AutoCloner

Multiple sequence alignment - TraesCS6D01G003100

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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	TraesCS6D01G003100	chr6D	100.000	2933	0	0	1	2933	1759637	1762569	0.000000e+00	5417.0
1	TraesCS6D01G003100	chr6D	92.338	1775	89	23	697	2462	1903689	1901953	0.000000e+00	2481.0
2	TraesCS6D01G003100	chr6D	88.901	1775	141	19	437	2201	1850541	1848813	0.000000e+00	2135.0
3	TraesCS6D01G003100	chr6D	86.120	1232	151	15	993	2209	1799984	1798758	0.000000e+00	1310.0
4	TraesCS6D01G003100	chr6D	84.863	1242	147	25	979	2206	1635721	1636935	0.000000e+00	1214.0
5	TraesCS6D01G003100	chr6D	82.992	976	124	23	1250	2209	1809413	1808464	0.000000e+00	845.0
6	TraesCS6D01G003100	chr6D	93.412	425	25	2	1	424	1911003	1910581	6.900000e-176	627.0
7	TraesCS6D01G003100	chr6D	90.397	479	32	7	2466	2933	1848404	1847929	4.150000e-173	617.0
8	TraesCS6D01G003100	chr6D	85.067	596	89	0	993	1588	1627581	1628176	2.500000e-170	608.0
9	TraesCS6D01G003100	chr6D	93.399	303	17	3	2165	2465	1848804	1848503	2.070000e-121	446.0
10	TraesCS6D01G003100	chr6D	96.667	270	6	1	437	706	1910597	1910331	2.070000e-121	446.0
11	TraesCS6D01G003100	chr6D	89.251	307	31	2	1	306	1851522	1851217	1.650000e-102	383.0
12	TraesCS6D01G003100	chr6D	81.211	479	65	16	2471	2933	1807989	1807520	2.150000e-96	363.0
13	TraesCS6D01G003100	chr6D	90.638	235	10	5	2466	2700	1901853	1901631	4.750000e-78	302.0
14	TraesCS6D01G003100	chr6D	78.252	469	75	17	2470	2931	1637301	1637749	2.880000e-70	276.0
15	TraesCS6D01G003100	chr6D	78.288	479	52	26	2466	2933	1798409	1797972	8.060000e-66	261.0
16	TraesCS6D01G003100	chr6D	91.946	149	12	0	505	653	1635314	1635462	2.960000e-50	209.0
17	TraesCS6D01G003100	chr6A	90.081	2480	175	38	1	2462	931303	933729	0.000000e+00	3151.0
18	TraesCS6D01G003100	chr6A	85.368	1237	157	16	993	2209	968805	967573	0.000000e+00	1260.0
19	TraesCS6D01G003100	chr6A	91.064	235	8	4	2466	2700	933820	934041	3.670000e-79	305.0
20	TraesCS6D01G003100	chr6A	78.085	470	76	18	2470	2931	967210	966760	3.720000e-69	272.0
21	TraesCS6D01G003100	chr6B	89.294	1784	149	25	437	2206	4855954	4857709	0.000000e+00	2198.0
22	TraesCS6D01G003100	chr6B	89.581	1526	127	21	689	2206	4885589	4884088	0.000000e+00	1908.0
23	TraesCS6D01G003100	chr6B	88.443	424	45	3	4	426	4886271	4885851	2.610000e-140	508.0
24	TraesCS6D01G003100	chr6B	92.748	262	17	2	437	698	4885869	4885610	7.670000e-101	377.0
25	TraesCS6D01G003100	chr6B	83.257	436	41	11	447	853	4847520	4847952	3.570000e-99	372.0
26	TraesCS6D01G003100	chr6B	96.000	175	5	2	2164	2337	4884085	4883912	1.720000e-72	283.0
27	TraesCS6D01G003100	chr3D	82.747	910	125	21	1019	1922	582909598	582908715	0.000000e+00	782.0
28	TraesCS6D01G003100	chr3D	82.947	862	115	21	1019	1874	582922020	582921185	0.000000e+00	749.0
29	TraesCS6D01G003100	chr2A	94.595	37	2	0	2688	2724	650624065	650624029	1.140000e-04	58.4
30	TraesCS6D01G003100	chr4D	100.000	30	0	0	2695	2724	37611205	37611176	4.080000e-04	56.5
31	TraesCS6D01G003100	chr3B	100.000	30	0	0	2695	2724	56343424	56343395	4.080000e-04	56.5
32	TraesCS6D01G003100	chr2B	90.698	43	3	1	2682	2724	218292598	218292557	4.080000e-04	56.5
33	TraesCS6D01G003100	chr7B	100.000	29	0	0	2696	2724	199976070	199976042	1.000000e-03	54.7

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	TraesCS6D01G003100	chr6D	1759637	1762569	2932	False	5417.000000	5417	100.000000	1	2933	1	chr6D.!!$F2	2932
1	TraesCS6D01G003100	chr6D	1901631	1903689	2058	True	1391.500000	2481	91.488000	697	2700	2	chr6D.!!$R4	2003
2	TraesCS6D01G003100	chr6D	1847929	1851522	3593	True	895.250000	2135	90.487000	1	2933	4	chr6D.!!$R3	2932
3	TraesCS6D01G003100	chr6D	1797972	1799984	2012	True	785.500000	1310	82.204000	993	2933	2	chr6D.!!$R1	1940
4	TraesCS6D01G003100	chr6D	1627581	1628176	595	False	608.000000	608	85.067000	993	1588	1	chr6D.!!$F1	595
5	TraesCS6D01G003100	chr6D	1807520	1809413	1893	True	604.000000	845	82.101500	1250	2933	2	chr6D.!!$R2	1683
6	TraesCS6D01G003100	chr6D	1635314	1637749	2435	False	566.333333	1214	85.020333	505	2931	3	chr6D.!!$F3	2426
7	TraesCS6D01G003100	chr6D	1910331	1911003	672	True	536.500000	627	95.039500	1	706	2	chr6D.!!$R5	705
8	TraesCS6D01G003100	chr6A	931303	934041	2738	False	1728.000000	3151	90.572500	1	2700	2	chr6A.!!$F1	2699
9	TraesCS6D01G003100	chr6A	966760	968805	2045	True	766.000000	1260	81.726500	993	2931	2	chr6A.!!$R1	1938
10	TraesCS6D01G003100	chr6B	4855954	4857709	1755	False	2198.000000	2198	89.294000	437	2206	1	chr6B.!!$F2	1769
11	TraesCS6D01G003100	chr6B	4883912	4886271	2359	True	769.000000	1908	91.693000	4	2337	4	chr6B.!!$R1	2333
12	TraesCS6D01G003100	chr3D	582908715	582909598	883	True	782.000000	782	82.747000	1019	1922	1	chr3D.!!$R1	903
13	TraesCS6D01G003100	chr3D	582921185	582922020	835	True	749.000000	749	82.947000	1019	1874	1	chr3D.!!$R2	855

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
914	1548	0.185901	CCCATCCATTCCCCGTTGAT	59.814	55.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	3023	0.38539	CCAAGAACTTTTGCGTGCCT	59.615	50.0	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
30	31	7.203255	AGTCTTTGCTTTACTATTTGACACC	57.797	36.000	0.00	0.00	0.00	4.16
59	60	3.194755	ACAAGAAGTGTGAACCAAAACCC	59.805	43.478	0.00	0.00	39.72	4.11
66	67	5.697067	AGTGTGAACCAAAACCCATAACTA	58.303	37.500	0.00	0.00	0.00	2.24
70	71	5.867174	GTGAACCAAAACCCATAACTATTGC	59.133	40.000	0.00	0.00	0.00	3.56
76	77	0.586319	CCCATAACTATTGCGCACCG	59.414	55.000	11.12	3.50	0.00	4.94
149	150	1.033746	CATGCCGACAAGGGAGCAAT	61.034	55.000	0.00	0.00	46.12	3.56
349	927	5.457140	GTGCTCGTGTCCAAATAATGAAAA	58.543	37.500	0.00	0.00	0.00	2.29
350	928	5.569059	GTGCTCGTGTCCAAATAATGAAAAG	59.431	40.000	0.00	0.00	0.00	2.27
351	929	5.095490	GCTCGTGTCCAAATAATGAAAAGG	58.905	41.667	0.00	0.00	0.00	3.11
352	930	5.637006	TCGTGTCCAAATAATGAAAAGGG	57.363	39.130	0.00	0.00	0.00	3.95
378	956	1.501582	GGGAGTGCAGAAGGGTCTAT	58.498	55.000	0.00	0.00	30.85	1.98
444	1022	5.137551	TGTTCCCCTAAGAAAAAGGTTGAG	58.862	41.667	0.00	0.00	31.70	3.02
445	1023	5.138276	GTTCCCCTAAGAAAAAGGTTGAGT	58.862	41.667	0.00	0.00	31.70	3.41
695	1319	4.766404	AGAAAAGAAAAGGTACGCCATG	57.234	40.909	0.00	0.00	37.19	3.66
894	1528	1.741706	CCAGACCAGCAGCTACAAATG	59.258	52.381	0.00	0.00	0.00	2.32
909	1543	0.760189	AAATGCCCATCCATTCCCCG	60.760	55.000	0.00	0.00	34.50	5.73
914	1548	0.185901	CCCATCCATTCCCCGTTGAT	59.814	55.000	0.00	0.00	0.00	2.57
1013	1680	1.993653	CAAGCATGGAGGGGTCAGA	59.006	57.895	0.00	0.00	0.00	3.27
1176	1843	1.611419	CATCCACCATGTCCCTGCT	59.389	57.895	0.00	0.00	0.00	4.24
1195	1862	2.515057	TTGAAACTGGCGCCGTGT	60.515	55.556	23.90	20.33	0.00	4.49
1287	1954	1.515020	GCTCATCTCCACGCTCTGT	59.485	57.895	0.00	0.00	0.00	3.41
1678	2350	4.473477	TGCATGCATGATTTGGATTGAA	57.527	36.364	30.64	0.00	33.53	2.69
1683	2355	6.292865	GCATGCATGATTTGGATTGAATCTTG	60.293	38.462	30.64	0.00	39.63	3.02
1705	2377	7.876582	TCTTGGTATCATTGATGTCTGATGATC	59.123	37.037	9.46	0.00	40.14	2.92
1775	2450	1.137872	GGTGCTCATGGAGAAGACGAT	59.862	52.381	0.00	0.00	0.00	3.73
1782	2457	3.117474	TCATGGAGAAGACGATAGGAGGT	60.117	47.826	0.00	0.00	43.77	3.85
1826	2501	0.107945	ATCTTCAAGACAGAGGCGGC	60.108	55.000	0.00	0.00	0.00	6.53
1933	2609	1.466025	AACCAACGTCACCGCCTAGA	61.466	55.000	0.00	0.00	37.70	2.43
1935	2611	1.445582	CAACGTCACCGCCTAGACC	60.446	63.158	0.00	0.00	37.70	3.85
1970	2651	5.757320	GGAATCAATCATCGTCTTGTCTCAT	59.243	40.000	0.00	0.00	0.00	2.90
1973	2654	5.482006	TCAATCATCGTCTTGTCTCATTGT	58.518	37.500	0.00	0.00	0.00	2.71
2012	2693	3.118775	CCAGATCTACCGGATTTGTGACA	60.119	47.826	9.46	0.00	35.52	3.58
2237	3023	4.697828	TGTGCTTGTTAGACAGAACAAACA	59.302	37.500	3.58	2.76	45.98	2.83
2262	3199	4.506288	GCACGCAAAAGTTCTTGGTTTATT	59.494	37.500	0.00	0.00	0.00	1.40
2405	3346	4.760204	CCCATCACCGATTATTTTCCCTAC	59.240	45.833	0.00	0.00	0.00	3.18
2407	3348	5.373222	CATCACCGATTATTTTCCCTACCA	58.627	41.667	0.00	0.00	0.00	3.25
2411	3354	6.893005	TCACCGATTATTTTCCCTACCATTTT	59.107	34.615	0.00	0.00	0.00	1.82
2413	3356	8.688151	CACCGATTATTTTCCCTACCATTTTAA	58.312	33.333	0.00	0.00	0.00	1.52
2595	3650	8.645487	CACTACTTCAAATACTAACCGAAGTTC	58.355	37.037	8.24	0.00	42.69	3.01
2620	3675	3.363341	TTCGTTTTCATTGGGTCAAGC	57.637	42.857	0.00	0.00	0.00	4.01
2624	3679	1.533625	TTTCATTGGGTCAAGCCTCG	58.466	50.000	0.00	0.00	37.43	4.63
2625	3680	0.400213	TTCATTGGGTCAAGCCTCGT	59.600	50.000	0.00	0.00	37.43	4.18
2626	3681	1.271856	TCATTGGGTCAAGCCTCGTA	58.728	50.000	0.00	0.00	37.43	3.43
2627	3682	1.837439	TCATTGGGTCAAGCCTCGTAT	59.163	47.619	0.00	0.00	37.43	3.06
2629	3684	0.251916	TTGGGTCAAGCCTCGTATGG	59.748	55.000	0.00	0.00	37.43	2.74
2748	3823	0.096976	CCAGCGAACAACCTTATGCG	59.903	55.000	0.00	0.00	0.00	4.73
2774	3849	0.037326	ATCCCGCGCACGAATCATAT	60.037	50.000	8.75	0.00	43.93	1.78
2787	3866	5.155509	CGAATCATATTTCGCTCCAAACA	57.844	39.130	0.00	0.00	41.61	2.83
2796	3875	2.176045	TCGCTCCAAACACATCCTCTA	58.824	47.619	0.00	0.00	0.00	2.43
2803	3882	3.941483	CCAAACACATCCTCTAAGCGAAT	59.059	43.478	0.00	0.00	0.00	3.34
2817	3896	7.201478	CCTCTAAGCGAATTACAAGAAGACAAG	60.201	40.741	0.00	0.00	0.00	3.16
2840	3919	6.878317	AGAGTGATTCGTTCATTTAGGATGA	58.122	36.000	0.00	0.00	36.54	2.92
2851	3930	5.052481	TCATTTAGGATGACAATCTGAGCG	58.948	41.667	0.00	0.00	32.95	5.03
2906	3986	3.192466	GGCATGGCAATTCTCACAATTC	58.808	45.455	15.47	0.00	0.00	2.17
2910	3990	4.933505	TGGCAATTCTCACAATTCAACA	57.066	36.364	0.00	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	2.201732	AGTCGGTGCGCAATAGTTATG	58.798	47.619	14.00	0.00	0.00	1.90
66	67	0.732571	CCAAATAGTCGGTGCGCAAT	59.267	50.000	14.00	0.00	0.00	3.56
70	71	1.396996	CTTTCCCAAATAGTCGGTGCG	59.603	52.381	0.00	0.00	0.00	5.34
76	77	7.722363	TCCTTTGTTTTCTTTCCCAAATAGTC	58.278	34.615	0.00	0.00	0.00	2.59
105	106	2.260844	AACCATGTCACACTGTCTGG	57.739	50.000	0.00	0.00	0.00	3.86
149	150	2.975489	GGAGGGAGATGCCTAATTCAGA	59.025	50.000	0.00	0.00	36.66	3.27
197	198	0.319900	AGGCACATGACACGTCACTC	60.320	55.000	0.00	0.00	43.11	3.51
357	935	2.936032	ACCCTTCTGCACTCCCCC	60.936	66.667	0.00	0.00	0.00	5.40
378	956	2.048597	GTCACCCATGTCGCGACA	60.049	61.111	40.57	40.57	46.44	4.35
453	1031	9.507329	ACTTTGAAACTACACATATCAGATTGT	57.493	29.630	0.00	0.00	0.00	2.71
456	1034	9.376075	CTGACTTTGAAACTACACATATCAGAT	57.624	33.333	0.00	0.00	32.30	2.90
695	1319	7.957484	CGCAATACATTGTATCCTGCTAAATAC	59.043	37.037	22.07	2.87	39.88	1.89
894	1528	2.127232	CAACGGGGAATGGATGGGC	61.127	63.158	0.00	0.00	0.00	5.36
909	1543	3.868077	CGAGACTGGGATGAAGAATCAAC	59.132	47.826	0.00	0.00	39.49	3.18
914	1548	1.478510	GAGCGAGACTGGGATGAAGAA	59.521	52.381	0.00	0.00	0.00	2.52
1013	1680	2.506217	CGCGCACGGTCATAGTGT	60.506	61.111	8.75	0.00	41.36	3.55
1176	1843	2.110213	ACGGCGCCAGTTTCAAGA	59.890	55.556	28.98	0.00	0.00	3.02
1287	1954	2.031314	TAGACGCCGCCTTGCAAA	59.969	55.556	0.00	0.00	0.00	3.68
1678	2350	7.742767	TCATCAGACATCAATGATACCAAGAT	58.257	34.615	0.00	0.00	34.42	2.40
1683	2355	5.579904	CCGATCATCAGACATCAATGATACC	59.420	44.000	0.00	0.00	39.58	2.73
1705	2377	0.108709	CCACCCATGACAAATTGCCG	60.109	55.000	0.00	0.00	0.00	5.69
1775	2450	0.828022	CATGGGCACGTTACCTCCTA	59.172	55.000	6.81	0.00	0.00	2.94
1845	2520	0.539669	TCTTGACGAGCCTCTCACCA	60.540	55.000	0.00	0.00	0.00	4.17
1933	2609	1.806496	TGATTCCTGGATGGATCGGT	58.194	50.000	0.00	0.00	45.68	4.69
1935	2611	4.011966	TGATTGATTCCTGGATGGATCG	57.988	45.455	0.00	0.00	45.68	3.69
1970	2651	2.223386	GGCTAACAAGCAACACGAACAA	60.223	45.455	0.00	0.00	36.33	2.83
1973	2654	1.601903	CTGGCTAACAAGCAACACGAA	59.398	47.619	0.00	0.00	36.33	3.85
2038	2719	5.743636	ATTTGGCTCCAACATAACATTGT	57.256	34.783	0.00	0.00	35.46	2.71
2219	3005	4.095782	GTGCCTGTTTGTTCTGTCTAACAA	59.904	41.667	0.00	0.00	45.20	2.83
2237	3023	0.385390	CCAAGAACTTTTGCGTGCCT	59.615	50.000	0.00	0.00	0.00	4.75
2262	3199	3.999229	AACGTTTGCGCAATTTCAAAA	57.001	33.333	25.64	3.58	42.83	2.44
2347	3286	4.460382	GGAAAGTGCATGAAGGAGATCAAA	59.540	41.667	0.00	0.00	32.06	2.69
2624	3679	3.056322	GGGGTATGTCCGTATGTCCATAC	60.056	52.174	7.27	7.27	39.13	2.39
2625	3680	3.167485	GGGGTATGTCCGTATGTCCATA	58.833	50.000	0.00	0.00	37.00	2.74
2626	3681	1.975680	GGGGTATGTCCGTATGTCCAT	59.024	52.381	0.00	0.00	37.00	3.41
2627	3682	1.343176	TGGGGTATGTCCGTATGTCCA	60.343	52.381	0.00	0.00	37.00	4.02
2629	3684	1.758280	TGTGGGGTATGTCCGTATGTC	59.242	52.381	0.00	0.00	37.00	3.06
2739	3814	1.609208	GGATCCAATGCGCATAAGGT	58.391	50.000	29.88	19.79	0.00	3.50
2748	3823	4.256090	GTGCGCGGGATCCAATGC	62.256	66.667	15.23	13.82	0.00	3.56
2774	3849	2.151202	GAGGATGTGTTTGGAGCGAAA	58.849	47.619	0.00	0.00	0.00	3.46
2787	3866	6.222038	TCTTGTAATTCGCTTAGAGGATGT	57.778	37.500	0.00	0.00	0.00	3.06
2796	3875	5.992217	ACTCTTGTCTTCTTGTAATTCGCTT	59.008	36.000	0.00	0.00	0.00	4.68
2803	3882	6.513180	ACGAATCACTCTTGTCTTCTTGTAA	58.487	36.000	0.00	0.00	0.00	2.41
2817	3896	6.535150	TGTCATCCTAAATGAACGAATCACTC	59.465	38.462	0.00	0.00	41.93	3.51
2851	3930	2.122783	TTCCATCCCCGAATGTGTTC	57.877	50.000	0.00	0.00	0.00	3.18
2906	3986	8.658609	GGGAATTTTCATGTTACATCAATGTTG	58.341	33.333	0.20	0.00	41.97	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.