AutoCloner

Multiple sequence alignment - TraesCS6D01G121700

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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	TraesCS6D01G121700	chr6D	100.000	2984	0	0	1	2984	86603518	86600535	0.000000e+00	5511.0
1	TraesCS6D01G121700	chr6A	92.036	3026	161	44	1	2984	104115043	104112056	0.000000e+00	4180.0
2	TraesCS6D01G121700	chr6B	92.903	2043	81	15	1	2027	164035962	164033968	0.000000e+00	2911.0
3	TraesCS6D01G121700	chr6B	86.632	965	86	27	2025	2984	164033926	164033000	0.000000e+00	1027.0
4	TraesCS6D01G121700	chr7B	87.879	462	48	8	1263	1722	597082597	597082142	1.220000e-148	536.0
5	TraesCS6D01G121700	chr7B	79.835	243	38	6	1736	1968	597081994	597081753	1.840000e-37	167.0
6	TraesCS6D01G121700	chr7A	87.527	465	50	8	1263	1725	637864972	637864514	5.660000e-147	531.0
7	TraesCS6D01G121700	chr7A	79.832	238	38	5	1736	1963	637864395	637864158	6.620000e-37	165.0
8	TraesCS6D01G121700	chr7A	86.486	74	8	2	2239	2311	126962286	126962358	2.470000e-11	80.5
9	TraesCS6D01G121700	chr7D	87.229	462	51	8	1263	1722	552164993	552164538	1.230000e-143	520.0
10	TraesCS6D01G121700	chr7D	79.747	237	38	5	1736	1962	552164391	552164155	2.380000e-36	163.0
11	TraesCS6D01G121700	chr4A	79.532	171	25	6	2152	2320	140988628	140988790	2.430000e-21	113.0
12	TraesCS6D01G121700	chr3A	83.784	111	11	5	2211	2320	610045188	610045084	6.810000e-17	99.0
13	TraesCS6D01G121700	chr5A	89.706	68	6	1	2251	2317	683270961	683271028	5.300000e-13	86.1
14	TraesCS6D01G121700	chr1A	75.439	171	30	6	2151	2320	381313783	381313624	4.130000e-09	73.1

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	TraesCS6D01G121700	chr6D	86600535	86603518	2983	True	5511.0	5511	100.0000	1	2984	1	chr6D.!!$R1	2983
1	TraesCS6D01G121700	chr6A	104112056	104115043	2987	True	4180.0	4180	92.0360	1	2984	1	chr6A.!!$R1	2983
2	TraesCS6D01G121700	chr6B	164033000	164035962	2962	True	1969.0	2911	89.7675	1	2984	2	chr6B.!!$R1	2983
3	TraesCS6D01G121700	chr7B	597081753	597082597	844	True	351.5	536	83.8570	1263	1968	2	chr7B.!!$R1	705
4	TraesCS6D01G121700	chr7A	637864158	637864972	814	True	348.0	531	83.6795	1263	1963	2	chr7A.!!$R1	700
5	TraesCS6D01G121700	chr7D	552164155	552164993	838	True	341.5	520	83.4880	1263	1962	2	chr7D.!!$R1	699

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
66	67	0.103208	CGAAGGCAACGGAGCTCTAT	59.897	55.0	14.64	0.0	46.39	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1986	2173	0.035439	GGAAAGCCGATTCCCTGACA	60.035	55.0	2.82	0.0	42.57	3.58	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
61	62	2.048127	ACTCGAAGGCAACGGAGC	60.048	61.111	3.84	0.00	46.39	4.70
62	63	2.262915	CTCGAAGGCAACGGAGCT	59.737	61.111	0.00	0.00	46.39	4.09
63	64	1.807573	CTCGAAGGCAACGGAGCTC	60.808	63.158	4.71	4.71	46.39	4.09
64	65	2.219325	CTCGAAGGCAACGGAGCTCT	62.219	60.000	14.64	0.00	46.39	4.09
65	66	0.963856	TCGAAGGCAACGGAGCTCTA	60.964	55.000	14.64	0.00	46.39	2.43
66	67	0.103208	CGAAGGCAACGGAGCTCTAT	59.897	55.000	14.64	0.00	46.39	1.98
80	81	4.258543	GAGCTCTATATAGACCGACAGCT	58.741	47.826	17.29	17.29	31.63	4.24
84	85	4.841422	TCTATATAGACCGACAGCTACCC	58.159	47.826	8.44	0.00	0.00	3.69
166	167	2.294512	CCAAGTGGCCAGTCTTCTTTTC	59.705	50.000	15.03	0.00	0.00	2.29
167	168	3.217626	CAAGTGGCCAGTCTTCTTTTCT	58.782	45.455	15.03	0.00	0.00	2.52
220	221	7.536895	TGTTCAACAATTTTCTCACCAAATG	57.463	32.000	0.00	0.00	0.00	2.32
283	284	1.379576	GATGGCCAGAAAGCTGCCT	60.380	57.895	13.05	0.00	40.91	4.75
296	301	2.659428	AGCTGCCTGTCTTCAAAGTTT	58.341	42.857	0.00	0.00	0.00	2.66
302	307	5.167845	TGCCTGTCTTCAAAGTTTCAAAAC	58.832	37.500	0.00	0.00	39.17	2.43
304	309	5.109210	CCTGTCTTCAAAGTTTCAAAACCC	58.891	41.667	2.08	0.00	39.71	4.11
394	400	4.641396	CCGTGATGTGTTCCATATACCAT	58.359	43.478	0.00	0.00	32.56	3.55
397	403	6.455647	CGTGATGTGTTCCATATACCATACT	58.544	40.000	0.00	0.00	32.56	2.12
470	479	3.197790	CGGGGTTCATCGCAGCTG	61.198	66.667	10.11	10.11	0.00	4.24
649	658	1.197721	AGATTGCTTTCTCGCCAAACG	59.802	47.619	0.00	0.00	45.62	3.60
768	780	1.378882	CCATCACATCCCAACCTGCG	61.379	60.000	0.00	0.00	0.00	5.18
822	839	3.513912	AGATGTCATTCTGGTACGGTGAA	59.486	43.478	0.00	0.00	35.30	3.18
855	872	0.610785	CCGCACCACCCCTTGTATTT	60.611	55.000	0.00	0.00	0.00	1.40
902	920	3.501828	AGCACAAGATCACACGCATAAAA	59.498	39.130	0.00	0.00	0.00	1.52
1008	1030	1.692762	GGGTAGGGAGAGATGAAGGCA	60.693	57.143	0.00	0.00	0.00	4.75
1018	1040	1.728490	GATGAAGGCAATGTCCGGGC	61.728	60.000	0.00	0.00	0.00	6.13
1837	2012	4.704103	AGCGGGAGGTGGAGAGCA	62.704	66.667	0.00	0.00	40.33	4.26
1977	2164	2.342279	CCGACCACGAAGAAGGCA	59.658	61.111	0.00	0.00	42.66	4.75
1986	2173	3.555168	CCACGAAGAAGGCAAACTAGTCT	60.555	47.826	0.00	0.00	0.00	3.24
1996	2183	3.307762	GGCAAACTAGTCTGTCAGGGAAT	60.308	47.826	0.00	0.00	0.00	3.01
2007	2194	0.035439	TCAGGGAATCGGCTTTCCAC	60.035	55.000	15.33	7.19	45.89	4.02
2087	2318	0.173481	ATGTGGTGTGGTCTCGATCG	59.827	55.000	9.36	9.36	0.00	3.69
2128	2359	6.253512	GTGGAACAACTGAACAAGTGATTTTC	59.746	38.462	0.00	0.00	44.16	2.29
2217	2450	8.512956	GGATCACACTACAAGTCACGTATATAT	58.487	37.037	0.00	0.00	0.00	0.86
2222	2455	8.615211	ACACTACAAGTCACGTATATATCGAAA	58.385	33.333	10.29	0.00	0.00	3.46
2231	2464	7.529519	GTCACGTATATATCGAAATGGCAAAAC	59.470	37.037	10.29	0.00	0.00	2.43
2234	2467	7.439955	ACGTATATATCGAAATGGCAAAACTGA	59.560	33.333	10.29	0.00	0.00	3.41
2321	2555	3.710209	AAGACCAAAGGATCCTCTGTG	57.290	47.619	16.52	13.36	0.00	3.66
2330	2564	1.634702	GATCCTCTGTGACGAGCAAC	58.365	55.000	0.00	0.00	0.00	4.17
2357	2591	4.445718	AGAATGACATATTTAGCGCTCACG	59.554	41.667	16.34	0.00	44.07	4.35
2507	2743	8.209917	AGAAAAGAGTCGTTGTGTTCTAATTT	57.790	30.769	0.00	0.00	0.00	1.82
2604	2841	4.284490	AGCTCAAGAGAATGAAGTACCACA	59.716	41.667	0.32	0.00	0.00	4.17
2606	2843	6.155221	AGCTCAAGAGAATGAAGTACCACATA	59.845	38.462	0.32	0.00	0.00	2.29
2653	2890	5.357878	TCCATCAAACACCAGCAATTATCTC	59.642	40.000	0.00	0.00	0.00	2.75
2657	2894	3.627395	ACACCAGCAATTATCTCGGAA	57.373	42.857	0.00	0.00	0.00	4.30
2658	2895	4.156455	ACACCAGCAATTATCTCGGAAT	57.844	40.909	0.00	0.00	0.00	3.01
2687	2924	5.635549	TCAAGAATACGTTGCACATATCG	57.364	39.130	0.00	0.00	0.00	2.92
2744	2981	0.246635	CATGTCGACCCCGAGTTCTT	59.753	55.000	14.12	0.00	46.52	2.52
2747	2984	1.271543	TGTCGACCCCGAGTTCTTCTA	60.272	52.381	14.12	0.00	46.52	2.10
2783	3020	5.989249	GCAAATGCATGAACGATATACAGA	58.011	37.500	0.00	0.00	41.59	3.41
2784	3021	6.605849	GCAAATGCATGAACGATATACAGAT	58.394	36.000	0.00	0.00	41.59	2.90
2785	3022	7.742151	GCAAATGCATGAACGATATACAGATA	58.258	34.615	0.00	0.00	41.59	1.98
2786	3023	8.393366	GCAAATGCATGAACGATATACAGATAT	58.607	33.333	0.00	0.00	41.59	1.63
2907	3147	5.921962	ATGTTGAATTAAGGGGAGAAAGC	57.078	39.130	0.00	0.00	0.00	3.51
2936	3180	8.497910	TCTGCCAAAAGATAGGATTATACTCT	57.502	34.615	0.00	0.00	0.00	3.24
2973	3217	6.207691	TGAGTTTTTCCAAAGTTTCTCCAG	57.792	37.500	0.00	0.00	0.00	3.86
2975	3219	6.607198	TGAGTTTTTCCAAAGTTTCTCCAGAT	59.393	34.615	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	2.477972	GAAGCCTCGGCAAAAGCACC	62.478	60.000	11.02	0.00	44.88	5.01
61	62	4.877251	GGGTAGCTGTCGGTCTATATAGAG	59.123	50.000	12.87	2.87	32.01	2.43
62	63	4.324099	GGGGTAGCTGTCGGTCTATATAGA	60.324	50.000	8.44	8.44	0.00	1.98
63	64	3.946558	GGGGTAGCTGTCGGTCTATATAG	59.053	52.174	3.10	3.10	0.00	1.31
64	65	3.308688	GGGGGTAGCTGTCGGTCTATATA	60.309	52.174	0.00	0.00	0.00	0.86
65	66	2.557005	GGGGGTAGCTGTCGGTCTATAT	60.557	54.545	0.00	0.00	0.00	0.86
66	67	1.202976	GGGGGTAGCTGTCGGTCTATA	60.203	57.143	0.00	0.00	0.00	1.31
84	85	3.937079	GGAACTAACGTTTGTAGATGGGG	59.063	47.826	15.57	0.00	32.39	4.96
129	130	2.005451	CTTGGGATTCAAGCGACTCAG	58.995	52.381	0.00	0.00	45.24	3.35
283	284	4.381079	CCGGGTTTTGAAACTTTGAAGACA	60.381	41.667	0.00	0.00	38.89	3.41
296	301	0.035439	GAGATGGCTCCGGGTTTTGA	60.035	55.000	0.00	0.00	35.01	2.69
376	382	8.902540	TTTCAGTATGGTATATGGAACACATC	57.097	34.615	0.00	0.00	37.96	3.06
420	429	3.967332	AATTTCTTGGGCAATGTGAGG	57.033	42.857	0.00	0.00	0.00	3.86
421	430	3.998341	CCAAATTTCTTGGGCAATGTGAG	59.002	43.478	0.00	0.00	35.96	3.51
422	431	3.390639	ACCAAATTTCTTGGGCAATGTGA	59.609	39.130	8.32	0.00	43.71	3.58
423	432	3.742385	ACCAAATTTCTTGGGCAATGTG	58.258	40.909	8.32	0.00	43.71	3.21
649	658	2.412847	GCGTTTGATCAGTAGTTGGCAC	60.413	50.000	0.00	0.00	0.00	5.01
768	780	2.671963	GTGAGTTGGCCGGGGAAC	60.672	66.667	2.18	0.00	0.00	3.62
822	839	0.179000	GTGCGGATGGAGAGAATGGT	59.821	55.000	0.00	0.00	0.00	3.55
855	872	0.894835	TGAAGAGCAGCGATGGTGTA	59.105	50.000	11.37	0.00	33.19	2.90
955	973	2.156917	CAAACCAATGAGCAGAGCAGA	58.843	47.619	0.00	0.00	0.00	4.26
985	1003	0.105658	TTCATCTCTCCCTACCCCGG	60.106	60.000	0.00	0.00	0.00	5.73
1008	1030	3.717294	AGCTTCGGCCCGGACATT	61.717	61.111	0.73	0.00	43.01	2.71
1134	1156	4.681978	AGGGACGCGCAGGTGAAC	62.682	66.667	5.73	0.00	0.00	3.18
1837	2012	2.125512	GAACTCCCTCGCGCACAT	60.126	61.111	8.75	0.00	0.00	3.21
1873	2048	2.933287	TGTGCCGGTCCCCTCAAT	60.933	61.111	1.90	0.00	0.00	2.57
1977	2164	3.195825	CCGATTCCCTGACAGACTAGTTT	59.804	47.826	3.32	0.00	0.00	2.66
1986	2173	0.035439	GGAAAGCCGATTCCCTGACA	60.035	55.000	2.82	0.00	42.57	3.58
1996	2183	1.314730	GAACCAAAGTGGAAAGCCGA	58.685	50.000	0.18	0.00	40.96	5.54
2007	2194	3.473625	ACCGAAGTACAAGGAACCAAAG	58.526	45.455	8.05	0.00	0.00	2.77
2087	2318	4.142271	TGTTCCACAAGTGTCATTTTGTCC	60.142	41.667	0.00	0.00	35.46	4.02
2249	2483	3.375610	TCTTTGTGCAAAGTTAGCGTTCA	59.624	39.130	20.02	0.20	45.88	3.18
2258	2492	5.047660	TGGTTAGTGTTTCTTTGTGCAAAGT	60.048	36.000	20.02	6.53	45.88	2.66
2259	2493	5.406649	TGGTTAGTGTTTCTTTGTGCAAAG	58.593	37.500	16.16	16.16	46.82	2.77
2300	2534	4.223032	GTCACAGAGGATCCTTTGGTCTTA	59.777	45.833	30.19	12.07	33.66	2.10
2311	2545	1.203523	AGTTGCTCGTCACAGAGGATC	59.796	52.381	0.00	0.00	38.37	3.36
2321	2555	5.786401	ATGTCATTCTAAAGTTGCTCGTC	57.214	39.130	0.00	0.00	0.00	4.20
2330	2564	8.006590	GTGAGCGCTAAATATGTCATTCTAAAG	58.993	37.037	11.50	0.00	0.00	1.85
2579	2816	6.014584	TGTGGTACTTCATTCTCTTGAGCTAA	60.015	38.462	0.00	0.00	0.00	3.09
2604	2841	2.880268	CGAACACACATGATGCCCATAT	59.120	45.455	0.00	0.00	33.31	1.78
2606	2843	1.097232	CGAACACACATGATGCCCAT	58.903	50.000	0.00	0.00	35.44	4.00
2653	2890	7.740346	GCAACGTATTCTTGATTACATATTCCG	59.260	37.037	0.00	0.00	0.00	4.30
2657	2894	8.432110	TGTGCAACGTATTCTTGATTACATAT	57.568	30.769	0.00	0.00	42.39	1.78
2658	2895	7.835634	TGTGCAACGTATTCTTGATTACATA	57.164	32.000	0.00	0.00	42.39	2.29
2687	2924	4.823989	AGTCAATTTCACATAGCCTATGCC	59.176	41.667	11.65	0.00	39.79	4.40
2732	2969	3.917300	AGATCATAGAAGAACTCGGGGT	58.083	45.455	0.00	0.00	0.00	4.95
2824	3061	8.258007	TCGATTGTTAACTAGGAATGACTTCAT	58.742	33.333	7.22	0.00	38.41	2.57
2833	3073	6.460781	TGAAGCTTCGATTGTTAACTAGGAA	58.539	36.000	21.11	6.65	0.00	3.36
2842	3082	7.769272	TCAAAATTTTGAAGCTTCGATTGTT	57.231	28.000	27.22	11.36	43.62	2.83
2888	3128	4.735369	TGTGCTTTCTCCCCTTAATTCAA	58.265	39.130	0.00	0.00	0.00	2.69
2907	3147	7.756395	ATAATCCTATCTTTTGGCAGATGTG	57.244	36.000	0.00	0.00	35.08	3.21
2941	3185	9.936759	AAACTTTGGAAAAACTCAAACAAGATA	57.063	25.926	0.00	0.00	0.00	1.98
2950	3194	5.949354	TCTGGAGAAACTTTGGAAAAACTCA	59.051	36.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.