AAGGTGGAAGCCAATCGCAT	60.324	50.000	0.00	0.00	41.38	4.73
1847	2394	6.072508	GCAAAGGTTGAATTCACAGTATGAGA	60.073	38.462	7.89	0.00	39.69	3.27
2046	9024	1.396648	GCTGGGTGCAAACAAAACAAC	59.603	47.619	0.00	0.00	42.31	3.32
2112	9091	1.381056	ACCACAGCCTTGCCAACAA	60.381	52.632	0.00	0.00	0.00	2.83
2206	9185	4.595198	CACTATCATGTGTGTGCTCAAG	57.405	45.455	0.00	0.00	33.61	3.02
2269	9248	6.119144	TCTCGCTCAATTAACTTATTTGGC	57.881	37.500	4.39	5.71	0.00	4.52
2283	9262	5.369685	TTTGCATGTAATTTCTCGCTCAA	57.630	34.783	0.00	0.00	0.00	3.02
2389	9368	7.277319	CCTGTGATGACGAATGATTATATGAGG	59.723	40.741	0.00	0.00	0.00	3.86
2461	9440	7.411486	TGCATCTAGTTAGCTCTTAGTTCTT	57.589	36.000	0.00	0.00	0.00	2.52
2512	9491	2.700897	AGCTTATGTTAGGATGCCTCGT	59.299	45.455	0.00	0.00	34.61	4.18
2524	9503	3.689832	CCCCCACCAAGCTTATGTT	57.310	52.632	0.00	0.00	0.00	2.71
2671	9652	4.532834	ACCTACCTTCACAAAAAGAAGCA	58.467	39.130	0.00	0.00	40.83	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.