AutoCloner

Multiple sequence alignment - TraesCS6B01G315100

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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	TraesCS6B01G315100	chr6B	100.000	3275	0	0	1	3275	563128821	563132095	0.000000e+00	6048.0
1	TraesCS6B01G315100	chr6B	88.571	875	61	16	2437	3275	563143120	563143991	0.000000e+00	1026.0
2	TraesCS6B01G315100	chr6A	94.753	2001	71	16	744	2716	518545151	518547145	0.000000e+00	3083.0
3	TraesCS6B01G315100	chr6A	88.010	809	55	13	2493	3275	518595491	518596283	0.000000e+00	918.0
4	TraesCS6B01G315100	chr6A	86.805	773	50	21	2437	3175	518547312	518548066	0.000000e+00	815.0
5	TraesCS6B01G315100	chr6A	85.952	541	30	12	4	529	518544252	518544761	1.340000e-148	536.0
6	TraesCS6B01G315100	chr6A	91.818	220	11	3	535	747	518544808	518545027	1.910000e-77	300.0
7	TraesCS6B01G315100	chr6A	88.785	214	16	2	900	1111	585467263	585467470	4.190000e-64	255.0
8	TraesCS6B01G315100	chr6D	94.990	1956	55	19	779	2700	376940920	376942866	0.000000e+00	3029.0
9	TraesCS6B01G315100	chr6D	87.941	879	55	18	2437	3275	376971929	376972796	0.000000e+00	989.0
10	TraesCS6B01G315100	chr6D	87.115	877	61	20	2437	3275	376943040	376943902	0.000000e+00	946.0
11	TraesCS6B01G315100	chr6D	89.895	762	28	9	4	747	376940046	376940776	0.000000e+00	935.0
12	TraesCS6B01G315100	chr6D	85.870	184	18	6	3090	3266	29116912	29116730	4.310000e-44	189.0
13	TraesCS6B01G315100	chr2D	91.121	214	11	2	900	1111	461804964	461805171	1.920000e-72	283.0
14	TraesCS6B01G315100	chr3A	86.667	240	24	4	893	1132	503028991	503029222	3.240000e-65	259.0
15	TraesCS6B01G315100	chr3A	90.426	94	9	0	900	993	164400609	164400516	1.230000e-24	124.0
16	TraesCS6B01G315100	chr7A	91.837	98	7	1	893	990	62891226	62891322	5.700000e-28	135.0
17	TraesCS6B01G315100	chr7A	83.582	67	11	0	2141	2207	645039714	645039780	2.730000e-06	63.9
18	TraesCS6B01G315100	chr4D	84.375	64	10	0	2144	2207	323604180	323604243	2.730000e-06	63.9
19	TraesCS6B01G315100	chr4B	84.375	64	10	0	2144	2207	404124959	404125022	2.730000e-06	63.9
20	TraesCS6B01G315100	chr4A	84.375	64	10	0	2144	2207	147652640	147652577	2.730000e-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	TraesCS6B01G315100	chr6B	563128821	563132095	3274	False	6048.000000	6048	100.000000	1	3275	1	chr6B.!!$F1	3274
1	TraesCS6B01G315100	chr6B	563143120	563143991	871	False	1026.000000	1026	88.571000	2437	3275	1	chr6B.!!$F2	838
2	TraesCS6B01G315100	chr6A	518544252	518548066	3814	False	1183.500000	3083	89.832000	4	3175	4	chr6A.!!$F3	3171
3	TraesCS6B01G315100	chr6A	518595491	518596283	792	False	918.000000	918	88.010000	2493	3275	1	chr6A.!!$F1	782
4	TraesCS6B01G315100	chr6D	376940046	376943902	3856	False	1636.666667	3029	90.666667	4	3275	3	chr6D.!!$F2	3271
5	TraesCS6B01G315100	chr6D	376971929	376972796	867	False	989.000000	989	87.941000	2437	3275	1	chr6D.!!$F1	838

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
484	515	0.031721	GCTCAGTTGCTTGCTTGCTT	59.968	50.0	3.47	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2478	3171	0.806102	CTCGAACGGCCTGGTGTATG	60.806	60.0	0.0	0.0	0.0	2.39	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
66	67	2.645567	CACTGCTCGGACACGTCT	59.354	61.111	0.00	0.00	41.85	4.18
136	144	1.295792	TCTTGTTCACAGGTTCGTGC	58.704	50.000	0.00	0.00	36.80	5.34
168	176	2.308690	CTGGGGGTGTAGTAGACTAGC	58.691	57.143	0.00	0.00	0.00	3.42
207	215	2.656646	CGGGCTTTTGGGCTTTCC	59.343	61.111	0.00	0.00	40.65	3.13
209	217	1.543944	CGGGCTTTTGGGCTTTCCAT	61.544	55.000	0.00	0.00	46.52	3.41
274	286	3.850273	GCAAACATCTGCGATTCTCAAAG	59.150	43.478	0.00	0.00	31.50	2.77
444	475	4.711949	CAAGCCAGCCACTCCGCT	62.712	66.667	0.00	0.00	40.65	5.52
484	515	0.031721	GCTCAGTTGCTTGCTTGCTT	59.968	50.000	3.47	0.00	0.00	3.91
485	516	1.767289	CTCAGTTGCTTGCTTGCTTG	58.233	50.000	3.47	0.84	0.00	4.01
486	517	0.249155	TCAGTTGCTTGCTTGCTTGC	60.249	50.000	3.47	0.00	0.00	4.01
487	518	0.249322	CAGTTGCTTGCTTGCTTGCT	60.249	50.000	10.35	0.00	0.00	3.91
520	551	2.512692	TACCATGCATGCCACTCTTT	57.487	45.000	21.69	0.11	0.00	2.52
525	556	0.322816	TGCATGCCACTCTTTCCCTC	60.323	55.000	16.68	0.00	0.00	4.30
529	560	0.473694	TGCCACTCTTTCCCTCTCCA	60.474	55.000	0.00	0.00	0.00	3.86
531	562	1.134250	GCCACTCTTTCCCTCTCCATC	60.134	57.143	0.00	0.00	0.00	3.51
601	673	3.585862	TGCAAAAGTAGATCGAGGACAC	58.414	45.455	0.00	0.00	0.00	3.67
626	698	2.165641	AGTATCTTTCCATCGACGCACA	59.834	45.455	0.00	0.00	0.00	4.57
650	725	2.490168	GGTTAAGGGGAGAGGCAACAAA	60.490	50.000	0.00	0.00	41.41	2.83
747	826	5.414454	TGTTAGTCTGGGTTTGTTATGCATC	59.586	40.000	0.19	0.00	0.00	3.91
748	827	3.356290	AGTCTGGGTTTGTTATGCATCC	58.644	45.455	0.19	0.00	0.00	3.51
750	829	3.701040	GTCTGGGTTTGTTATGCATCCAT	59.299	43.478	0.19	0.00	35.44	3.41
835	1046	1.804326	CACCGGCTAAACGACTCGG	60.804	63.158	0.00	0.00	45.42	4.63
839	1050	2.263540	GCTAAACGACTCGGGGCA	59.736	61.111	2.98	0.00	0.00	5.36
850	1061	0.600255	CTCGGGGCACGGCTTTATAG	60.600	60.000	10.28	0.00	44.45	1.31
1044	1258	2.440430	CTCCTCTTCTCCGCCGGA	60.440	66.667	5.05	5.37	0.00	5.14
1437	1660	2.285069	ATGGACCGGTACTGGGCA	60.285	61.111	28.22	14.47	39.59	5.36
1674	1897	3.362399	CTGCCAGTGGTCGCTCGAT	62.362	63.158	11.74	0.00	0.00	3.59
2250	2476	2.244651	GCCGCTGCCGTTCGATTAT	61.245	57.895	0.00	0.00	0.00	1.28
2284	2510	1.444119	GAGGCGCTGACAACCAAACA	61.444	55.000	7.64	0.00	0.00	2.83
2366	2597	1.003839	TCGCTGGTGGGTTTAGCAG	60.004	57.895	0.00	0.00	46.19	4.24
2414	2645	4.396166	GGGTTCAGTACATTTGATGTCTGG	59.604	45.833	14.57	2.26	43.67	3.86
2487	3180	1.527034	AGTTGCACAGCATACACCAG	58.473	50.000	0.00	0.00	38.76	4.00
2569	3298	8.670521	AAGAAAAGAACCAGGGATATTTGATT	57.329	30.769	0.00	0.00	0.00	2.57
2591	3320	6.545504	TTGTTTTAGACAGCAGATTCTCAC	57.454	37.500	0.00	0.00	39.94	3.51
2636	3367	7.978414	TGAAACAAACAACTATTTGAATCAGCA	59.022	29.630	5.30	0.00	41.28	4.41
2665	3396	5.517054	CAGTGAAGCTAAATCTAGTTCCGAC	59.483	44.000	0.00	0.00	0.00	4.79
2716	3447	1.670087	CCAGACGTACTTCAGTGGCAG	60.670	57.143	1.85	0.00	0.00	4.85
2717	3448	0.038159	AGACGTACTTCAGTGGCAGC	60.038	55.000	1.85	0.00	0.00	5.25
2778	3516	3.262915	AGGTCAGAGAAAGGACTCAATGG	59.737	47.826	0.00	0.00	39.14	3.16
2805	3543	3.441500	AGGAAAACAGGGATGTCTTCC	57.558	47.619	5.52	5.52	44.62	3.46
2987	3732	9.846248	CTTTATGTTGGATTCCTAAGAACAAAG	57.154	33.333	9.59	6.91	33.97	2.77
3001	3746	5.228945	AGAACAAAGTGCTTAGCTAAGGA	57.771	39.130	29.93	26.39	33.95	3.36
3025	3770	7.148507	GGATTGCTTTGATGTATAGGATTCTCG	60.149	40.741	0.00	0.00	0.00	4.04
3206	3953	5.730550	TGTTGGATTGCTAATCGTTCTAGT	58.269	37.500	0.00	0.00	38.82	2.57
3215	3962	5.062558	TGCTAATCGTTCTAGTTAAAACCGC	59.937	40.000	0.00	0.00	0.00	5.68
3239	3986	4.155826	TGAACCTACAAATTCATTCTGCCG	59.844	41.667	0.00	0.00	29.89	5.69
3256	4003	2.970639	GTACCAGAGCTGCCGTCA	59.029	61.111	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	2.141122	AACATGCCCACGGAAAAGCG	62.141	55.000	0.00	0.00	0.00	4.68
66	67	3.435026	GGCTAATTTGACCCCTCATAGCA	60.435	47.826	0.00	0.00	35.49	3.49
136	144	2.186903	CCCCAGTGATTCCGACCG	59.813	66.667	0.00	0.00	0.00	4.79
207	215	2.323213	TGCTCATGCATGCCGTATG	58.677	52.632	22.25	12.59	45.31	2.39
284	302	9.720809	CAGAATACTGAGAGCAGAATTTTGCGG	62.721	44.444	14.62	7.18	45.98	5.69
484	515	0.871722	GTAAATCGTGTGTGGCAGCA	59.128	50.000	0.00	0.00	0.00	4.41
485	516	0.168128	GGTAAATCGTGTGTGGCAGC	59.832	55.000	0.00	0.00	0.00	5.25
486	517	1.518325	TGGTAAATCGTGTGTGGCAG	58.482	50.000	0.00	0.00	0.00	4.85
487	518	1.809547	CATGGTAAATCGTGTGTGGCA	59.190	47.619	0.00	0.00	0.00	4.92
520	551	1.933051	TGAAGGAGAGATGGAGAGGGA	59.067	52.381	0.00	0.00	0.00	4.20
525	556	2.100584	CCGAACTGAAGGAGAGATGGAG	59.899	54.545	0.00	0.00	0.00	3.86
529	560	4.467795	TGAATTCCGAACTGAAGGAGAGAT	59.532	41.667	2.27	0.00	37.88	2.75
531	562	4.081972	TCTGAATTCCGAACTGAAGGAGAG	60.082	45.833	2.27	0.00	37.88	3.20
601	673	3.061139	GCGTCGATGGAAAGATACTTTCG	60.061	47.826	6.79	7.32	0.00	3.46
621	693	1.094785	CTCCCCTTAACCAATGTGCG	58.905	55.000	0.00	0.00	0.00	5.34
626	698	1.681229	TGCCTCTCCCCTTAACCAAT	58.319	50.000	0.00	0.00	0.00	3.16
748	827	3.254060	ACTCGATCAACTCCAAACGATG	58.746	45.455	0.00	0.00	0.00	3.84
750	829	3.380479	AACTCGATCAACTCCAAACGA	57.620	42.857	0.00	0.00	0.00	3.85
835	1046	1.897137	GGCCTATAAAGCCGTGCCC	60.897	63.158	0.00	0.00	41.41	5.36
1020	1234	2.701780	GGAGAAGAGGAGCGCGTCA	61.702	63.158	8.43	0.00	0.00	4.35
1060	1274	2.746671	CAGGGTGAGCAGCAGCAG	60.747	66.667	3.17	0.00	46.67	4.24
1482	1705	2.923035	ACCCACCAGACCCACTCG	60.923	66.667	0.00	0.00	0.00	4.18
1674	1897	2.361104	GCCCAGGCGTCCATGAAA	60.361	61.111	0.00	0.00	0.00	2.69
1754	1977	1.485066	ACTCGTTGAACACCTTGTCCT	59.515	47.619	0.00	0.00	0.00	3.85
2107	2333	1.679977	CGGAGTAGTCCCGGTTCCA	60.680	63.158	11.16	0.00	43.05	3.53
2311	2537	3.252400	CACAGCAGCACAAAGACAAAAA	58.748	40.909	0.00	0.00	0.00	1.94
2414	2645	5.554822	TGGTACAAGAAAATGGATAACGC	57.445	39.130	0.00	0.00	31.92	4.84
2478	3171	0.806102	CTCGAACGGCCTGGTGTATG	60.806	60.000	0.00	0.00	0.00	2.39
2487	3180	1.712018	GCATAAACCCTCGAACGGCC	61.712	60.000	0.00	0.00	0.00	6.13
2569	3298	5.610398	TGTGAGAATCTGCTGTCTAAAACA	58.390	37.500	0.00	0.00	34.92	2.83
2636	3367	5.749462	ACTAGATTTAGCTTCACTGGCAAT	58.251	37.500	0.00	0.00	0.00	3.56
2665	3396	3.127895	CAGCCAATTGCATTGAAAATGGG	59.872	43.478	12.55	7.38	44.83	4.00
2716	3447	0.169009	GCTTTGAATCACCTGTCGGC	59.831	55.000	0.00	0.00	0.00	5.54
2717	3448	0.804989	GGCTTTGAATCACCTGTCGG	59.195	55.000	0.00	0.00	0.00	4.79
2748	3479	4.273724	GTCCTTTCTCTGACCTGTTTGTTC	59.726	45.833	0.00	0.00	0.00	3.18
2778	3516	5.046231	AGACATCCCTGTTTTCCTAGTTCTC	60.046	44.000	0.00	0.00	35.14	2.87
2805	3543	1.134946	CGCTAAGCAAATTCCCCCTTG	59.865	52.381	0.00	0.00	0.00	3.61
2810	3548	1.816224	TGAACCGCTAAGCAAATTCCC	59.184	47.619	0.00	0.00	0.00	3.97
2851	3589	4.702131	ACTGATAGGTGATCAAAGTTTGCC	59.298	41.667	10.90	6.33	44.14	4.52
2918	3659	5.919755	TGGTTTTATTTTTCACCCTTCACC	58.080	37.500	0.00	0.00	0.00	4.02
2961	3706	9.846248	CTTTGTTCTTAGGAATCCAACATAAAG	57.154	33.333	0.61	1.78	33.71	1.85
2987	3732	4.396166	TCAAAGCAATCCTTAGCTAAGCAC	59.604	41.667	25.38	12.89	40.90	4.40
3001	3746	7.445121	TCGAGAATCCTATACATCAAAGCAAT	58.555	34.615	0.00	0.00	0.00	3.56
3025	3770	9.559958	CATGTGTTTATTCTATTCCTGTGTTTC	57.440	33.333	0.00	0.00	0.00	2.78
3061	3806	9.733556	TGTTTCATACATTGTTATTCCTGTAGT	57.266	29.630	0.00	0.00	0.00	2.73
3141	3887	9.862371	TTGAATTTGTAGTTTCAGCAGTTTTAA	57.138	25.926	0.00	0.00	33.68	1.52
3170	3916	6.541907	AGCAATCCAACATAAAACCCATTTT	58.458	32.000	0.00	0.00	41.07	1.82
3186	3933	8.662141	GTTTTAACTAGAACGATTAGCAATCCA	58.338	33.333	0.00	0.00	34.35	3.41
3206	3953	6.039493	TGAATTTGTAGGTTCAGCGGTTTTAA	59.961	34.615	0.00	0.00	31.24	1.52
3215	3962	5.644644	GGCAGAATGAATTTGTAGGTTCAG	58.355	41.667	0.00	0.00	39.69	3.02
3239	3986	1.014564	GTTGACGGCAGCTCTGGTAC	61.015	60.000	0.00	0.00	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.