AutoCloner

Multiple sequence alignment - TraesCS6A01G240300

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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	TraesCS6A01G240300	chr6A	100.000	2408	0	0	1	2408	450684655	450682248	0.000000e+00	4447
1	TraesCS6A01G240300	chr6A	90.051	1980	181	13	426	2396	441150314	441148342	0.000000e+00	2551
2	TraesCS6A01G240300	chr6A	89.955	1981	183	14	426	2396	441032989	441031015	0.000000e+00	2542
3	TraesCS6A01G240300	chr6A	89.747	1980	189	10	426	2396	441084652	441082678	0.000000e+00	2519
4	TraesCS6A01G240300	chr6A	90.466	965	89	3	1443	2406	450775924	450774962	0.000000e+00	1269
5	TraesCS6A01G240300	chr6A	90.000	570	57	0	1357	1926	444070396	444070965	0.000000e+00	737
6	TraesCS6A01G240300	chr6A	90.353	539	43	7	426	958	444069862	444070397	0.000000e+00	699
7	TraesCS6A01G240300	chr6A	75.304	1150	243	35	409	1543	505898124	505897001	1.650000e-141	512
8	TraesCS6A01G240300	chr6A	91.351	370	27	4	513	878	441250805	441250437	3.570000e-138	501
9	TraesCS6A01G240300	chr6D	92.836	2415	163	8	1	2406	313721797	313719384	0.000000e+00	3493
10	TraesCS6A01G240300	chr6D	92.023	2407	178	11	10	2406	313796087	313793685	0.000000e+00	3369
11	TraesCS6A01G240300	chr6B	89.559	2404	220	25	14	2396	689661455	689659062	0.000000e+00	3020
12	TraesCS6A01G240300	chr6B	90.662	1360	125	2	1038	2396	689656887	689655529	0.000000e+00	1807
13	TraesCS6A01G240300	chr6B	92.453	212	15	1	8	218	351243069	351243280	3.890000e-78	302
14	TraesCS6A01G240300	chr3A	76.618	757	160	13	1648	2396	305323531	305322784	3.730000e-108	401
15	TraesCS6A01G240300	chr3B	78.080	625	129	6	1774	2396	454988018	454987400	2.900000e-104	388
16	TraesCS6A01G240300	chr3D	92.925	212	14	1	8	218	124476822	124476611	8.360000e-80	307
17	TraesCS6A01G240300	chr3D	92.453	212	15	1	8	218	418241348	418241559	3.890000e-78	302
18	TraesCS6A01G240300	chr2B	91.818	220	16	2	8	226	314646920	314647138	3.010000e-79	305
19	TraesCS6A01G240300	chr1D	92.417	211	15	1	8	217	85509584	85509794	1.400000e-77	300
20	TraesCS6A01G240300	chr2D	89.177	231	23	2	8	237	331437854	331437625	1.090000e-73	287

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	TraesCS6A01G240300	chr6A	450682248	450684655	2407	True	4447.0	4447	100.0000	1	2408	1	chr6A.!!$R5	2407
1	TraesCS6A01G240300	chr6A	441148342	441150314	1972	True	2551.0	2551	90.0510	426	2396	1	chr6A.!!$R3	1970
2	TraesCS6A01G240300	chr6A	441031015	441032989	1974	True	2542.0	2542	89.9550	426	2396	1	chr6A.!!$R1	1970
3	TraesCS6A01G240300	chr6A	441082678	441084652	1974	True	2519.0	2519	89.7470	426	2396	1	chr6A.!!$R2	1970
4	TraesCS6A01G240300	chr6A	450774962	450775924	962	True	1269.0	1269	90.4660	1443	2406	1	chr6A.!!$R6	963
5	TraesCS6A01G240300	chr6A	444069862	444070965	1103	False	718.0	737	90.1765	426	1926	2	chr6A.!!$F1	1500
6	TraesCS6A01G240300	chr6A	505897001	505898124	1123	True	512.0	512	75.3040	409	1543	1	chr6A.!!$R7	1134
7	TraesCS6A01G240300	chr6D	313719384	313721797	2413	True	3493.0	3493	92.8360	1	2406	1	chr6D.!!$R1	2405
8	TraesCS6A01G240300	chr6D	313793685	313796087	2402	True	3369.0	3369	92.0230	10	2406	1	chr6D.!!$R2	2396
9	TraesCS6A01G240300	chr6B	689655529	689661455	5926	True	2413.5	3020	90.1105	14	2396	2	chr6B.!!$R1	2382
10	TraesCS6A01G240300	chr3A	305322784	305323531	747	True	401.0	401	76.6180	1648	2396	1	chr3A.!!$R1	748
11	TraesCS6A01G240300	chr3B	454987400	454988018	618	True	388.0	388	78.0800	1774	2396	1	chr3B.!!$R1	622

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
808	823	0.826715	CCTCTGGAGCGGATTTCTCA	59.173	55.0	0.0	0.0	32.38	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1866	5422	1.361204	TGGAAGAGACCATTGCTGGA	58.639	50.0	0.0	0.0	46.37	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
46	47	7.906527	GTGCACTTTATTTACCATTACCGTTAG	59.093	37.037	10.32	0.00	0.00	2.34
66	67	7.582679	CCGTTAGTTGCTCATTACAAATTATCG	59.417	37.037	0.00	0.00	0.00	2.92
118	120	3.010420	AGCGCTTGGAGAAAATACCTTC	58.990	45.455	2.64	0.00	0.00	3.46
119	121	3.010420	GCGCTTGGAGAAAATACCTTCT	58.990	45.455	0.00	0.00	38.39	2.85
206	208	6.888632	GGACTACGATTGATCCCCTATACTTA	59.111	42.308	0.00	0.00	0.00	2.24
218	220	6.032039	TCCCCTATACTTATGGCTCATCAAT	58.968	40.000	0.00	0.00	0.00	2.57
232	234	8.640063	TGGCTCATCAATAGTATTTATGCAAT	57.360	30.769	10.88	0.00	0.00	3.56
252	254	5.464168	CAATAGTTTTTGGACCAAGCTCAG	58.536	41.667	7.07	0.00	0.00	3.35
306	313	2.128507	GCCCCTAGCGCTAGACAGT	61.129	63.158	39.42	7.20	35.21	3.55
307	314	1.736586	CCCCTAGCGCTAGACAGTG	59.263	63.158	39.42	24.25	35.21	3.66
377	384	1.229625	AGGATGACCACAGGAGGCA	60.230	57.895	0.00	0.00	38.94	4.75
703	715	7.892771	TGGATTTAATGCATATAAGGCCACATA	59.107	33.333	5.01	1.52	0.00	2.29
808	823	0.826715	CCTCTGGAGCGGATTTCTCA	59.173	55.000	0.00	0.00	32.38	3.27
858	873	8.712285	AGAATATCAAAAATTCCAACATGCAG	57.288	30.769	0.00	0.00	34.50	4.41
954	971	3.797865	GCATAGCCTTTTGATGTGCATCC	60.798	47.826	9.39	0.00	37.02	3.51
966	985	1.009829	GTGCATCCATTCCACTCGTC	58.990	55.000	0.00	0.00	0.00	4.20
1005	1024	6.745794	TTTTTCATTCCTGAAGAAATGGGT	57.254	33.333	0.00	0.00	42.19	4.51
1029	1048	1.838112	TCAAGGTGCCAAGCCTATTG	58.162	50.000	0.00	0.00	34.81	1.90
1067	1086	5.473504	TCATGCCACTTCTTTTAGTTCCTTC	59.526	40.000	0.00	0.00	0.00	3.46
1089	1108	8.436200	CCTTCTAAGTATTGTCTGAAAACTTCG	58.564	37.037	0.00	0.00	32.85	3.79
1095	1114	5.633830	ATTGTCTGAAAACTTCGCATGAT	57.366	34.783	0.00	0.00	0.00	2.45
1099	1118	5.181811	TGTCTGAAAACTTCGCATGATGAAT	59.818	36.000	0.00	0.00	0.00	2.57
1100	1119	5.510674	GTCTGAAAACTTCGCATGATGAATG	59.489	40.000	0.00	0.00	39.49	2.67
1204	4756	8.556589	TCTTTTTGGATGGAACTTCATAGGATA	58.443	33.333	0.00	0.00	0.00	2.59
1211	4763	6.672266	TGGAACTTCATAGGATATGAGTCC	57.328	41.667	13.80	13.80	38.62	3.85
1350	4902	2.576648	CAAGGAGGGCTTTACTAAGGGT	59.423	50.000	0.00	0.00	31.76	4.34
1425	4977	8.017587	AGTGTTAAACAAAGAAAAAGTTGCAG	57.982	30.769	0.00	0.00	0.00	4.41
1461	5013	9.450807	GATGTGTGATGTAACAAATAATAAGGC	57.549	33.333	0.00	0.00	27.69	4.35
1511	5063	4.142730	GCAATGACAGAAGTTGAGTCCATC	60.143	45.833	0.00	0.00	0.00	3.51
1512	5064	4.897509	ATGACAGAAGTTGAGTCCATCA	57.102	40.909	0.00	0.00	35.62	3.07
1519	5071	6.998074	ACAGAAGTTGAGTCCATCACAAATAA	59.002	34.615	0.00	0.00	37.77	1.40
1575	5131	4.858692	GCTCACATGCAAATACGACAAAAT	59.141	37.500	0.00	0.00	0.00	1.82
1624	5180	4.832248	ACGTCAACATCTTCACCATATGT	58.168	39.130	1.24	0.00	35.40	2.29
1733	5289	4.327680	GTTTCTCCAAGCTCATAGGTGTT	58.672	43.478	0.00	0.00	0.00	3.32
1744	5300	3.420893	TCATAGGTGTTTTTGCCCTCTG	58.579	45.455	0.00	0.00	0.00	3.35
1797	5353	8.495554	CTACATTAGTAGCAGTGTAAGAATCG	57.504	38.462	0.00	0.00	41.12	3.34
1809	5365	1.148310	AAGAATCGTCTGGTTGTGCG	58.852	50.000	0.00	0.00	33.05	5.34
1822	5378	3.628032	TGGTTGTGCGACTTCATTAAACA	59.372	39.130	0.00	0.00	0.00	2.83
1853	5409	7.041916	ACTCTCCTCGAACTATTGTAATACTCG	60.042	40.741	0.00	0.00	0.00	4.18
1859	5415	4.939052	ACTATTGTAATACTCGCCAGCT	57.061	40.909	0.00	0.00	0.00	4.24
1866	5422	1.826385	ATACTCGCCAGCTTTGCTTT	58.174	45.000	3.68	0.00	36.40	3.51
1869	5425	1.518056	CTCGCCAGCTTTGCTTTCCA	61.518	55.000	3.68	0.00	36.40	3.53
1918	5474	3.196463	TGTGTTGCTTGATTTGCCAAAG	58.804	40.909	0.00	0.00	0.00	2.77
2006	5562	9.527157	TTTGGGTTTTGAGATCATGATAAACTA	57.473	29.630	22.18	13.80	0.00	2.24
2030	5586	9.309516	CTAGTTATACCAACGACAACATAACAT	57.690	33.333	12.74	5.09	33.39	2.71
2122	5678	7.672239	AGCATACATTTTAGTTCCCACCTTTTA	59.328	33.333	0.00	0.00	0.00	1.52
2193	5750	2.006888	CGTGTGCAAGGGTATTGTAGG	58.993	52.381	0.00	0.00	0.00	3.18
2235	5792	6.396829	GCAAGATGCATAATTACTTTCCCT	57.603	37.500	0.00	0.00	44.26	4.20
2313	5870	2.419021	CCCGCATCTTTTTACCCTACGA	60.419	50.000	0.00	0.00	0.00	3.43
2317	5874	5.699458	CCGCATCTTTTTACCCTACGATTAT	59.301	40.000	0.00	0.00	0.00	1.28
2336	5893	9.234384	ACGATTATAAAGTAGACAAGTTGATCG	57.766	33.333	10.54	11.07	0.00	3.69
2406	5967	5.819991	TCTTACATGGCTCAAATCCTTTCT	58.180	37.500	0.00	0.00	0.00	2.52
2407	5968	5.649395	TCTTACATGGCTCAAATCCTTTCTG	59.351	40.000	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	6.258160	AGCACGATAATTTGTAATGAGCAAC	58.742	36.000	0.00	0.00	0.00	4.17
66	67	4.565564	CGGTAACAGGTAGTTTGATAGCAC	59.434	45.833	0.00	0.00	41.64	4.40
118	120	5.906073	AGGAAATGACAAGTGGTTTTCAAG	58.094	37.500	0.00	0.00	0.00	3.02
119	121	5.930837	AGGAAATGACAAGTGGTTTTCAA	57.069	34.783	0.00	0.00	0.00	2.69
206	208	8.640063	TTGCATAAATACTATTGATGAGCCAT	57.360	30.769	9.59	0.00	0.00	4.40
232	234	4.389374	CTCTGAGCTTGGTCCAAAAACTA	58.611	43.478	5.64	0.00	0.00	2.24
252	254	1.475213	GGTCGGGTCAATTCATCCCTC	60.475	57.143	7.31	2.17	39.10	4.30
269	271	2.483889	GGCAGAGCTATAGTGTTGGGTC	60.484	54.545	0.84	0.00	0.00	4.46
270	272	1.486726	GGCAGAGCTATAGTGTTGGGT	59.513	52.381	0.84	0.00	0.00	4.51
303	310	1.003545	CAAAACTCACGCCACTCACTG	60.004	52.381	0.00	0.00	0.00	3.66
306	313	1.013596	CACAAAACTCACGCCACTCA	58.986	50.000	0.00	0.00	0.00	3.41
307	314	0.317020	GCACAAAACTCACGCCACTC	60.317	55.000	0.00	0.00	0.00	3.51
377	384	4.881157	ATAAAAGGCCATTGGAGTACCT	57.119	40.909	5.01	0.00	37.04	3.08
516	527	6.980397	AGATATTTTGTTTTTGATCCATCGCC	59.020	34.615	0.00	0.00	0.00	5.54
590	601	6.097696	ACCTATTAAAGTTGTTGCACAAAGGT	59.902	34.615	10.75	10.75	40.15	3.50
695	707	7.118390	GTGATGTTCTATGTAGAATATGTGGCC	59.882	40.741	14.29	0.00	42.00	5.36
808	823	6.737720	TCTGAAAGATGTGGCTATATCTGT	57.262	37.500	10.06	4.59	38.67	3.41
858	873	8.306038	AGATTGTGTGATGCTATCTAGAAGATC	58.694	37.037	0.00	0.00	36.20	2.75
954	971	3.238108	AGCAAGTAGACGAGTGGAATG	57.762	47.619	0.00	0.00	0.00	2.67
966	985	8.490355	GGAATGAAAAATCACAAAAGCAAGTAG	58.510	33.333	0.00	0.00	0.00	2.57
1005	1024	0.895100	GGCTTGGCACCTTGATGTCA	60.895	55.000	0.00	0.00	30.64	3.58
1029	1048	2.168521	TGGCATGAGTAGTAGAAGGCAC	59.831	50.000	0.00	0.00	0.00	5.01
1067	1086	7.117241	TGCGAAGTTTTCAGACAATACTTAG	57.883	36.000	0.00	0.00	0.00	2.18
1089	1108	2.034305	GGAAGTGCCTCATTCATCATGC	59.966	50.000	0.00	0.00	32.13	4.06
1095	1114	4.701651	CACATTTAGGAAGTGCCTCATTCA	59.298	41.667	0.00	0.00	46.97	2.57
1099	1118	3.788227	ACACATTTAGGAAGTGCCTCA	57.212	42.857	0.00	0.00	46.97	3.86
1100	1119	4.327680	AGAACACATTTAGGAAGTGCCTC	58.672	43.478	0.00	0.00	46.97	4.70
1425	4977	3.198068	ACATCACACATCCTATGCGAAC	58.802	45.455	0.00	0.00	0.00	3.95
1461	5013	9.948964	TCATTATCAATTCATCATACTACCCAG	57.051	33.333	0.00	0.00	0.00	4.45
1543	5097	6.293027	CGTATTTGCATGTGAGCATTCATAGA	60.293	38.462	0.00	0.00	45.19	1.98
1547	5101	3.688673	TCGTATTTGCATGTGAGCATTCA	59.311	39.130	0.00	0.00	45.19	2.57
1575	5131	6.204688	GGTGTTGCGGATAATGATTAGATTGA	59.795	38.462	0.00	0.00	0.00	2.57
1588	5144	0.033642	TGACGTTGGTGTTGCGGATA	59.966	50.000	0.00	0.00	0.00	2.59
1733	5289	6.889177	TGTTTATGATATGTCAGAGGGCAAAA	59.111	34.615	0.00	0.00	37.87	2.44
1744	5300	8.127327	GCATGCCATAGATGTTTATGATATGTC	58.873	37.037	6.36	0.00	33.75	3.06
1797	5353	1.512926	ATGAAGTCGCACAACCAGAC	58.487	50.000	0.00	0.00	35.30	3.51
1853	5409	1.373873	GCTGGAAAGCAAAGCTGGC	60.374	57.895	2.51	2.51	39.62	4.85
1866	5422	1.361204	TGGAAGAGACCATTGCTGGA	58.639	50.000	0.00	0.00	46.37	3.86
1869	5425	3.328931	TCTTCTTGGAAGAGACCATTGCT	59.671	43.478	5.96	0.00	39.82	3.91
1918	5474	3.777465	TCACACAGACGAGCCTTATAC	57.223	47.619	0.00	0.00	0.00	1.47
2006	5562	9.656040	TTATGTTATGTTGTCGTTGGTATAACT	57.344	29.630	0.00	0.00	34.06	2.24
2193	5750	2.264813	GCATTGTTCATGATGTGTGCC	58.735	47.619	0.00	0.00	34.31	5.01
2235	5792	5.138276	CACTAGCAATGGGTCCTAGTACTA	58.862	45.833	1.89	1.89	39.64	1.82
2313	5870	8.204836	AGGCGATCAACTTGTCTACTTTATAAT	58.795	33.333	0.00	0.00	0.00	1.28
2317	5874	5.401531	AGGCGATCAACTTGTCTACTTTA	57.598	39.130	0.00	0.00	0.00	1.85
2321	5878	3.851098	AGAAGGCGATCAACTTGTCTAC	58.149	45.455	3.82	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.