AutoCloner

Multiple sequence alignment - TraesCS6A01G233300

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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	TraesCS6A01G233300	chr6A	100.000	8237	0	0	614	8850	441434072	441425836	0.000000e+00	15211.0
1	TraesCS6A01G233300	chr6A	95.386	3338	100	12	5352	8661	410906451	410909762	0.000000e+00	5262.0
2	TraesCS6A01G233300	chr6A	94.691	2863	107	13	651	3481	410895975	410898824	0.000000e+00	4403.0
3	TraesCS6A01G233300	chr6A	96.142	1892	57	10	3481	5370	410899624	410901501	0.000000e+00	3075.0
4	TraesCS6A01G233300	chr6A	100.000	345	0	0	1	345	441434685	441434341	9.690000e-179	638.0
5	TraesCS6A01G233300	chr6A	93.671	237	8	3	1	232	410895688	410895922	1.830000e-91	348.0
6	TraesCS6A01G233300	chr6A	96.196	184	5	2	2096	2278	262043745	262043927	5.190000e-77	300.0
7	TraesCS6A01G233300	chr6A	92.929	198	13	1	8651	8847	410909902	410910099	4.040000e-73	287.0
8	TraesCS6A01G233300	chr6B	98.263	8000	84	15	651	8616	470130544	470122566	0.000000e+00	13952.0
9	TraesCS6A01G233300	chr6B	96.532	346	9	2	1	345	470131328	470130985	3.590000e-158	569.0
10	TraesCS6A01G233300	chr6B	97.354	189	5	0	8662	8850	470122556	470122368	1.110000e-83	322.0
11	TraesCS6A01G233300	chr6D	96.006	5108	160	19	653	5729	304286434	304281340	0.000000e+00	8263.0
12	TraesCS6A01G233300	chr6D	95.384	2881	76	12	5801	8661	304281339	304278496	0.000000e+00	4530.0
13	TraesCS6A01G233300	chr6D	93.948	347	16	4	1	345	304287190	304286847	3.660000e-143	520.0
14	TraesCS6A01G233300	chr6D	93.035	201	13	1	8651	8850	304278357	304278157	8.690000e-75	292.0
15	TraesCS6A01G233300	chr6D	90.217	92	6	2	7645	7733	292073459	292073368	5.610000e-22	117.0
16	TraesCS6A01G233300	chr6D	90.000	90	6	2	7643	7729	292073368	292073457	7.260000e-21	113.0
17	TraesCS6A01G233300	chr6D	86.792	53	5	2	7701	7751	363032562	363032510	3.450000e-04	58.4
18	TraesCS6A01G233300	chrUn	100.000	414	0	0	2373	2786	477402502	477402089	0.000000e+00	765.0
19	TraesCS6A01G233300	chrUn	88.660	194	20	2	8651	8843	87229936	87229744	1.490000e-57	235.0
20	TraesCS6A01G233300	chr1B	74.404	1301	225	59	6342	7602	673970907	673969675	8.100000e-125	459.0
21	TraesCS6A01G233300	chr1B	97.753	178	4	0	2113	2290	321238406	321238229	3.100000e-79	307.0
22	TraesCS6A01G233300	chr4B	93.970	199	11	1	2113	2310	553510684	553510486	5.190000e-77	300.0
23	TraesCS6A01G233300	chr4A	94.416	197	8	3	2113	2308	658953765	658953959	5.190000e-77	300.0
24	TraesCS6A01G233300	chr2B	95.722	187	5	3	2099	2285	184124042	184124225	1.870000e-76	298.0
25	TraesCS6A01G233300	chr2B	88.945	199	19	2	8651	8848	394138358	394138162	8.880000e-60	243.0
26	TraesCS6A01G233300	chr2B	89.362	47	3	2	7702	7747	616968513	616968468	3.450000e-04	58.4
27	TraesCS6A01G233300	chr3B	98.795	166	2	0	2113	2278	520146252	520146417	6.720000e-76	296.0
28	TraesCS6A01G233300	chr3B	90.769	195	14	4	8651	8843	97755898	97756090	3.170000e-64	257.0
29	TraesCS6A01G233300	chr3B	89.340	197	18	3	8648	8843	519860665	519860859	2.470000e-60	244.0
30	TraesCS6A01G233300	chr3A	90.256	195	15	4	8651	8843	69662548	69662740	1.470000e-62	252.0
31	TraesCS6A01G233300	chr3A	87.912	91	6	3	7642	7729	679696556	679696644	1.570000e-17	102.0
32	TraesCS6A01G233300	chr3A	88.000	50	3	3	7703	7750	510594377	510594425	1.000000e-03	56.5
33	TraesCS6A01G233300	chr7B	88.384	198	21	2	8651	8847	414049840	414049644	4.130000e-58	237.0
34	TraesCS6A01G233300	chr3D	87.778	90	7	3	7643	7729	47480782	47480694	1.570000e-17	102.0
35	TraesCS6A01G233300	chr3D	86.538	52	5	2	7695	7744	419594262	419594211	1.000000e-03	56.5
36	TraesCS6A01G233300	chr1D	88.372	86	7	1	7647	7729	249025325	249025240	5.650000e-17	100.0
37	TraesCS6A01G233300	chr1A	87.640	89	8	1	7644	7729	298608403	298608491	5.650000e-17	100.0
38	TraesCS6A01G233300	chr4D	86.667	60	4	3	7695	7752	85586331	85586274	7.420000e-06	63.9

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	TraesCS6A01G233300	chr6A	441425836	441434685	8849	True	7924.500000	15211	100.000000	1	8850	2	chr6A.!!$R1	8849
1	TraesCS6A01G233300	chr6A	410906451	410910099	3648	False	2774.500000	5262	94.157500	5352	8847	2	chr6A.!!$F3	3495
2	TraesCS6A01G233300	chr6A	410895688	410901501	5813	False	2608.666667	4403	94.834667	1	5370	3	chr6A.!!$F2	5369
3	TraesCS6A01G233300	chr6B	470122368	470131328	8960	True	4947.666667	13952	97.383000	1	8850	3	chr6B.!!$R1	8849
4	TraesCS6A01G233300	chr6D	304278157	304287190	9033	True	3401.250000	8263	94.593250	1	8850	4	chr6D.!!$R3	8849
5	TraesCS6A01G233300	chr1B	673969675	673970907	1232	True	459.000000	459	74.404000	6342	7602	1	chr1B.!!$R2	1260

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
38	39	1.202428	AGGTTCGCTAAATCGGAGCTC	60.202	52.381	4.71	4.71	41.45	4.09	F
181	184	1.341581	CCGAATTTCTGGCCCCCTTAA	60.342	52.381	0.00	0.00	0.00	1.85	F
320	327	3.118408	TGGAGAATGTTCCCTATTCGGTG	60.118	47.826	0.00	0.00	39.07	4.94	F
1969	2131	0.853530	AGCCCCAGGTCCATATTTCC	59.146	55.000	0.00	0.00	0.00	3.13	F
2786	2949	2.103094	TGCGCTACATTCCTTCATAGCT	59.897	45.455	9.73	0.00	38.31	3.32	F
2935	3111	2.486472	AGCAACTTGGAGGACATCAG	57.514	50.000	0.00	0.00	0.00	2.90	F
3218	3394	7.650504	GCACTATCAGGAATACAACGTGTATAA	59.349	37.037	9.91	0.00	42.29	0.98	F
4249	5244	3.503748	GCTTCCACAGCTTTGAGTTATGT	59.496	43.478	0.17	0.00	46.27	2.29	F
5259	6256	2.671396	CGTACCTTTAGTTGCATCGCTT	59.329	45.455	0.00	0.00	0.00	4.68	F
5892	6892	0.542805	ATTGGGATGGTTGCATTGCC	59.457	50.000	6.12	0.00	0.00	4.52	F
5893	6893	0.544833	TTGGGATGGTTGCATTGCCT	60.545	50.000	6.12	0.00	0.00	4.75	F
6803	7806	0.606401	CGGGTGAAGCTGTTCCACAT	60.606	55.000	9.85	0.00	0.00	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1487	1646	4.393062	GTCCATATGCCATCTTGTAATCCG	59.607	45.833	0.00	0.00	0.00	4.18	R
1853	2015	4.768448	TGCTAGTAACAGTAACTAGTGCCA	59.232	41.667	0.00	0.34	45.43	4.92	R
2312	2474	6.439636	AAGGCCATTCATAAGCTGTCTATA	57.560	37.500	5.01	0.00	0.00	1.31	R
3714	4708	0.871163	CGTTTGCCAAGCTGGTTGTG	60.871	55.000	17.30	10.38	40.46	3.33	R
4104	5099	5.812642	CACAGTTAGCGACAGGAATTTAGAT	59.187	40.000	0.00	0.00	0.00	1.98	R
4249	5244	6.720309	TGATTTTGTTGGATCTATGAGTGGA	58.280	36.000	0.00	0.00	0.00	4.02	R
5259	6256	4.389890	AAACTGAGCTCATGTTTGCAAA	57.610	36.364	28.22	8.05	33.36	3.68	R
5889	6889	5.070847	TGAAGCATGACATATTAGAGAGGCA	59.929	40.000	0.00	0.00	0.00	4.75	R
6690	7693	1.743996	GTGAAATCCTCAGACCAGGC	58.256	55.000	0.00	0.00	33.60	4.85	R
7044	8059	2.950309	GAGTCGTCCCTTAGCATGAGTA	59.050	50.000	0.00	0.00	0.00	2.59	R
7697	8737	3.650139	GATCCATAATAAGTGTCGCGGT	58.350	45.455	6.13	0.00	0.00	5.68	R
8014	9056	1.182667	AGGTAAAATTGGAAGGCCGC	58.817	50.000	0.00	0.00	36.79	6.53	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
38	39	1.202428	AGGTTCGCTAAATCGGAGCTC	60.202	52.381	4.71	4.71	41.45	4.09
39	40	1.202428	GGTTCGCTAAATCGGAGCTCT	60.202	52.381	14.64	0.00	37.81	4.09
181	184	1.341581	CCGAATTTCTGGCCCCCTTAA	60.342	52.381	0.00	0.00	0.00	1.85
320	327	3.118408	TGGAGAATGTTCCCTATTCGGTG	60.118	47.826	0.00	0.00	39.07	4.94
338	345	5.597806	TCGGTGTACATATGAACCTCATTC	58.402	41.667	10.38	0.00	38.26	2.67
767	925	5.107065	CCGCTAAAAGTTTCAGGACTACTTG	60.107	44.000	0.00	0.00	32.76	3.16
1390	1549	9.889128	TCAATTGTTCTCTTCTTTTTCCATTTT	57.111	25.926	5.13	0.00	0.00	1.82
1459	1618	4.408921	GGGCAATTATTTCCCTTTAGGCTT	59.591	41.667	5.40	0.00	37.08	4.35
1585	1744	8.935741	GTTCTCTATTTCCCTATTTCCTTCCTA	58.064	37.037	0.00	0.00	0.00	2.94
1593	1752	6.699688	TCCCTATTTCCTTCCTAATGGAGTA	58.300	40.000	0.00	0.00	44.24	2.59
1596	1755	8.448816	CCCTATTTCCTTCCTAATGGAGTATTT	58.551	37.037	0.00	0.00	44.24	1.40
1597	1756	9.868160	CCTATTTCCTTCCTAATGGAGTATTTT	57.132	33.333	0.00	0.00	44.24	1.82
1603	1762	6.480320	CCTTCCTAATGGAGTATTTTGAGACG	59.520	42.308	0.00	0.00	44.24	4.18
1604	1763	6.540438	TCCTAATGGAGTATTTTGAGACGT	57.460	37.500	0.00	0.00	37.46	4.34
1605	1764	7.649533	TCCTAATGGAGTATTTTGAGACGTA	57.350	36.000	0.00	0.00	37.46	3.57
1853	2015	1.390565	ATAACGCTCGAGTGCTAGGT	58.609	50.000	25.38	2.85	0.00	3.08
1969	2131	0.853530	AGCCCCAGGTCCATATTTCC	59.146	55.000	0.00	0.00	0.00	3.13
2371	2534	6.856895	ACTGCCTTATTAATTCAAGCAGTTC	58.143	36.000	20.43	0.66	36.56	3.01
2786	2949	2.103094	TGCGCTACATTCCTTCATAGCT	59.897	45.455	9.73	0.00	38.31	3.32
2935	3111	2.486472	AGCAACTTGGAGGACATCAG	57.514	50.000	0.00	0.00	0.00	2.90
3218	3394	7.650504	GCACTATCAGGAATACAACGTGTATAA	59.349	37.037	9.91	0.00	42.29	0.98
4104	5099	7.933033	CCCAACTAGTTAAACAAGGTACAGTAA	59.067	37.037	8.04	0.00	0.00	2.24
4249	5244	3.503748	GCTTCCACAGCTTTGAGTTATGT	59.496	43.478	0.17	0.00	46.27	2.29
4487	5482	7.684062	AAACTTCTTTCATGATTTTCACACG	57.316	32.000	0.00	0.00	0.00	4.49
5259	6256	2.671396	CGTACCTTTAGTTGCATCGCTT	59.329	45.455	0.00	0.00	0.00	4.68
5306	6303	7.225784	TGTATTGTAACCATTTTCATGCACT	57.774	32.000	0.00	0.00	0.00	4.40
5889	6889	4.288398	TGTGATATTGGGATGGTTGCATT	58.712	39.130	0.00	0.00	0.00	3.56
5892	6892	0.542805	ATTGGGATGGTTGCATTGCC	59.457	50.000	6.12	0.00	0.00	4.52
5893	6893	0.544833	TTGGGATGGTTGCATTGCCT	60.545	50.000	6.12	0.00	0.00	4.75
6346	7348	3.806380	TGCATTTCATTGTTTTGCACCT	58.194	36.364	0.00	0.00	38.32	4.00
6561	7564	7.306807	CGCAATCGTCTCATTGATGTAATACTT	60.307	37.037	0.00	0.00	36.03	2.24
6690	7693	5.290158	GCAAAATCAACATAAGACAGCCATG	59.710	40.000	0.00	0.00	0.00	3.66
6801	7804	1.966451	CCGGGTGAAGCTGTTCCAC	60.966	63.158	0.00	0.00	0.00	4.02
6803	7806	0.606401	CGGGTGAAGCTGTTCCACAT	60.606	55.000	9.85	0.00	0.00	3.21
6945	7948	6.000219	AGCTATAAATGAAATGCCTGTCGAT	59.000	36.000	0.00	0.00	0.00	3.59
7070	8085	1.174783	GCTAAGGGACGACTCTCACA	58.825	55.000	0.00	0.00	0.00	3.58
7125	8149	2.519377	TCCGTGTCTTCGATGTTTGT	57.481	45.000	0.00	0.00	0.00	2.83
7743	8783	7.124599	TCGGAGGGAGTAATATTTTACTGTTGA	59.875	37.037	12.58	1.34	46.32	3.18
7965	9007	4.813697	GCCTGTAAGATCCTTTCAGCTAAG	59.186	45.833	7.53	0.00	34.07	2.18
7997	9039	3.145286	TCATTTGAACGTCCAATGCTGA	58.855	40.909	0.00	0.00	0.00	4.26
8014	9056	8.961092	CCAATGCTGATCTGTTTTATAAATTCG	58.039	33.333	0.00	0.00	0.00	3.34
8335	9386	8.731605	CAGTTCTACCTCATCGAGCTTTATATA	58.268	37.037	0.00	0.00	0.00	0.86
8649	9700	2.192624	CAACTTTGTGTTTTCGGGCAG	58.807	47.619	0.00	0.00	36.63	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	0.373716	CGATTTAGCGAACCTGTGGC	59.626	55.000	0.00	0.00	0.00	5.01
38	39	1.079543	CCTTCTGGACGGCACTCAG	60.080	63.158	0.00	0.00	34.57	3.35
39	40	3.059982	CCTTCTGGACGGCACTCA	58.940	61.111	0.00	0.00	34.57	3.41
181	184	7.971722	GGTAAGTCGGCATAAATGTACAAAAAT	59.028	33.333	0.00	0.00	0.00	1.82
270	277	9.542462	TCTTCATAACTAAAATAATCACGGAGG	57.458	33.333	0.00	0.00	0.00	4.30
320	327	6.174720	TCCCAGAATGAGGTTCATATGTAC	57.825	41.667	1.90	3.04	39.69	2.90
624	712	3.758023	CTGAACCTGCCATTTGACATGTA	59.242	43.478	0.00	0.00	0.00	2.29
767	925	6.477360	GCTACCTAAACTTGATAAGTGAGAGC	59.523	42.308	0.00	0.27	41.91	4.09
1024	1183	5.629435	GCTGTGATACAAGGCTTTTTACAAC	59.371	40.000	0.00	0.00	0.00	3.32
1136	1295	4.757149	GGGACAGATATAATGAGTTGGTGC	59.243	45.833	0.00	0.00	0.00	5.01
1487	1646	4.393062	GTCCATATGCCATCTTGTAATCCG	59.607	45.833	0.00	0.00	0.00	4.18
1597	1756	8.662141	GCAATACCTTAAGAAAAATACGTCTCA	58.338	33.333	3.36	0.00	0.00	3.27
1598	1757	8.662141	TGCAATACCTTAAGAAAAATACGTCTC	58.338	33.333	3.36	0.00	0.00	3.36
1603	1762	9.678941	GCCTATGCAATACCTTAAGAAAAATAC	57.321	33.333	3.36	0.00	37.47	1.89
1604	1763	9.640952	AGCCTATGCAATACCTTAAGAAAAATA	57.359	29.630	3.36	0.00	41.13	1.40
1605	1764	8.539117	AGCCTATGCAATACCTTAAGAAAAAT	57.461	30.769	3.36	0.00	41.13	1.82
1667	1826	6.037500	ACATTGACATCACCTTATCATCAACG	59.962	38.462	0.00	0.00	0.00	4.10
1853	2015	4.768448	TGCTAGTAACAGTAACTAGTGCCA	59.232	41.667	0.00	0.34	45.43	4.92
1969	2131	6.728200	TGTGTTCTGCTTCTGTTTATTTGAG	58.272	36.000	0.00	0.00	0.00	3.02
2311	2473	6.633325	AGGCCATTCATAAGCTGTCTATAT	57.367	37.500	5.01	0.00	0.00	0.86
2312	2474	6.439636	AAGGCCATTCATAAGCTGTCTATA	57.560	37.500	5.01	0.00	0.00	1.31
2786	2949	5.273674	TGGAAATGAAGCAATGTGTCAAA	57.726	34.783	0.00	0.00	0.00	2.69
2935	3111	5.522824	GTCCTATCTTGACGTGGGAAATTAC	59.477	44.000	0.00	0.00	0.00	1.89
3218	3394	3.558746	GCAATAGATAGTCTGCAGGCCAT	60.559	47.826	16.31	6.88	34.87	4.40
3714	4708	0.871163	CGTTTGCCAAGCTGGTTGTG	60.871	55.000	17.30	10.38	40.46	3.33
4104	5099	5.812642	CACAGTTAGCGACAGGAATTTAGAT	59.187	40.000	0.00	0.00	0.00	1.98
4249	5244	6.720309	TGATTTTGTTGGATCTATGAGTGGA	58.280	36.000	0.00	0.00	0.00	4.02
5259	6256	4.389890	AAACTGAGCTCATGTTTGCAAA	57.610	36.364	28.22	8.05	33.36	3.68
5889	6889	5.070847	TGAAGCATGACATATTAGAGAGGCA	59.929	40.000	0.00	0.00	0.00	4.75
6561	7564	5.250543	TGATAAGTCCCCAACAGAAGAATGA	59.749	40.000	0.00	0.00	0.00	2.57
6690	7693	1.743996	GTGAAATCCTCAGACCAGGC	58.256	55.000	0.00	0.00	33.60	4.85
6861	7864	4.007457	GCATGCTGCCCTTCTTCA	57.993	55.556	11.37	0.00	37.42	3.02
6945	7948	5.306937	TGATCCCACAACTTGTAGAAAGAGA	59.693	40.000	0.00	0.00	0.00	3.10
7044	8059	2.950309	GAGTCGTCCCTTAGCATGAGTA	59.050	50.000	0.00	0.00	0.00	2.59
7697	8737	3.650139	GATCCATAATAAGTGTCGCGGT	58.350	45.455	6.13	0.00	0.00	5.68
7997	9039	4.578928	AGGCCGCGAATTTATAAAACAGAT	59.421	37.500	8.23	0.00	0.00	2.90
8014	9056	1.182667	AGGTAAAATTGGAAGGCCGC	58.817	50.000	0.00	0.00	36.79	6.53
8335	9386	3.439857	ACCTGCATGAAACATGGTACT	57.560	42.857	12.56	0.00	0.00	2.73
8681	9883	4.421058	GTCAAAGTTTGTGAGGTTTGACC	58.579	43.478	15.08	0.00	46.89	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.