AutoCloner

Multiple sequence alignment - TraesCS7D01G519200

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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	TraesCS7D01G519200	chr7D	100.000	2591	0	0	1	2591	617117982	617115392	0.000000e+00	4785.0
1	TraesCS7D01G519200	chr7D	84.529	711	82	20	866	1571	616908052	616908739	0.000000e+00	678.0
2	TraesCS7D01G519200	chr7D	88.562	577	41	10	797	1367	617374551	617373994	0.000000e+00	676.0
3	TraesCS7D01G519200	chr7D	95.285	403	18	1	1	402	136680383	136679981	2.810000e-179	638.0
4	TraesCS7D01G519200	chr7B	91.930	1834	91	23	797	2591	711485681	711483866	0.000000e+00	2514.0
5	TraesCS7D01G519200	chr7B	94.062	421	22	3	1	420	335830577	335830159	1.010000e-178	636.0
6	TraesCS7D01G519200	chr7B	88.356	438	42	6	1134	1571	711000738	711001166	3.820000e-143	518.0
7	TraesCS7D01G519200	chr7A	95.167	869	21	10	817	1683	709999072	709998223	0.000000e+00	1352.0
8	TraesCS7D01G519200	chr7A	92.072	555	43	1	1	554	710080801	710080247	0.000000e+00	780.0
9	TraesCS7D01G519200	chr7A	85.775	710	75	16	866	1571	709674312	709674999	0.000000e+00	728.0
10	TraesCS7D01G519200	chr7A	93.351	376	21	3	1720	2093	709992906	709992533	1.050000e-153	553.0
11	TraesCS7D01G519200	chr7A	90.397	302	24	5	2110	2407	709992220	709991920	2.420000e-105	392.0
12	TraesCS7D01G519200	chr7A	96.067	178	7	0	2414	2591	709991667	709991490	9.070000e-75	291.0
13	TraesCS7D01G519200	chr7A	87.554	233	17	2	552	783	710079961	710079740	2.560000e-65	259.0
14	TraesCS7D01G519200	chr7A	93.750	48	3	0	1675	1722	709993034	709992987	3.580000e-09	73.1
15	TraesCS7D01G519200	chr6B	95.980	398	16	0	2	399	306760064	306760461	0.000000e+00	647.0
16	TraesCS7D01G519200	chr4D	95.718	397	17	0	1	397	473126722	473127118	7.820000e-180	640.0
17	TraesCS7D01G519200	chr1B	95.285	403	17	2	1	402	390739862	390739461	2.810000e-179	638.0
18	TraesCS7D01G519200	chr1D	95.274	402	18	1	2	402	318221372	318221773	1.010000e-178	636.0
19	TraesCS7D01G519200	chr1D	95.477	398	18	0	1	398	355514617	355515014	1.010000e-178	636.0
20	TraesCS7D01G519200	chr3D	93.824	421	23	3	1	420	365104703	365105121	4.710000e-177	630.0
21	TraesCS7D01G519200	chr2D	90.395	177	13	3	1795	1970	435149434	435149261	2.010000e-56	230.0
22	TraesCS7D01G519200	chr5D	86.957	184	21	2	1788	1970	112953774	112953593	1.220000e-48	204.0
23	TraesCS7D01G519200	chr5A	85.792	183	24	1	1788	1970	118388908	118388728	2.630000e-45	193.0
24	TraesCS7D01G519200	chr3B	85.088	114	10	1	1787	1893	32445398	32445285	2.730000e-20	110.0

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	TraesCS7D01G519200	chr7D	617115392	617117982	2590	True	4785.000	4785	100.00000	1	2591	1	chr7D.!!$R2	2590
1	TraesCS7D01G519200	chr7D	616908052	616908739	687	False	678.000	678	84.52900	866	1571	1	chr7D.!!$F1	705
2	TraesCS7D01G519200	chr7D	617373994	617374551	557	True	676.000	676	88.56200	797	1367	1	chr7D.!!$R3	570
3	TraesCS7D01G519200	chr7B	711483866	711485681	1815	True	2514.000	2514	91.93000	797	2591	1	chr7B.!!$R2	1794
4	TraesCS7D01G519200	chr7A	709998223	709999072	849	True	1352.000	1352	95.16700	817	1683	1	chr7A.!!$R1	866
5	TraesCS7D01G519200	chr7A	709674312	709674999	687	False	728.000	728	85.77500	866	1571	1	chr7A.!!$F1	705
6	TraesCS7D01G519200	chr7A	710079740	710080801	1061	True	519.500	780	89.81300	1	783	2	chr7A.!!$R3	782
7	TraesCS7D01G519200	chr7A	709991490	709993034	1544	True	327.275	553	93.39125	1675	2591	4	chr7A.!!$R2	916

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
787	1078	0.313987	GTGCTTCTTTTTGACCCCCG	59.686	55.0	0.0	0.0	0.0	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1937	2356	0.032403	CACACACGGACCCTTTACGA	59.968	55.0	0.0	0.0	0.0	3.43	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
58	59	4.926238	GGGAGTTGCATAATCTCATAGTCG	59.074	45.833	0.00	0.00	0.00	4.18
123	124	8.461249	AAACTGAATGATCATTATGCTAAGCT	57.539	30.769	20.75	0.00	34.37	3.74
132	133	6.096673	TCATTATGCTAAGCTAACGGATGA	57.903	37.500	0.00	0.00	0.00	2.92
144	145	2.969628	ACGGATGAGTCTTGTCCATC	57.030	50.000	9.45	0.00	36.78	3.51
145	146	2.179427	ACGGATGAGTCTTGTCCATCA	58.821	47.619	0.00	0.00	38.65	3.07
154	155	5.169992	AGTCTTGTCCATCACATCATTCA	57.830	39.130	0.00	0.00	33.90	2.57
171	172	5.954296	CATTCACCTAATGATGTGATCCC	57.046	43.478	0.00	0.00	46.81	3.85
184	185	6.298361	TGATGTGATCCCGTTATCAAATGAT	58.702	36.000	4.98	1.01	34.56	2.45
208	209	4.589908	ACTCATGTCCATGGTTAGGAAAC	58.410	43.478	12.58	0.61	39.24	2.78
260	261	3.900971	AGTAGAGGCTTACTAGGGACAC	58.099	50.000	7.35	0.00	32.25	3.67
261	262	3.528491	AGTAGAGGCTTACTAGGGACACT	59.472	47.826	7.35	0.00	32.25	3.55
264	265	2.166664	GAGGCTTACTAGGGACACTGTG	59.833	54.545	6.19	6.19	0.00	3.66
403	404	1.876156	GCATATTTCCTTCAGCTCCGG	59.124	52.381	0.00	0.00	0.00	5.14
448	450	1.675641	GCGATGAGGGTGGCAAAGT	60.676	57.895	0.00	0.00	0.00	2.66
465	467	1.889545	AGTTGAAGCAGAAGCAGGAC	58.110	50.000	0.00	0.00	45.49	3.85
466	468	0.877743	GTTGAAGCAGAAGCAGGACC	59.122	55.000	0.00	0.00	45.49	4.46
469	471	4.749310	AGCAGAAGCAGGACCGCG	62.749	66.667	0.00	0.00	45.49	6.46
486	488	2.387445	CGTCATCCGGCGCTTCAAA	61.387	57.895	7.64	0.00	0.00	2.69
504	506	4.442706	TCAAAGGCTAATTCGTCATCTCC	58.557	43.478	0.00	0.00	0.00	3.71
554	556	0.531532	GATGGCTCTGACGATGGTGG	60.532	60.000	0.00	0.00	0.00	4.61
556	558	0.977627	TGGCTCTGACGATGGTGGAT	60.978	55.000	0.00	0.00	0.00	3.41
557	559	0.531532	GGCTCTGACGATGGTGGATG	60.532	60.000	0.00	0.00	0.00	3.51
558	560	1.156645	GCTCTGACGATGGTGGATGC	61.157	60.000	0.00	0.00	0.00	3.91
559	561	0.873312	CTCTGACGATGGTGGATGCG	60.873	60.000	0.00	0.00	0.00	4.73
560	562	1.884464	CTGACGATGGTGGATGCGG	60.884	63.158	0.00	0.00	0.00	5.69
561	563	3.272334	GACGATGGTGGATGCGGC	61.272	66.667	0.00	0.00	0.00	6.53
599	889	3.345808	GCAGACGCGGCTGAAACA	61.346	61.111	44.63	0.00	38.14	2.83
605	895	4.683334	GCGGCTGAAACACGCCAC	62.683	66.667	0.00	0.00	46.62	5.01
609	899	4.025401	CTGAAACACGCCACGGGC	62.025	66.667	4.96	4.96	46.75	6.13
646	936	2.806608	TGACAAGTCCGGTTGTAGAC	57.193	50.000	10.19	0.00	40.83	2.59
648	938	0.319297	ACAAGTCCGGTTGTAGACGC	60.319	55.000	8.59	0.00	38.92	5.19
783	1074	3.905784	CATCAGGTGCTTCTTTTTGACC	58.094	45.455	0.00	0.00	0.00	4.02
784	1075	2.306847	TCAGGTGCTTCTTTTTGACCC	58.693	47.619	0.00	0.00	0.00	4.46
785	1076	1.341209	CAGGTGCTTCTTTTTGACCCC	59.659	52.381	0.00	0.00	0.00	4.95
786	1077	0.679505	GGTGCTTCTTTTTGACCCCC	59.320	55.000	0.00	0.00	0.00	5.40
787	1078	0.313987	GTGCTTCTTTTTGACCCCCG	59.686	55.000	0.00	0.00	0.00	5.73
788	1079	1.289066	GCTTCTTTTTGACCCCCGC	59.711	57.895	0.00	0.00	0.00	6.13
789	1080	1.460273	GCTTCTTTTTGACCCCCGCA	61.460	55.000	0.00	0.00	0.00	5.69
790	1081	1.036707	CTTCTTTTTGACCCCCGCAA	58.963	50.000	0.00	0.00	0.00	4.85
791	1082	1.410882	CTTCTTTTTGACCCCCGCAAA	59.589	47.619	0.00	0.00	33.76	3.68
792	1083	1.486211	TCTTTTTGACCCCCGCAAAA	58.514	45.000	0.00	0.00	41.81	2.44
793	1084	1.831736	TCTTTTTGACCCCCGCAAAAA	59.168	42.857	12.04	12.04	46.78	1.94
848	1143	4.162812	TGAATAAATCGCTGGCGTTTTTC	58.837	39.130	22.67	17.10	40.39	2.29
853	1148	1.833860	TCGCTGGCGTTTTTCTTTTG	58.166	45.000	14.55	0.00	40.74	2.44
854	1149	1.133407	TCGCTGGCGTTTTTCTTTTGT	59.867	42.857	14.55	0.00	40.74	2.83
855	1150	1.255084	CGCTGGCGTTTTTCTTTTGTG	59.745	47.619	6.83	0.00	34.35	3.33
1107	1416	4.866224	TGCACCCACACCCACACG	62.866	66.667	0.00	0.00	0.00	4.49
1139	1475	3.706373	CCACGACCTCCCCCACAG	61.706	72.222	0.00	0.00	0.00	3.66
1168	1504	1.961277	CACCACGTCCACTCCAAGC	60.961	63.158	0.00	0.00	0.00	4.01
1737	2156	6.346919	GCATAGTTACATTGGATGCTAACTCG	60.347	42.308	13.81	10.35	39.81	4.18
1819	2238	3.970640	AGACTCAGGGAGGGATTGATTAC	59.029	47.826	0.00	0.00	33.35	1.89
1894	2313	2.355115	GTCCACCCCCGCTGAATT	59.645	61.111	0.00	0.00	0.00	2.17
1937	2356	8.379457	AGTTAGAAGAAAATCACGTAAAAGCT	57.621	30.769	0.00	0.00	0.00	3.74
1954	2373	1.012486	GCTCGTAAAGGGTCCGTGTG	61.012	60.000	0.00	0.00	0.00	3.82
1955	2374	0.316204	CTCGTAAAGGGTCCGTGTGT	59.684	55.000	0.00	0.00	0.00	3.72
1972	2391	3.306166	GTGTGTGTGTAGGATTATCGTGC	59.694	47.826	0.00	0.00	0.00	5.34
1981	2400	9.256477	TGTGTAGGATTATCGTGCTATTTAAAG	57.744	33.333	4.82	0.00	0.00	1.85
2097	2527	0.548031	TCAAAGCCCAGGCATAGAGG	59.452	55.000	12.03	0.00	44.88	3.69
2108	2538	3.379688	CAGGCATAGAGGAAAGAAAAGGC	59.620	47.826	0.00	0.00	0.00	4.35
2131	2847	4.069869	CCAGTTCAGGGCAGTGTG	57.930	61.111	0.00	0.00	0.00	3.82
2150	2866	1.762370	TGAGTGCACGGATATGTCCAT	59.238	47.619	12.01	0.00	45.37	3.41
2215	2932	1.710244	TGGATTGAACCTGTGGGTGAT	59.290	47.619	0.00	0.00	46.67	3.06
2217	2934	2.369394	GATTGAACCTGTGGGTGATCC	58.631	52.381	0.00	0.00	46.67	3.36
2236	2953	4.360951	TCCCGTCAACTAGAACCATTTT	57.639	40.909	0.00	0.00	0.00	1.82
2252	2969	5.938322	ACCATTTTAGTATGTGCAGTTTCG	58.062	37.500	0.00	0.00	0.00	3.46
2271	2988	5.749596	TTCGTCTGCTCAATTTCTTTTCA	57.250	34.783	0.00	0.00	0.00	2.69
2291	3008	3.165071	CACCCCCTAATTTTGCTCAACT	58.835	45.455	0.00	0.00	0.00	3.16
2331	3051	4.647424	TTTGTTTCCAGTCCATCACAAC	57.353	40.909	0.00	0.00	0.00	3.32
2392	3112	4.162812	CAAATAAACCGACACCATTTCCG	58.837	43.478	0.00	0.00	0.00	4.30
2397	3117	1.095228	CCGACACCATTTCCGGGATG	61.095	60.000	0.00	6.69	38.42	3.51
2514	3482	1.222113	GGCTAGCAGGGACCAGAAC	59.778	63.158	18.24	0.00	0.00	3.01
2532	3500	3.721575	AGAACCCACAATATGCCCTCATA	59.278	43.478	0.00	0.00	39.31	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	4.926238	CGACTATGAGATTATGCAACTCCC	59.074	45.833	0.00	0.00	0.00	4.30
42	43	9.029243	CATATTCCTTCGACTATGAGATTATGC	57.971	37.037	0.00	0.00	34.92	3.14
106	107	6.096673	TCCGTTAGCTTAGCATAATGATCA	57.903	37.500	7.07	0.00	0.00	2.92
123	124	3.767131	TGATGGACAAGACTCATCCGTTA	59.233	43.478	0.00	0.00	37.17	3.18
132	133	4.940046	GTGAATGATGTGATGGACAAGACT	59.060	41.667	0.00	0.00	38.36	3.24
154	155	5.306937	TGATAACGGGATCACATCATTAGGT	59.693	40.000	0.00	0.00	30.75	3.08
184	185	6.177610	GTTTCCTAACCATGGACATGAGTTA	58.822	40.000	21.47	16.03	41.20	2.24
208	209	5.404968	GCTCGTTGATCAGAGATGATTAAGG	59.595	44.000	14.47	8.35	36.65	2.69
214	215	4.203226	ACTAGCTCGTTGATCAGAGATGA	58.797	43.478	14.47	2.44	36.65	2.92
220	221	5.986741	TCTACTAGACTAGCTCGTTGATCAG	59.013	44.000	9.52	0.00	0.00	2.90
260	261	8.904712	CATGTGTGAATACATAAACAAACACAG	58.095	33.333	10.57	1.22	46.74	3.66
403	404	1.880340	CGGACTCTCAATGCCGAGC	60.880	63.158	0.00	0.00	46.29	5.03
407	408	1.880340	CGCTCGGACTCTCAATGCC	60.880	63.158	0.00	0.00	0.00	4.40
434	436	1.691196	CTTCAACTTTGCCACCCTCA	58.309	50.000	0.00	0.00	0.00	3.86
448	450	0.603707	CGGTCCTGCTTCTGCTTCAA	60.604	55.000	0.00	0.00	40.48	2.69
469	471	1.425428	CTTTGAAGCGCCGGATGAC	59.575	57.895	5.05	0.00	0.00	3.06
483	485	4.446371	AGGAGATGACGAATTAGCCTTTG	58.554	43.478	0.00	0.00	0.00	2.77
486	488	3.571590	AGAGGAGATGACGAATTAGCCT	58.428	45.455	0.00	0.00	0.00	4.58
504	506	2.483583	CGTCATCGGAGAAGGAAGAG	57.516	55.000	0.00	0.00	43.58	2.85
534	536	0.873312	CACCATCGTCAGAGCCATCG	60.873	60.000	0.00	0.00	0.00	3.84
554	556	2.515991	TCCCCAAATCGCCGCATC	60.516	61.111	0.00	0.00	0.00	3.91
556	558	3.969250	GACTCCCCAAATCGCCGCA	62.969	63.158	0.00	0.00	0.00	5.69
557	559	3.202706	GACTCCCCAAATCGCCGC	61.203	66.667	0.00	0.00	0.00	6.53
558	560	2.106683	GTGACTCCCCAAATCGCCG	61.107	63.158	0.00	0.00	0.00	6.46
559	561	1.026718	CAGTGACTCCCCAAATCGCC	61.027	60.000	0.00	0.00	0.00	5.54
560	562	0.321653	ACAGTGACTCCCCAAATCGC	60.322	55.000	0.00	0.00	0.00	4.58
561	563	1.676014	GGACAGTGACTCCCCAAATCG	60.676	57.143	0.00	0.00	0.00	3.34
609	899	3.074412	GTCAAATCCGGCACCCTATATG	58.926	50.000	0.00	0.00	0.00	1.78
610	900	2.708861	TGTCAAATCCGGCACCCTATAT	59.291	45.455	0.00	0.00	0.00	0.86
637	927	3.243336	CACAGTTAGAGCGTCTACAACC	58.757	50.000	0.00	0.00	0.00	3.77
646	936	7.772332	ATAAAAATCCTACACAGTTAGAGCG	57.228	36.000	0.00	0.00	0.00	5.03
689	979	5.364778	GGGCAAAAATCCTACACAGTTTTT	58.635	37.500	0.00	0.00	34.98	1.94
690	980	4.202315	GGGGCAAAAATCCTACACAGTTTT	60.202	41.667	0.00	0.00	0.00	2.43
691	981	3.323691	GGGGCAAAAATCCTACACAGTTT	59.676	43.478	0.00	0.00	0.00	2.66
692	982	2.897326	GGGGCAAAAATCCTACACAGTT	59.103	45.455	0.00	0.00	0.00	3.16
748	1038	1.398390	CCTGATGCAAACTACTTCGCC	59.602	52.381	0.00	0.00	0.00	5.54
793	1084	5.994668	TGTTTGTCAAAAAGAAGCACCTTTT	59.005	32.000	0.00	9.42	45.28	2.27
794	1085	5.546526	TGTTTGTCAAAAAGAAGCACCTTT	58.453	33.333	0.00	0.00	37.94	3.11
795	1086	5.146010	TGTTTGTCAAAAAGAAGCACCTT	57.854	34.783	0.00	0.00	0.00	3.50
814	1105	9.520204	CCAGCGATTTATTCATCTATTTTTGTT	57.480	29.630	0.00	0.00	0.00	2.83
848	1143	2.218603	AGCCACTACCGTTCACAAAAG	58.781	47.619	0.00	0.00	0.00	2.27
853	1148	0.320697	AGGAAGCCACTACCGTTCAC	59.679	55.000	0.00	0.00	0.00	3.18
854	1149	0.606604	GAGGAAGCCACTACCGTTCA	59.393	55.000	0.00	0.00	0.00	3.18
855	1150	0.896226	AGAGGAAGCCACTACCGTTC	59.104	55.000	0.00	0.00	0.00	3.95
1595	1931	9.732130	AGTAAAATTCTGATGCTACTCTTTTCT	57.268	29.630	0.00	0.00	0.00	2.52
1737	2156	4.262463	GGTCCCAATTGACTTTTCTTTCCC	60.262	45.833	7.12	0.00	35.54	3.97
1819	2238	0.389426	CTGTTAGTCCGTGAACCCCG	60.389	60.000	0.00	0.00	0.00	5.73
1894	2313	3.019799	ACTAATCTCTCTCCCGCTGAA	57.980	47.619	0.00	0.00	0.00	3.02
1937	2356	0.032403	CACACACGGACCCTTTACGA	59.968	55.000	0.00	0.00	0.00	3.43
1954	2373	8.583810	TTAAATAGCACGATAATCCTACACAC	57.416	34.615	0.00	0.00	0.00	3.82
1955	2374	9.256477	CTTTAAATAGCACGATAATCCTACACA	57.744	33.333	0.00	0.00	0.00	3.72
1981	2400	9.173939	CACTCTCTGTCATTTTCACAAAATTAC	57.826	33.333	0.90	0.90	38.97	1.89
1991	2410	4.276926	AGGTTTGCACTCTCTGTCATTTTC	59.723	41.667	0.00	0.00	0.00	2.29
2126	2842	1.550524	ACATATCCGTGCACTCACACT	59.449	47.619	16.19	0.00	43.28	3.55
2146	2862	2.297895	CCCAAGTCCCCGTCATGGA	61.298	63.158	0.00	0.00	42.00	3.41
2150	2866	1.540367	ATTCCCCAAGTCCCCGTCA	60.540	57.895	0.00	0.00	0.00	4.35
2215	2932	4.360951	AAAATGGTTCTAGTTGACGGGA	57.639	40.909	0.00	0.00	0.00	5.14
2217	2934	7.548075	ACATACTAAAATGGTTCTAGTTGACGG	59.452	37.037	0.00	0.00	0.00	4.79
2252	2969	4.550422	GGGTGAAAAGAAATTGAGCAGAC	58.450	43.478	0.00	0.00	0.00	3.51
2271	2988	3.431415	GAGTTGAGCAAAATTAGGGGGT	58.569	45.455	0.00	0.00	0.00	4.95
2291	3008	1.320344	ATTGGACTAGAGCGGTGCGA	61.320	55.000	0.00	0.00	0.00	5.10
2331	3051	5.357032	GGTCTTTACATGGTTTCATAGTGGG	59.643	44.000	0.00	0.00	31.33	4.61
2514	3482	3.679389	GACTATGAGGGCATATTGTGGG	58.321	50.000	0.00	0.00	36.45	4.61
2532	3500	2.670148	GGGGCTCCAATGGACGACT	61.670	63.158	0.00	0.00	0.00	4.18
2562	3530	1.447314	CCTCGGCGGTTGTACCTTC	60.447	63.158	7.21	0.00	35.66	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.