AutoCloner

Multiple sequence alignment - TraesCS6D01G338000

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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	TraesCS6D01G338000	chr6D	100.000	3409	0	0	1	3409	438343512	438346920	0.000000e+00	6296
1	TraesCS6D01G338000	chr6D	86.235	1235	122	24	1266	2466	436373281	436374501	0.000000e+00	1295
2	TraesCS6D01G338000	chr6D	90.590	797	58	10	2616	3409	30224869	30224087	0.000000e+00	1040
3	TraesCS6D01G338000	chr6D	90.226	798	58	16	2616	3409	55385473	55384692	0.000000e+00	1024
4	TraesCS6D01G338000	chr6A	93.824	2623	136	16	2	2616	586854164	586856768	0.000000e+00	3923
5	TraesCS6D01G338000	chr6A	88.458	1083	108	8	1363	2432	584527997	584529075	0.000000e+00	1291
6	TraesCS6D01G338000	chr6A	85.881	1197	114	28	1266	2432	584504726	584505897	0.000000e+00	1223
7	TraesCS6D01G338000	chr6B	93.039	1336	76	12	1257	2591	663787625	663788944	0.000000e+00	1936
8	TraesCS6D01G338000	chr6B	91.781	1022	73	5	98	1117	663767379	663768391	0.000000e+00	1411
9	TraesCS6D01G338000	chr6B	87.547	1068	111	10	1385	2432	659592657	659593722	0.000000e+00	1216
10	TraesCS6D01G338000	chr6B	92.723	797	55	3	2616	3409	240299012	240298216	0.000000e+00	1147
11	TraesCS6D01G338000	chr6B	91.034	803	61	8	2612	3409	32965279	32966075	0.000000e+00	1074
12	TraesCS6D01G338000	chr6B	91.667	144	4	5	1117	1257	663786649	663786787	3.470000e-45	193
13	TraesCS6D01G338000	chr3B	90.977	798	62	8	2616	3409	88670111	88669320	0.000000e+00	1066
14	TraesCS6D01G338000	chr3B	80.968	310	35	15	2613	2918	10574344	10574633	1.230000e-54	224
15	TraesCS6D01G338000	chr4B	90.375	800	65	10	2616	3409	93731734	93730941	0.000000e+00	1040
16	TraesCS6D01G338000	chr4B	91.242	765	55	9	2649	3409	630463454	630462698	0.000000e+00	1031
17	TraesCS6D01G338000	chr7B	91.146	768	51	13	2649	3409	740400204	740400961	0.000000e+00	1026
18	TraesCS6D01G338000	chr7B	75.758	264	45	10	398	644	244567857	244568118	7.730000e-22	115
19	TraesCS6D01G338000	chr3A	89.526	802	71	10	2613	3409	668628709	668629502	0.000000e+00	1003
20	TraesCS6D01G338000	chr3A	75.106	707	125	24	292	969	588516971	588516287	2.000000e-72	283
21	TraesCS6D01G338000	chr3D	74.808	913	189	27	80	969	605062447	605061553	1.160000e-99	374
22	TraesCS6D01G338000	chr3D	75.260	768	145	26	226	969	539576746	539576000	1.180000e-84	324
23	TraesCS6D01G338000	chr7D	75.911	768	141	26	226	968	186006212	186006960	1.500000e-93	353
24	TraesCS6D01G338000	chr7D	78.054	442	85	9	528	968	4391031	4390601	5.610000e-68	268
25	TraesCS6D01G338000	chrUn	75.815	736	137	28	253	968	324145763	324145049	5.450000e-88	335
26	TraesCS6D01G338000	chr1B	75.385	715	143	21	255	957	32371319	32372012	7.100000e-82	315
27	TraesCS6D01G338000	chr1B	78.586	481	72	19	505	969	43957962	43958427	4.300000e-74	289
28	TraesCS6D01G338000	chr1B	75.592	549	101	23	436	968	667370606	667371137	1.220000e-59	241
29	TraesCS6D01G338000	chr2B	73.781	923	178	39	79	969	232247574	232248464	4.270000e-79	305
30	TraesCS6D01G338000	chr5A	75.234	747	123	43	253	969	680271580	680270866	7.150000e-77	298
31	TraesCS6D01G338000	chr5B	78.602	472	76	19	509	969	485872186	485872643	4.300000e-74	289
32	TraesCS6D01G338000	chr7A	78.407	477	78	17	505	973	709675774	709675315	1.550000e-73	287
33	TraesCS6D01G338000	chr7A	73.948	737	139	32	257	969	410719257	410718550	7.310000e-62	248

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	TraesCS6D01G338000	chr6D	438343512	438346920	3408	False	6296.0	6296	100.000	1	3409	1	chr6D.!!$F2	3408
1	TraesCS6D01G338000	chr6D	436373281	436374501	1220	False	1295.0	1295	86.235	1266	2466	1	chr6D.!!$F1	1200
2	TraesCS6D01G338000	chr6D	30224087	30224869	782	True	1040.0	1040	90.590	2616	3409	1	chr6D.!!$R1	793
3	TraesCS6D01G338000	chr6D	55384692	55385473	781	True	1024.0	1024	90.226	2616	3409	1	chr6D.!!$R2	793
4	TraesCS6D01G338000	chr6A	586854164	586856768	2604	False	3923.0	3923	93.824	2	2616	1	chr6A.!!$F3	2614
5	TraesCS6D01G338000	chr6A	584527997	584529075	1078	False	1291.0	1291	88.458	1363	2432	1	chr6A.!!$F2	1069
6	TraesCS6D01G338000	chr6A	584504726	584505897	1171	False	1223.0	1223	85.881	1266	2432	1	chr6A.!!$F1	1166
7	TraesCS6D01G338000	chr6B	663767379	663768391	1012	False	1411.0	1411	91.781	98	1117	1	chr6B.!!$F3	1019
8	TraesCS6D01G338000	chr6B	659592657	659593722	1065	False	1216.0	1216	87.547	1385	2432	1	chr6B.!!$F2	1047
9	TraesCS6D01G338000	chr6B	240298216	240299012	796	True	1147.0	1147	92.723	2616	3409	1	chr6B.!!$R1	793
10	TraesCS6D01G338000	chr6B	32965279	32966075	796	False	1074.0	1074	91.034	2612	3409	1	chr6B.!!$F1	797
11	TraesCS6D01G338000	chr6B	663786649	663788944	2295	False	1064.5	1936	92.353	1117	2591	2	chr6B.!!$F4	1474
12	TraesCS6D01G338000	chr3B	88669320	88670111	791	True	1066.0	1066	90.977	2616	3409	1	chr3B.!!$R1	793
13	TraesCS6D01G338000	chr4B	93730941	93731734	793	True	1040.0	1040	90.375	2616	3409	1	chr4B.!!$R1	793
14	TraesCS6D01G338000	chr4B	630462698	630463454	756	True	1031.0	1031	91.242	2649	3409	1	chr4B.!!$R2	760
15	TraesCS6D01G338000	chr7B	740400204	740400961	757	False	1026.0	1026	91.146	2649	3409	1	chr7B.!!$F2	760
16	TraesCS6D01G338000	chr3A	668628709	668629502	793	False	1003.0	1003	89.526	2613	3409	1	chr3A.!!$F1	796
17	TraesCS6D01G338000	chr3A	588516287	588516971	684	True	283.0	283	75.106	292	969	1	chr3A.!!$R1	677
18	TraesCS6D01G338000	chr3D	605061553	605062447	894	True	374.0	374	74.808	80	969	1	chr3D.!!$R2	889
19	TraesCS6D01G338000	chr3D	539576000	539576746	746	True	324.0	324	75.260	226	969	1	chr3D.!!$R1	743
20	TraesCS6D01G338000	chr7D	186006212	186006960	748	False	353.0	353	75.911	226	968	1	chr7D.!!$F1	742
21	TraesCS6D01G338000	chrUn	324145049	324145763	714	True	335.0	335	75.815	253	968	1	chrUn.!!$R1	715
22	TraesCS6D01G338000	chr1B	32371319	32372012	693	False	315.0	315	75.385	255	957	1	chr1B.!!$F1	702
23	TraesCS6D01G338000	chr1B	667370606	667371137	531	False	241.0	241	75.592	436	968	1	chr1B.!!$F3	532
24	TraesCS6D01G338000	chr2B	232247574	232248464	890	False	305.0	305	73.781	79	969	1	chr2B.!!$F1	890
25	TraesCS6D01G338000	chr5A	680270866	680271580	714	True	298.0	298	75.234	253	969	1	chr5A.!!$R1	716
26	TraesCS6D01G338000	chr7A	410718550	410719257	707	True	248.0	248	73.948	257	969	1	chr7A.!!$R1	712

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
903	964	0.239347	GGTGTGTGCTCATTGTGCTC	59.761	55.0	11.58	8.67	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2808	3755	0.240945	CGGTTCAAGCCACCAATCAC	59.759	55.0	0.0	0.0	33.36	3.06	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
73	74	3.768922	GCTGCAGCGAGGAGGTCT	61.769	66.667	25.23	0.00	35.99	3.85
172	174	1.512735	GGCCTCAATAGGGGTCTCTT	58.487	55.000	0.00	0.00	43.87	2.85
224	226	3.186909	TCATCATCGTTGTTGATCCGTC	58.813	45.455	3.63	0.00	31.50	4.79
343	353	1.068588	CTTGGGCCATGAGATGCAATG	59.931	52.381	13.94	0.00	0.00	2.82
345	355	0.672342	GGGCCATGAGATGCAATGTC	59.328	55.000	4.39	0.00	37.09	3.06
383	395	3.002656	CGCAGAGGGTATAATTGTGCAAG	59.997	47.826	0.00	0.00	0.00	4.01
386	398	4.818546	CAGAGGGTATAATTGTGCAAGGAG	59.181	45.833	0.00	0.00	0.00	3.69
423	437	1.098050	AGATGCTGGGATCGCAAAAC	58.902	50.000	14.01	6.99	41.26	2.43
425	439	1.406539	GATGCTGGGATCGCAAAACAT	59.593	47.619	14.01	15.95	41.26	2.71
623	656	5.393068	TCTGGCCTTTGATAATTGGATCT	57.607	39.130	3.32	0.00	0.00	2.75
866	924	0.813210	TGTGTTGCTCGTGTGCATCA	60.813	50.000	0.00	4.15	42.96	3.07
900	961	1.575922	CGGGTGTGTGCTCATTGTG	59.424	57.895	0.00	0.00	0.00	3.33
901	962	1.286880	GGGTGTGTGCTCATTGTGC	59.713	57.895	3.79	3.79	0.00	4.57
902	963	1.174712	GGGTGTGTGCTCATTGTGCT	61.175	55.000	11.58	0.00	0.00	4.40
903	964	0.239347	GGTGTGTGCTCATTGTGCTC	59.761	55.000	11.58	8.67	0.00	4.26
904	965	0.946528	GTGTGTGCTCATTGTGCTCA	59.053	50.000	11.58	10.98	0.00	4.26
905	966	1.538512	GTGTGTGCTCATTGTGCTCAT	59.461	47.619	15.78	0.00	36.54	2.90
906	967	2.030540	GTGTGTGCTCATTGTGCTCATT	60.031	45.455	15.78	0.00	36.54	2.57
907	968	2.624364	TGTGTGCTCATTGTGCTCATTT	59.376	40.909	15.78	0.00	36.54	2.32
908	969	3.819902	TGTGTGCTCATTGTGCTCATTTA	59.180	39.130	15.78	6.17	36.54	1.40
941	1003	9.807649	ATTATCTTGATGCTTTATTTTGTGTCC	57.192	29.630	0.00	0.00	0.00	4.02
960	1022	5.925969	GTGTCCATAAAATCAACCCTTTGTG	59.074	40.000	0.00	0.00	34.02	3.33
995	1057	9.340695	CTTGATCGATATGTACTCATCTCTTTC	57.659	37.037	0.00	0.00	35.70	2.62
997	1059	7.448469	TGATCGATATGTACTCATCTCTTTCCA	59.552	37.037	0.00	0.00	35.70	3.53
1023	1085	3.735591	ACAAAAAGAGACGGATTTCGGA	58.264	40.909	0.00	0.00	44.45	4.55
1062	1125	8.430063	GTGTTTGTTTATCTTGATGCTTCATTG	58.570	33.333	2.75	0.56	0.00	2.82
1783	2714	1.000739	AATACGACTCGGGACCCCA	59.999	57.895	4.46	0.00	35.37	4.96
1960	2900	1.681793	CACCTACTCCTATCACACGGG	59.318	57.143	0.00	0.00	0.00	5.28
2256	3196	2.355818	GGTAGGTTTTGCCTCTGGGTAG	60.356	54.545	0.00	0.00	46.96	3.18
2353	3299	3.426568	GCTGGAGCGCCAACTCAC	61.427	66.667	11.38	0.00	45.41	3.51
2370	3316	0.821517	CACCGACTACATGCTACCCA	59.178	55.000	0.00	0.00	0.00	4.51
2378	3324	2.533266	ACATGCTACCCATAAGCTCG	57.467	50.000	0.00	0.00	40.73	5.03
2562	3509	2.606519	TTGGGTGGCGAGGCTAGT	60.607	61.111	0.00	0.00	0.00	2.57
2599	3546	2.601481	CGGACAGCAAGATTTGTGTC	57.399	50.000	12.15	12.15	39.13	3.67
2620	3567	8.676454	GTGTCAGACACTTTAGACATTAGTAG	57.324	38.462	24.23	0.00	45.27	2.57
2776	3723	2.426887	GGACGAACCGGGACCAAA	59.573	61.111	6.32	0.00	0.00	3.28
2808	3755	0.466007	TGGCCCATCATCATTGGTCG	60.466	55.000	0.00	0.00	31.99	4.79
2811	3758	1.746861	GCCCATCATCATTGGTCGTGA	60.747	52.381	0.00	0.00	31.99	4.35
2835	3782	1.304134	GGCTTGAACCGGGACCAAT	60.304	57.895	6.32	0.00	0.00	3.16
2924	3873	2.653115	CGAGCAGAGCACTCCACA	59.347	61.111	0.00	0.00	0.00	4.17
2925	3874	1.735920	CGAGCAGAGCACTCCACAC	60.736	63.158	0.00	0.00	0.00	3.82
2926	3875	1.670590	GAGCAGAGCACTCCACACT	59.329	57.895	0.00	0.00	0.00	3.55
2927	3876	0.669932	GAGCAGAGCACTCCACACTG	60.670	60.000	0.00	0.00	0.00	3.66
2932	3881	1.206610	AGAGCACTCCACACTGCTATG	59.793	52.381	0.00	0.00	43.94	2.23
3047	3997	2.488204	GCTTTCTCCTCTCCAAGCTT	57.512	50.000	0.00	0.00	38.89	3.74
3099	4049	0.248377	CTAGGTTTAGCGGTCCGTCG	60.248	60.000	13.94	0.00	0.00	5.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	4.738998	CCATCCCGGCAGCACCAA	62.739	66.667	0.00	0.00	39.03	3.67
30	31	3.242291	CCCTAGGCCGACCATCCC	61.242	72.222	2.05	0.00	39.06	3.85
38	39	2.768344	ACCCATGACCCTAGGCCG	60.768	66.667	2.05	0.00	0.00	6.13
42	43	1.153086	GCAGCACCCATGACCCTAG	60.153	63.158	0.00	0.00	0.00	3.02
44	45	3.259314	TGCAGCACCCATGACCCT	61.259	61.111	0.00	0.00	0.00	4.34
73	74	3.884774	AGGAACCAAGGCGCCACA	61.885	61.111	31.54	0.00	0.00	4.17
172	174	0.897621	TCTGATTGCTCTCTTGCCGA	59.102	50.000	0.00	0.00	0.00	5.54
181	183	3.406764	AGAACACCACTTCTGATTGCTC	58.593	45.455	0.00	0.00	0.00	4.26
248	256	2.894257	ATTCCACAGCGAGGCCACA	61.894	57.895	5.01	0.00	0.00	4.17
343	353	1.668151	GTCAAGCCGTGGTCCAGAC	60.668	63.158	0.00	0.00	0.00	3.51
345	355	2.738521	CGTCAAGCCGTGGTCCAG	60.739	66.667	0.00	0.00	0.00	3.86
423	437	5.746721	CCATCATGTGTTACTGCAATCAATG	59.253	40.000	0.00	0.00	0.00	2.82
425	439	5.008980	TCCATCATGTGTTACTGCAATCAA	58.991	37.500	0.00	0.00	0.00	2.57
561	594	6.320672	CCTGAAGAACCAATTTGAGCATATCT	59.679	38.462	0.00	0.00	0.00	1.98
623	656	1.332375	GCTTAAGCGTTGTTGTCACCA	59.668	47.619	12.53	0.00	0.00	4.17
866	924	3.245658	ACACCCGGCCTCTACATAGATAT	60.246	47.826	0.00	0.00	0.00	1.63
941	1003	8.430801	TTTTCACACAAAGGGTTGATTTTATG	57.569	30.769	0.00	0.00	38.20	1.90
969	1031	9.340695	GAAAGAGATGAGTACATATCGATCAAG	57.659	37.037	0.00	0.00	45.76	3.02
995	1057	4.252971	TCCGTCTCTTTTTGTACTCTGG	57.747	45.455	0.00	0.00	0.00	3.86
997	1059	5.634020	CGAAATCCGTCTCTTTTTGTACTCT	59.366	40.000	0.00	0.00	0.00	3.24
1062	1125	0.799534	GCGCATGAATCTTGGTGCAC	60.800	55.000	8.80	8.80	37.44	4.57
1108	1171	3.119743	ACACAATGACATCAATTCGCAGG	60.120	43.478	0.00	0.00	0.00	4.85
1640	2563	3.138798	TCGTAGAGCAGGGTCCGC	61.139	66.667	0.00	0.00	0.00	5.54
1783	2714	1.603236	CTGCTGGAGAGCCTCGAACT	61.603	60.000	0.00	0.00	45.57	3.01
1922	2862	3.467226	CCCTGGTACCGCACGGAT	61.467	66.667	17.40	2.73	38.96	4.18
2256	3196	0.310543	TTGCTGTTGTCGTGATTGGC	59.689	50.000	0.00	0.00	0.00	4.52
2353	3299	3.861131	GCTTATGGGTAGCATGTAGTCGG	60.861	52.174	0.00	0.00	38.51	4.79
2378	3324	1.133025	ACATCAGCACCAAAATAGCGC	59.867	47.619	0.00	0.00	0.00	5.92
2505	3452	1.066716	GCCAAAGCTTGATGCATTCCA	60.067	47.619	0.00	0.00	45.94	3.53
2512	3459	3.624861	AGAATCTACGCCAAAGCTTGATG	59.375	43.478	0.00	0.00	36.60	3.07
2562	3509	2.875485	CTCGGACGGCGAGAAAGA	59.125	61.111	16.62	4.52	35.69	2.52
2612	3559	7.114529	CGAACGTAAGCCCTATTTCTACTAATG	59.885	40.741	0.00	0.00	45.62	1.90
2613	3560	7.144000	CGAACGTAAGCCCTATTTCTACTAAT	58.856	38.462	0.00	0.00	45.62	1.73
2614	3561	6.460123	CCGAACGTAAGCCCTATTTCTACTAA	60.460	42.308	0.00	0.00	45.62	2.24
2616	3563	4.202090	CCGAACGTAAGCCCTATTTCTACT	60.202	45.833	0.00	0.00	45.62	2.57
2617	3564	4.047142	CCGAACGTAAGCCCTATTTCTAC	58.953	47.826	0.00	0.00	45.62	2.59
2618	3565	3.068590	CCCGAACGTAAGCCCTATTTCTA	59.931	47.826	0.00	0.00	45.62	2.10
2619	3566	2.159000	CCCGAACGTAAGCCCTATTTCT	60.159	50.000	0.00	0.00	45.62	2.52
2620	3567	2.207590	CCCGAACGTAAGCCCTATTTC	58.792	52.381	0.00	0.00	45.62	2.17
2624	3571	2.724273	GGCCCGAACGTAAGCCCTA	61.724	63.158	6.77	0.00	45.62	3.53
2737	3684	3.585428	AACCGGGACCAATGCCCA	61.585	61.111	6.32	0.00	46.36	5.36
2796	3743	3.009026	CACCAATCACGACCAATGATGA	58.991	45.455	0.00	0.00	36.89	2.92
2808	3755	0.240945	CGGTTCAAGCCACCAATCAC	59.759	55.000	0.00	0.00	33.36	3.06
2811	3758	1.606313	CCCGGTTCAAGCCACCAAT	60.606	57.895	0.00	0.00	33.36	3.16
2835	3782	1.263356	CCGGGACTAAAGGACACTCA	58.737	55.000	0.00	0.00	0.00	3.41
2924	3873	1.812571	CGGCCAGAAAAACATAGCAGT	59.187	47.619	2.24	0.00	0.00	4.40
2925	3874	1.133025	CCGGCCAGAAAAACATAGCAG	59.867	52.381	2.24	0.00	0.00	4.24
2926	3875	1.173043	CCGGCCAGAAAAACATAGCA	58.827	50.000	2.24	0.00	0.00	3.49
2927	3876	0.179137	GCCGGCCAGAAAAACATAGC	60.179	55.000	18.11	0.00	0.00	2.97
2932	3881	2.561373	CTCGCCGGCCAGAAAAAC	59.439	61.111	23.46	0.00	0.00	2.43
3047	3997	3.075283	TGGAAAATGGAGCTTGGAGGTTA	59.925	43.478	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.