AutoCloner

Multiple sequence alignment - TraesCS3B01G009200

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	TraesCS3B01G009200	chr3B	100.000	2414	0	0	1	2414	4435096	4432683	0.000000e+00	4458.0
1	TraesCS3B01G009200	chr3B	86.068	1615	150	43	639	2234	4421965	4420407	0.000000e+00	1666.0
2	TraesCS3B01G009200	chr3B	77.888	1108	160	49	753	1840	4459654	4458612	5.710000e-171	610.0
3	TraesCS3B01G009200	chr3B	73.228	1143	207	64	747	1843	4490991	4489902	8.320000e-85	324.0
4	TraesCS3B01G009200	chr3B	88.889	153	12	3	350	498	4423531	4423380	1.470000e-42	183.0
5	TraesCS3B01G009200	chr3D	94.366	2059	84	15	241	2292	2244085	2242052	0.000000e+00	3131.0
6	TraesCS3B01G009200	chr3D	88.969	1115	100	11	945	2055	2239567	2238472	0.000000e+00	1356.0
7	TraesCS3B01G009200	chr3D	93.233	266	17	1	1427	1691	2200946	2200681	8.090000e-105	390.0
8	TraesCS3B01G009200	chr3D	89.437	284	18	8	642	915	2239845	2239564	4.940000e-92	348.0
9	TraesCS3B01G009200	chr3D	84.711	242	33	3	1007	1247	2201195	2200957	3.100000e-59	239.0
10	TraesCS3B01G009200	chr3D	83.794	253	37	3	357	605	2259788	2259536	1.120000e-58	237.0
11	TraesCS3B01G009200	chr3D	89.305	187	17	2	5	191	2244270	2244087	5.190000e-57	231.0
12	TraesCS3B01G009200	chr3D	78.780	377	45	21	128	498	2240901	2240554	1.120000e-53	220.0
13	TraesCS3B01G009200	chr3D	97.778	45	1	0	2335	2379	2242055	2242011	7.160000e-11	78.7
14	TraesCS3B01G009200	chr3A	91.068	1433	101	17	971	2379	1789558	1790987	0.000000e+00	1912.0
15	TraesCS3B01G009200	chr3A	91.139	869	69	6	113	976	1788624	1789489	0.000000e+00	1171.0
16	TraesCS3B01G009200	chr3A	85.727	1128	100	34	642	1757	1797095	1798173	0.000000e+00	1134.0
17	TraesCS3B01G009200	chr3A	81.368	848	125	20	849	1684	1780259	1781085	0.000000e+00	660.0
18	TraesCS3B01G009200	chr3A	87.600	500	46	11	1741	2234	1817317	1817806	1.250000e-157	566.0
19	TraesCS3B01G009200	chr3A	91.120	259	22	1	1427	1684	1859541	1859799	1.370000e-92	350.0
20	TraesCS3B01G009200	chr3A	90.421	261	20	3	274	530	1788341	1788600	2.970000e-89	339.0
21	TraesCS3B01G009200	chr3A	76.115	695	125	25	838	1516	1851822	1852491	2.310000e-85	326.0
22	TraesCS3B01G009200	chr3A	73.846	780	140	48	981	1741	1774068	1774802	3.980000e-63	252.0
23	TraesCS3B01G009200	chr3A	79.331	329	43	15	174	498	1792351	1792658	8.750000e-50	207.0
24	TraesCS3B01G009200	chr3A	94.286	35	2	0	2380	2414	531386191	531386157	1.000000e-03	54.7
25	TraesCS3B01G009200	chr1B	100.000	37	0	0	2378	2414	658287357	658287393	4.310000e-08	69.4
26	TraesCS3B01G009200	chrUn	100.000	30	0	0	2378	2407	103936195	103936224	3.350000e-04	56.5
27	TraesCS3B01G009200	chr4A	94.286	35	2	0	2370	2404	465894290	465894324	1.000000e-03	54.7
28	TraesCS3B01G009200	chr7A	100.000	28	0	0	2377	2404	403948255	403948228	4.000000e-03	52.8
29	TraesCS3B01G009200	chr2A	100.000	28	0	0	2377	2404	9321030	9321057	4.000000e-03	52.8

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	TraesCS3B01G009200	chr3B	4432683	4435096	2413	True	4458.000000	4458	100.00000	1	2414	1	chr3B.!!$R1	2413
1	TraesCS3B01G009200	chr3B	4420407	4423531	3124	True	924.500000	1666	87.47850	350	2234	2	chr3B.!!$R4	1884
2	TraesCS3B01G009200	chr3B	4458612	4459654	1042	True	610.000000	610	77.88800	753	1840	1	chr3B.!!$R2	1087
3	TraesCS3B01G009200	chr3B	4489902	4490991	1089	True	324.000000	324	73.22800	747	1843	1	chr3B.!!$R3	1096
4	TraesCS3B01G009200	chr3D	2238472	2244270	5798	True	894.116667	3131	89.77250	5	2379	6	chr3D.!!$R3	2374
5	TraesCS3B01G009200	chr3D	2200681	2201195	514	True	314.500000	390	88.97200	1007	1691	2	chr3D.!!$R2	684
6	TraesCS3B01G009200	chr3A	1797095	1798173	1078	False	1134.000000	1134	85.72700	642	1757	1	chr3A.!!$F3	1115
7	TraesCS3B01G009200	chr3A	1788341	1792658	4317	False	907.250000	1912	87.98975	113	2379	4	chr3A.!!$F7	2266
8	TraesCS3B01G009200	chr3A	1780259	1781085	826	False	660.000000	660	81.36800	849	1684	1	chr3A.!!$F2	835
9	TraesCS3B01G009200	chr3A	1851822	1852491	669	False	326.000000	326	76.11500	838	1516	1	chr3A.!!$F5	678
10	TraesCS3B01G009200	chr3A	1774068	1774802	734	False	252.000000	252	73.84600	981	1741	1	chr3A.!!$F1	760

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
398	571	2.033407	GTCAATTCATGCGATCTGGACG	60.033	50.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2370	4037	0.252103	AACGGAGGGAGTAGAAGCCA	60.252	55.0	0.0	0.0	0.0	4.75	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
35	36	7.606456	GTGTTAAGAAAGGAATCACCATGAGTA	59.394	37.037	0.00	0.00	42.04	2.59
37	38	9.832445	GTTAAGAAAGGAATCACCATGAGTATA	57.168	33.333	0.00	0.00	42.04	1.47
49	50	5.063944	CACCATGAGTATAAGTCACTTGCAC	59.936	44.000	0.00	0.00	29.04	4.57
55	56	4.943705	AGTATAAGTCACTTGCACATTGGG	59.056	41.667	0.00	0.00	0.00	4.12
66	67	2.290832	TGCACATTGGGCTACTCATCAA	60.291	45.455	12.93	0.00	0.00	2.57
95	96	8.081633	CCAAATTAACTAAAGTCAGTTCATGCA	58.918	33.333	0.00	0.00	39.45	3.96
105	106	5.950883	AGTCAGTTCATGCATTTGATTCTG	58.049	37.500	0.00	6.58	33.33	3.02
112	113	4.079844	TCATGCATTTGATTCTGAGGGGTA	60.080	41.667	0.00	0.00	0.00	3.69
114	115	3.523157	TGCATTTGATTCTGAGGGGTAGA	59.477	43.478	0.00	0.00	0.00	2.59
115	116	4.166725	TGCATTTGATTCTGAGGGGTAGAT	59.833	41.667	0.00	0.00	0.00	1.98
116	117	4.518211	GCATTTGATTCTGAGGGGTAGATG	59.482	45.833	0.00	0.00	0.00	2.90
119	291	7.456725	CATTTGATTCTGAGGGGTAGATGTAT	58.543	38.462	0.00	0.00	0.00	2.29
125	297	5.394738	TCTGAGGGGTAGATGTATTAGTGG	58.605	45.833	0.00	0.00	0.00	4.00
176	348	9.227777	CATAATATCATGTCACATGATGGAACT	57.772	33.333	34.48	16.86	38.98	3.01
191	363	7.943079	TGATGGAACTTATGAATCACAATGT	57.057	32.000	0.00	0.00	0.00	2.71
193	365	8.805175	TGATGGAACTTATGAATCACAATGTTT	58.195	29.630	0.00	0.00	0.00	2.83
203	375	6.290605	TGAATCACAATGTTTCTCAGTCTCA	58.709	36.000	0.36	0.00	29.82	3.27
208	380	5.699915	CACAATGTTTCTCAGTCTCACAGAT	59.300	40.000	0.00	0.00	0.00	2.90
296	469	6.606234	TCGCAGTTAACAAGTTAATGTTCA	57.394	33.333	8.61	0.00	42.33	3.18
398	571	2.033407	GTCAATTCATGCGATCTGGACG	60.033	50.000	0.00	0.00	0.00	4.79
432	605	7.703058	ATTAATGCACCACTTACTAAAAGCT	57.297	32.000	0.00	0.00	0.00	3.74
459	632	5.004448	TGCGAGTAAATCTAGGATCGATCT	58.996	41.667	23.96	12.90	32.13	2.75
565	1335	5.316987	AGTTAAGTGTCAAGCTAGCCATTT	58.683	37.500	12.13	7.81	0.00	2.32
572	1342	4.695455	TGTCAAGCTAGCCATTTAAGTGAC	59.305	41.667	12.13	12.01	34.76	3.67
600	1370	8.766151	GTTCTCTGGAGTAAAAGAAAAGTACAG	58.234	37.037	0.00	0.00	30.10	2.74
632	1824	6.723298	TGATTGTTCCCAAAACAGTGTTAT	57.277	33.333	9.37	0.00	33.44	1.89
708	2159	7.623089	GCTGTGAAAGTTCATACTTGAGATGTC	60.623	40.741	0.00	0.00	43.74	3.06
956	2439	4.103153	TCCAATCTTGACACCTTCTCTTGT	59.897	41.667	0.00	0.00	0.00	3.16
1066	2642	0.926155	CATGCTGATCACGTCTTCCG	59.074	55.000	0.00	0.00	44.03	4.30
1129	2706	2.556287	GTACCAACTGCACTGCGC	59.444	61.111	0.00	0.00	42.89	6.09
1283	2868	1.109323	AACACTGTGGCTGAAAGGGC	61.109	55.000	13.09	0.00	0.00	5.19
1292	2877	0.108945	GCTGAAAGGGCTTGCATGAC	60.109	55.000	3.33	0.00	0.00	3.06
1327	2912	1.818674	CCCTACAATGTGAACCTTGCC	59.181	52.381	0.00	0.00	0.00	4.52
1371	2956	2.170607	CGGTTCCACCTGTAGGAATGAT	59.829	50.000	4.64	0.00	46.08	2.45
1476	3083	1.372499	GGCTCGTTGTAGTCGTGCA	60.372	57.895	12.72	0.00	45.34	4.57
1779	3442	3.350219	AATACTTGGAGGTGATGCGTT	57.650	42.857	0.00	0.00	0.00	4.84
1827	3490	2.943033	CGTTGTTGAGGAAACTGACCTT	59.057	45.455	0.00	0.00	44.43	3.50
1875	3539	3.120060	CCCTGATATTAGAATGCTTGCGC	60.120	47.826	0.00	0.00	0.00	6.09
1943	3608	9.619316	CTGTATGTATTAGACTATGAGTGCTTC	57.381	37.037	0.00	0.00	0.00	3.86
1947	3612	8.526667	TGTATTAGACTATGAGTGCTTCTCTT	57.473	34.615	9.94	6.95	43.13	2.85
2176	3842	9.985318	CAAAAGAAGCAATAGTAGAAGATGAAG	57.015	33.333	0.00	0.00	0.00	3.02
2180	3846	9.810545	AGAAGCAATAGTAGAAGATGAAGTAAC	57.189	33.333	0.00	0.00	0.00	2.50
2181	3847	9.587772	GAAGCAATAGTAGAAGATGAAGTAACA	57.412	33.333	0.00	0.00	0.00	2.41
2182	3848	8.934507	AGCAATAGTAGAAGATGAAGTAACAC	57.065	34.615	0.00	0.00	0.00	3.32
2189	3856	8.085296	AGTAGAAGATGAAGTAACACAAGACAG	58.915	37.037	0.00	0.00	0.00	3.51
2209	3876	0.655733	ACAAGCTTTCCAACACGACG	59.344	50.000	0.00	0.00	0.00	5.12
2238	3905	3.136763	CAAGTGTGCTCATTCAGAGTGT	58.863	45.455	0.00	0.00	46.47	3.55
2263	3930	0.810648	CATGGTGTTTCCCGACATGG	59.189	55.000	0.00	0.00	36.25	3.66
2264	3931	0.404040	ATGGTGTTTCCCGACATGGT	59.596	50.000	0.00	0.00	35.15	3.55
2275	3942	3.976701	GACATGGTGTGGGGCTCCG	62.977	68.421	0.00	0.00	35.24	4.63
2370	4037	3.323751	GCAGATGCCATTTGGTTCTTT	57.676	42.857	0.00	0.00	37.57	2.52
2379	4046	4.809673	CCATTTGGTTCTTTGGCTTCTAC	58.190	43.478	0.00	0.00	0.00	2.59
2381	4048	5.335976	CCATTTGGTTCTTTGGCTTCTACTC	60.336	44.000	0.00	0.00	0.00	2.59
2382	4049	3.418684	TGGTTCTTTGGCTTCTACTCC	57.581	47.619	0.00	0.00	0.00	3.85
2383	4050	2.039879	TGGTTCTTTGGCTTCTACTCCC	59.960	50.000	0.00	0.00	0.00	4.30
2384	4051	2.306219	GGTTCTTTGGCTTCTACTCCCT	59.694	50.000	0.00	0.00	0.00	4.20
2386	4053	2.188817	TCTTTGGCTTCTACTCCCTCC	58.811	52.381	0.00	0.00	0.00	4.30
2387	4054	0.902531	TTTGGCTTCTACTCCCTCCG	59.097	55.000	0.00	0.00	0.00	4.63
2388	4055	0.252103	TTGGCTTCTACTCCCTCCGT	60.252	55.000	0.00	0.00	0.00	4.69
2390	4057	0.460722	GGCTTCTACTCCCTCCGTTC	59.539	60.000	0.00	0.00	0.00	3.95
2392	4059	0.739561	CTTCTACTCCCTCCGTTCCG	59.260	60.000	0.00	0.00	0.00	4.30
2393	4060	0.329261	TTCTACTCCCTCCGTTCCGA	59.671	55.000	0.00	0.00	0.00	4.55
2394	4061	0.329261	TCTACTCCCTCCGTTCCGAA	59.671	55.000	0.00	0.00	0.00	4.30
2397	7478	1.856629	ACTCCCTCCGTTCCGAATTA	58.143	50.000	0.00	0.00	0.00	1.40
2405	7486	2.349275	TCCGTTCCGAATTAATTGTCGC	59.651	45.455	5.17	0.00	35.93	5.19
2406	7487	2.094575	CCGTTCCGAATTAATTGTCGCA	59.905	45.455	5.17	0.00	35.93	5.10
2411	7492	5.811399	TCCGAATTAATTGTCGCAGAAAT	57.189	34.783	5.17	0.00	39.69	2.17
2412	7493	5.568482	TCCGAATTAATTGTCGCAGAAATG	58.432	37.500	5.17	0.00	39.69	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	3.439129	GGTGATTCCTTTCTTAACACCCG	59.561	47.826	0.00	0.00	39.91	5.28
7	8	4.403734	TGGTGATTCCTTTCTTAACACCC	58.596	43.478	0.00	0.00	43.53	4.61
8	9	5.710099	TCATGGTGATTCCTTTCTTAACACC	59.290	40.000	0.00	0.00	44.15	4.16
9	10	6.431234	ACTCATGGTGATTCCTTTCTTAACAC	59.569	38.462	0.00	0.00	37.07	3.32
35	36	2.493278	GCCCAATGTGCAAGTGACTTAT	59.507	45.455	0.00	0.00	0.00	1.73
37	38	0.675633	GCCCAATGTGCAAGTGACTT	59.324	50.000	0.00	0.00	0.00	3.01
38	39	0.178981	AGCCCAATGTGCAAGTGACT	60.179	50.000	0.00	0.00	0.00	3.41
49	50	3.209410	GGACTTGATGAGTAGCCCAATG	58.791	50.000	0.00	0.00	39.19	2.82
55	56	7.617041	AGTTAATTTGGACTTGATGAGTAGC	57.383	36.000	0.00	0.00	39.19	3.58
66	67	8.974060	TGAACTGACTTTAGTTAATTTGGACT	57.026	30.769	0.00	0.00	40.78	3.85
95	96	5.983333	ACATCTACCCCTCAGAATCAAAT	57.017	39.130	0.00	0.00	0.00	2.32
97	98	7.789831	ACTAATACATCTACCCCTCAGAATCAA	59.210	37.037	0.00	0.00	0.00	2.57
105	106	4.748701	TCCCACTAATACATCTACCCCTC	58.251	47.826	0.00	0.00	0.00	4.30
112	113	5.301298	GTCCGTACTTCCCACTAATACATCT	59.699	44.000	0.00	0.00	0.00	2.90
114	115	4.037208	CGTCCGTACTTCCCACTAATACAT	59.963	45.833	0.00	0.00	0.00	2.29
115	116	3.378112	CGTCCGTACTTCCCACTAATACA	59.622	47.826	0.00	0.00	0.00	2.29
116	117	3.378427	ACGTCCGTACTTCCCACTAATAC	59.622	47.826	0.00	0.00	0.00	1.89
119	291	1.909700	ACGTCCGTACTTCCCACTAA	58.090	50.000	0.00	0.00	0.00	2.24
125	297	1.202076	CGTAGGAACGTCCGTACTTCC	60.202	57.143	3.18	3.23	42.75	3.46
176	348	8.853077	AGACTGAGAAACATTGTGATTCATAA	57.147	30.769	0.00	0.00	32.41	1.90
191	363	6.762333	TCATTTCATCTGTGAGACTGAGAAA	58.238	36.000	0.00	0.00	35.39	2.52
193	365	5.624052	GCTCATTTCATCTGTGAGACTGAGA	60.624	44.000	5.84	0.00	41.38	3.27
203	375	6.016024	TGCTAACTTTTGCTCATTTCATCTGT	60.016	34.615	0.00	0.00	0.00	3.41
208	380	6.147864	ACTTGCTAACTTTTGCTCATTTCA	57.852	33.333	0.00	0.00	0.00	2.69
348	521	1.967779	GGTCTTCTCTAGCCCTCATCC	59.032	57.143	0.00	0.00	0.00	3.51
432	605	5.761726	TCGATCCTAGATTTACTCGCAACTA	59.238	40.000	0.00	0.00	0.00	2.24
542	1312	4.559862	ATGGCTAGCTTGACACTTAACT	57.440	40.909	15.72	0.00	0.00	2.24
565	1335	6.971726	TTTACTCCAGAGAACAGTCACTTA	57.028	37.500	0.70	0.00	0.00	2.24
572	1342	7.793927	ACTTTTCTTTTACTCCAGAGAACAG	57.206	36.000	0.70	0.00	34.03	3.16
632	1824	6.737608	AGGGGGTATTACTAAAATTGCTTGA	58.262	36.000	0.00	0.00	0.00	3.02
648	2099	1.768870	CTCACCGATCAAAGGGGGTAT	59.231	52.381	0.00	0.00	31.73	2.73
708	2159	1.228124	TTTCCCGGCACTGTCTTGG	60.228	57.895	0.00	0.00	0.00	3.61
778	2231	0.669318	ACGGCACCATGTTACAGTCG	60.669	55.000	0.00	0.00	0.00	4.18
876	2359	0.904649	TGGTGTGCCTCCTGATACTG	59.095	55.000	0.00	0.00	35.27	2.74
956	2439	5.710646	AGCTAGAGAGGTGAATATCTGGAA	58.289	41.667	0.00	0.00	30.28	3.53
1073	2649	1.451927	CTGCATAAAGGCCTCGGCA	60.452	57.895	5.23	12.98	44.11	5.69
1283	2868	0.376152	GTCGCTGATGGTCATGCAAG	59.624	55.000	0.00	0.00	0.00	4.01
1327	2912	1.262417	CTGGTTGTATATGCTGCGCTG	59.738	52.381	9.73	10.04	0.00	5.18
1476	3083	4.634443	GTCATGGCGGTTACAAAAGTCTAT	59.366	41.667	0.00	0.00	0.00	1.98
1779	3442	1.022451	GTAAATGGCACGGCGAAGGA	61.022	55.000	16.62	0.00	0.00	3.36
1875	3539	5.622770	AAACAGTTCTATAAACGCAAGGG	57.377	39.130	0.00	0.00	46.39	3.95
1947	3612	5.068198	GCCATTCTATCCATGCTCTTCAAAA	59.932	40.000	0.00	0.00	0.00	2.44
2116	3782	3.122480	TCCATGGTGATGTATGGACCTT	58.878	45.455	12.58	0.00	45.87	3.50
2176	3842	5.485662	AAAGCTTGTCTGTCTTGTGTTAC	57.514	39.130	0.00	0.00	0.00	2.50
2180	3846	2.945008	TGGAAAGCTTGTCTGTCTTGTG	59.055	45.455	0.00	0.00	0.00	3.33
2181	3847	3.281727	TGGAAAGCTTGTCTGTCTTGT	57.718	42.857	0.00	0.00	0.00	3.16
2182	3848	3.378112	TGTTGGAAAGCTTGTCTGTCTTG	59.622	43.478	0.00	0.00	0.00	3.02
2189	3856	1.332904	CGTCGTGTTGGAAAGCTTGTC	60.333	52.381	0.00	0.00	0.00	3.18
2238	3905	1.905894	TCGGGAAACACCATGAGATGA	59.094	47.619	0.00	0.00	41.20	2.92
2263	3930	2.358737	CAGTTCGGAGCCCCACAC	60.359	66.667	0.00	0.00	0.00	3.82
2264	3931	4.329545	GCAGTTCGGAGCCCCACA	62.330	66.667	0.00	0.00	0.00	4.17
2275	3942	3.426568	GAGGCGTGGCAGCAGTTC	61.427	66.667	10.33	2.81	39.27	3.01
2370	4037	0.252103	AACGGAGGGAGTAGAAGCCA	60.252	55.000	0.00	0.00	0.00	4.75
2387	4054	4.593597	TCTGCGACAATTAATTCGGAAC	57.406	40.909	10.65	0.00	35.02	3.62
2388	4055	5.614923	TTTCTGCGACAATTAATTCGGAA	57.385	34.783	10.65	7.84	35.02	4.30
2390	4057	4.734854	CCATTTCTGCGACAATTAATTCGG	59.265	41.667	10.65	0.57	35.73	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.