AutoCloner

Multiple sequence alignment - TraesCS6A01G123100

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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	TraesCS6A01G123100	chr6A	100.000	2648	0	0	1	2648	96771296	96773943	0.000000e+00	4891.0
1	TraesCS6A01G123100	chr6B	90.942	1380	75	27	692	2027	152631486	152630113	0.000000e+00	1810.0
2	TraesCS6A01G123100	chr6B	95.808	334	11	1	967	1297	152696001	152695668	1.080000e-148	536.0
3	TraesCS6A01G123100	chr6B	88.352	352	22	9	586	925	152696861	152696517	3.170000e-109	405.0
4	TraesCS6A01G123100	chr6B	77.522	347	43	19	2315	2645	152614599	152614272	2.710000e-40	176.0
5	TraesCS6A01G123100	chr6B	92.453	53	4	0	2049	2101	712633031	712633083	2.830000e-10	76.8
6	TraesCS6A01G123100	chr6D	90.789	1357	73	26	391	1719	79934855	79933523	0.000000e+00	1766.0
7	TraesCS6A01G123100	chr6D	90.383	1331	44	26	680	1950	80061026	80062332	0.000000e+00	1672.0
8	TraesCS6A01G123100	chr6D	88.369	705	59	12	1957	2648	80088263	80088957	0.000000e+00	826.0
9	TraesCS6A01G123100	chr6D	82.316	950	112	28	1729	2645	79933463	79932537	0.000000e+00	773.0
10	TraesCS6A01G123100	chr6D	87.111	225	15	8	452	667	80060542	80060761	2.630000e-60	243.0
11	TraesCS6A01G123100	chr6D	87.113	194	8	3	366	543	80060019	80060211	1.240000e-48	204.0
12	TraesCS6A01G123100	chr6D	92.453	53	4	0	2049	2101	294405020	294405072	2.830000e-10	76.8
13	TraesCS6A01G123100	chr2D	86.339	549	68	6	1095	1641	102725399	102725942	2.270000e-165	592.0
14	TraesCS6A01G123100	chr2A	85.974	549	70	6	1095	1641	101836457	101837000	4.910000e-162	580.0
15	TraesCS6A01G123100	chr2B	85.246	549	74	6	1095	1641	153903596	153904139	2.300000e-155	558.0
16	TraesCS6A01G123100	chr2B	94.915	59	3	0	1267	1325	74359081	74359139	2.810000e-15	93.5
17	TraesCS6A01G123100	chr2B	92.453	53	4	0	2049	2101	731023784	731023732	2.830000e-10	76.8
18	TraesCS6A01G123100	chr7D	92.432	370	16	6	1	364	77441054	77441417	3.910000e-143	518.0
19	TraesCS6A01G123100	chr4A	91.892	370	23	4	1	364	731948652	731949020	6.540000e-141	510.0
20	TraesCS6A01G123100	chr4A	91.870	369	21	6	3	364	547074065	547074431	8.460000e-140	507.0
21	TraesCS6A01G123100	chr3B	91.914	371	20	7	1	364	2117794	2117427	6.540000e-141	510.0
22	TraesCS6A01G123100	chr3B	92.453	53	4	0	2049	2101	468219540	468219592	2.830000e-10	76.8
23	TraesCS6A01G123100	chr4B	91.870	369	23	3	1	364	68087230	68087596	2.350000e-140	508.0
24	TraesCS6A01G123100	chr4B	91.375	371	24	5	1	364	68086795	68087164	3.930000e-138	501.0
25	TraesCS6A01G123100	chr4B	91.525	59	5	0	1267	1325	636684407	636684465	6.070000e-12	82.4
26	TraesCS6A01G123100	chr1B	91.667	372	22	5	1	364	667359732	667359362	8.460000e-140	507.0
27	TraesCS6A01G123100	chr1B	91.398	372	23	6	1	364	38021357	38020987	3.930000e-138	501.0
28	TraesCS6A01G123100	chr1B	91.398	372	23	6	1	364	166576132	166575762	3.930000e-138	501.0
29	TraesCS6A01G123100	chr7B	94.340	53	3	0	2049	2101	647684029	647683977	6.070000e-12	82.4
30	TraesCS6A01G123100	chr7B	92.453	53	4	0	2049	2101	397870467	397870519	2.830000e-10	76.8
31	TraesCS6A01G123100	chr7B	97.727	44	1	0	2058	2101	603569851	603569808	2.830000e-10	76.8
32	TraesCS6A01G123100	chr5B	91.525	59	5	0	1267	1325	418917194	418917136	6.070000e-12	82.4

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	TraesCS6A01G123100	chr6A	96771296	96773943	2647	False	4891.000000	4891	100.000000	1	2648	1	chr6A.!!$F1	2647
1	TraesCS6A01G123100	chr6B	152630113	152631486	1373	True	1810.000000	1810	90.942000	692	2027	1	chr6B.!!$R2	1335
2	TraesCS6A01G123100	chr6B	152695668	152696861	1193	True	470.500000	536	92.080000	586	1297	2	chr6B.!!$R3	711
3	TraesCS6A01G123100	chr6D	79932537	79934855	2318	True	1269.500000	1766	86.552500	391	2645	2	chr6D.!!$R1	2254
4	TraesCS6A01G123100	chr6D	80088263	80088957	694	False	826.000000	826	88.369000	1957	2648	1	chr6D.!!$F1	691
5	TraesCS6A01G123100	chr6D	80060019	80062332	2313	False	706.333333	1672	88.202333	366	1950	3	chr6D.!!$F3	1584
6	TraesCS6A01G123100	chr2D	102725399	102725942	543	False	592.000000	592	86.339000	1095	1641	1	chr2D.!!$F1	546
7	TraesCS6A01G123100	chr2A	101836457	101837000	543	False	580.000000	580	85.974000	1095	1641	1	chr2A.!!$F1	546
8	TraesCS6A01G123100	chr2B	153903596	153904139	543	False	558.000000	558	85.246000	1095	1641	1	chr2B.!!$F2	546
9	TraesCS6A01G123100	chr4B	68086795	68087596	801	False	504.500000	508	91.622500	1	364	2	chr4B.!!$F2	363

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
628	1515	0.59023	TTTGTACGTGTTGCAAGCGC	60.59	50.0	19.29	0.0	39.24	5.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2129	3865	0.529992	GATCGAACCCCTAACGCTGG	60.53	60.0	0.0	0.0	0.0	4.85	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
43	44	2.693074	GTTTCTGCCCAAACAAGGAAGA	59.307	45.455	3.35	0.00	36.44	2.87
56	492	5.941948	ACAAGGAAGAAAAGTTATGGACG	57.058	39.130	0.00	0.00	0.00	4.79
77	513	3.002862	CGTGATTCGGAAGGAAACAAACA	59.997	43.478	0.00	0.00	38.88	2.83
182	622	5.655488	CGTCAGTATGGAAAGTTCTGATCT	58.345	41.667	0.00	0.00	37.46	2.75
215	655	3.587797	TTCGTTGTATGAGAGGGTGAC	57.412	47.619	0.00	0.00	0.00	3.67
321	762	3.202151	ACCATGGTAGATGGGACGAAAAT	59.798	43.478	18.10	0.00	43.32	1.82
325	766	6.490040	CCATGGTAGATGGGACGAAAATAAAT	59.510	38.462	2.57	0.00	35.58	1.40
332	773	5.890424	TGGGACGAAAATAAATCTGGAAC	57.110	39.130	0.00	0.00	0.00	3.62
333	774	4.393680	TGGGACGAAAATAAATCTGGAACG	59.606	41.667	0.00	0.00	0.00	3.95
348	789	3.427573	TGGAACGGAGACTATCAACTGA	58.572	45.455	0.00	0.00	0.00	3.41
349	790	3.444034	TGGAACGGAGACTATCAACTGAG	59.556	47.826	0.00	0.00	0.00	3.35
350	791	3.695060	GGAACGGAGACTATCAACTGAGA	59.305	47.826	0.00	0.00	0.00	3.27
357	798	6.261158	CGGAGACTATCAACTGAGACATTAGA	59.739	42.308	0.00	0.00	0.00	2.10
359	800	8.470805	GGAGACTATCAACTGAGACATTAGAAA	58.529	37.037	0.00	0.00	0.00	2.52
375	816	5.890424	TTAGAAATAGACCCCGCAAAAAG	57.110	39.130	0.00	0.00	0.00	2.27
389	830	7.340999	ACCCCGCAAAAAGTATAATCAAAGTAT	59.659	33.333	0.00	0.00	0.00	2.12
450	901	1.510480	GCTGGCGGGACAAGCATATC	61.510	60.000	0.00	0.00	36.08	1.63
457	1336	3.338249	CGGGACAAGCATATCTTATGGG	58.662	50.000	0.00	0.00	32.74	4.00
505	1391	1.381928	ATGACGTGTCCGCCGACTAT	61.382	55.000	6.74	0.00	39.94	2.12
548	1434	3.523157	TCAACCTCAAGATCTATTGGCCA	59.477	43.478	0.00	0.00	0.00	5.36
556	1442	4.686191	AGATCTATTGGCCAAGTCTCTG	57.314	45.455	24.94	9.66	0.00	3.35
584	1470	6.212187	AGCTGCTCACAGGAATATGATGTATA	59.788	38.462	0.00	0.00	44.63	1.47
614	1500	4.385825	GTTCATGAGGGTGAGTGTTTGTA	58.614	43.478	0.00	0.00	0.00	2.41
620	1507	2.093341	AGGGTGAGTGTTTGTACGTGTT	60.093	45.455	0.00	0.00	0.00	3.32
622	1509	2.538132	GGTGAGTGTTTGTACGTGTTGC	60.538	50.000	0.00	0.00	0.00	4.17
623	1510	2.094575	GTGAGTGTTTGTACGTGTTGCA	59.905	45.455	0.00	0.00	0.00	4.08
628	1515	0.590230	TTTGTACGTGTTGCAAGCGC	60.590	50.000	19.29	0.00	39.24	5.92
641	1528	1.399727	GCAAGCGCATCGTAGTGTTTT	60.400	47.619	11.47	0.00	38.36	2.43
643	1530	2.080286	AGCGCATCGTAGTGTTTTCT	57.920	45.000	11.47	0.00	0.00	2.52
644	1531	1.993370	AGCGCATCGTAGTGTTTTCTC	59.007	47.619	11.47	0.00	0.00	2.87
645	1532	1.060698	GCGCATCGTAGTGTTTTCTCC	59.939	52.381	0.30	0.00	0.00	3.71
698	1839	2.548920	GCTGAGCCGGAGCATATAGTTT	60.549	50.000	5.05	0.00	43.56	2.66
735	1876	2.665649	TGCATTCCACGTTCGACTAT	57.334	45.000	0.00	0.00	0.00	2.12
736	1877	3.786516	TGCATTCCACGTTCGACTATA	57.213	42.857	0.00	0.00	0.00	1.31
737	1878	4.316205	TGCATTCCACGTTCGACTATAT	57.684	40.909	0.00	0.00	0.00	0.86
738	1879	5.441709	TGCATTCCACGTTCGACTATATA	57.558	39.130	0.00	0.00	0.00	0.86
811	1957	1.202651	GCCAGTGGCCACGAATATACT	60.203	52.381	29.68	7.25	44.06	2.12
812	1958	2.755650	CCAGTGGCCACGAATATACTC	58.244	52.381	29.68	2.00	36.20	2.59
941	2116	4.097012	GCGCGCTATATAAAGAGGTAGAC	58.903	47.826	26.67	0.00	0.00	2.59
942	2117	4.379186	GCGCGCTATATAAAGAGGTAGACA	60.379	45.833	26.67	0.00	0.00	3.41
943	2118	5.325494	CGCGCTATATAAAGAGGTAGACAG	58.675	45.833	5.56	0.00	0.00	3.51
948	2123	7.148154	CGCTATATAAAGAGGTAGACAGCTGAT	60.148	40.741	23.35	11.17	30.99	2.90
1064	2710	0.462759	GCCCAACAATCCTCTCCTCG	60.463	60.000	0.00	0.00	0.00	4.63
1066	2712	0.462759	CCAACAATCCTCTCCTCGCC	60.463	60.000	0.00	0.00	0.00	5.54
1675	3331	2.317609	CCAAACGTGGTGGAGCTCG	61.318	63.158	12.22	0.00	40.42	5.03
1685	3341	0.744771	GTGGAGCTCGTTCATTCCCC	60.745	60.000	7.83	0.00	0.00	4.81
1743	3456	5.109903	ACCAAACTAATACGAGAGCATCAC	58.890	41.667	0.00	0.00	37.82	3.06
1835	3557	2.982470	CCTTCTTCATTTCAAAGTGCGC	59.018	45.455	0.00	0.00	0.00	6.09
1856	3578	5.670341	GCGCGACTTTTAAACATGAGTACAT	60.670	40.000	12.10	0.00	37.19	2.29
2027	3753	8.772705	TCAATACAAATCCAAAAGCACATTTTC	58.227	29.630	0.00	0.00	39.11	2.29
2036	3764	7.315142	TCCAAAAGCACATTTTCTGTATCATC	58.685	34.615	0.00	0.00	39.11	2.92
2126	3862	1.274167	TCGTTCAAGCGTATCCCTTGT	59.726	47.619	0.00	0.00	40.35	3.16
2129	3865	1.448985	TCAAGCGTATCCCTTGTTGC	58.551	50.000	0.00	0.00	40.35	4.17
2130	3866	0.451783	CAAGCGTATCCCTTGTTGCC	59.548	55.000	0.00	0.00	35.97	4.52
2150	3886	1.140375	GCGTTAGGGGTTCGATCGT	59.860	57.895	15.94	0.00	0.00	3.73
2219	3955	3.776616	GCTAATGGCTGCTGAGACT	57.223	52.632	0.00	0.00	38.06	3.24
2261	3997	2.074576	GGTTTCTGACTAGTTTCGGGC	58.925	52.381	0.00	0.00	0.00	6.13
2264	4000	1.629043	TCTGACTAGTTTCGGGCACT	58.371	50.000	0.00	0.00	0.00	4.40
2267	4003	3.575256	TCTGACTAGTTTCGGGCACTTTA	59.425	43.478	0.00	0.00	0.00	1.85
2280	4016	4.809426	CGGGCACTTTATAGAAGGTTACAG	59.191	45.833	0.00	0.00	0.00	2.74
2283	4019	7.054751	GGGCACTTTATAGAAGGTTACAGAAT	58.945	38.462	0.00	0.00	0.00	2.40
2286	4022	7.516943	GCACTTTATAGAAGGTTACAGAATCGC	60.517	40.741	0.00	0.00	0.00	4.58
2366	4102	7.986085	TTTCAAAATTTTGTGGTCCTTTTCA	57.014	28.000	25.98	4.02	39.18	2.69
2382	4118	9.594478	GGTCCTTTTCAGTTTTTCATTTTCTAA	57.406	29.630	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	4.571919	TCCGAATCACGTCCATAACTTTT	58.428	39.130	0.00	0.00	40.78	2.27
56	492	4.561735	TGTTTGTTTCCTTCCGAATCAC	57.438	40.909	0.00	0.00	31.36	3.06
159	599	5.518128	CAGATCAGAACTTTCCATACTGACG	59.482	44.000	0.00	0.00	39.76	4.35
195	635	2.094906	CGTCACCCTCTCATACAACGAA	60.095	50.000	0.00	0.00	0.00	3.85
196	636	1.471287	CGTCACCCTCTCATACAACGA	59.529	52.381	0.00	0.00	0.00	3.85
199	639	0.172578	CGCGTCACCCTCTCATACAA	59.827	55.000	0.00	0.00	0.00	2.41
203	643	0.320374	TTTTCGCGTCACCCTCTCAT	59.680	50.000	5.77	0.00	0.00	2.90
215	655	3.778718	CACTTCATCGGTTTATTTTCGCG	59.221	43.478	0.00	0.00	0.00	5.87
300	741	3.275617	TTTTCGTCCCATCTACCATGG	57.724	47.619	11.19	11.19	38.88	3.66
309	750	5.065988	CGTTCCAGATTTATTTTCGTCCCAT	59.934	40.000	0.00	0.00	0.00	4.00
321	762	6.380274	AGTTGATAGTCTCCGTTCCAGATTTA	59.620	38.462	0.00	0.00	0.00	1.40
325	766	3.444034	CAGTTGATAGTCTCCGTTCCAGA	59.556	47.826	0.00	0.00	0.00	3.86
332	773	4.909696	ATGTCTCAGTTGATAGTCTCCG	57.090	45.455	0.00	0.00	0.00	4.63
333	774	7.575414	TCTAATGTCTCAGTTGATAGTCTCC	57.425	40.000	0.00	0.00	0.00	3.71
341	782	7.364762	GGGGTCTATTTCTAATGTCTCAGTTGA	60.365	40.741	0.00	0.00	0.00	3.18
348	789	3.709653	TGCGGGGTCTATTTCTAATGTCT	59.290	43.478	0.00	0.00	0.00	3.41
349	790	4.067972	TGCGGGGTCTATTTCTAATGTC	57.932	45.455	0.00	0.00	0.00	3.06
350	791	4.497291	TTGCGGGGTCTATTTCTAATGT	57.503	40.909	0.00	0.00	0.00	2.71
357	798	7.558444	TGATTATACTTTTTGCGGGGTCTATTT	59.442	33.333	0.00	0.00	0.00	1.40
359	800	6.597562	TGATTATACTTTTTGCGGGGTCTAT	58.402	36.000	0.00	0.00	0.00	1.98
364	805	5.961272	ACTTTGATTATACTTTTTGCGGGG	58.039	37.500	0.00	0.00	0.00	5.73
389	830	7.831691	TCCTCCATTTCAAAACATAAGACAA	57.168	32.000	0.00	0.00	0.00	3.18
548	1434	1.296068	GAGCAGCTGCCAGAGACTT	59.704	57.895	34.39	14.14	43.38	3.01
556	1442	0.107508	TATTCCTGTGAGCAGCTGCC	60.108	55.000	34.39	24.89	43.38	4.85
584	1470	0.036732	ACCCTCATGAACGTGCACAT	59.963	50.000	18.64	4.50	0.00	3.21
622	1509	2.157668	AGAAAACACTACGATGCGCTTG	59.842	45.455	9.73	0.00	0.00	4.01
623	1510	2.412089	GAGAAAACACTACGATGCGCTT	59.588	45.455	9.73	0.55	0.00	4.68
628	1515	6.539649	TTTTCTGGAGAAAACACTACGATG	57.460	37.500	9.95	0.00	45.76	3.84
735	1876	2.413796	CGGCAACAAGAAACTGCGTATA	59.586	45.455	0.00	0.00	36.93	1.47
736	1877	1.196808	CGGCAACAAGAAACTGCGTAT	59.803	47.619	0.00	0.00	36.93	3.06
737	1878	0.584396	CGGCAACAAGAAACTGCGTA	59.416	50.000	0.00	0.00	36.93	4.42
738	1879	1.355210	CGGCAACAAGAAACTGCGT	59.645	52.632	0.00	0.00	36.93	5.24
1152	2798	2.925706	TGGAAGGCCAGCACCGTA	60.926	61.111	5.01	0.00	39.92	4.02
1516	3162	3.812019	CTCCCTCGTGTCCGTCCG	61.812	72.222	0.00	0.00	35.01	4.79
1675	3331	2.040412	AGACAAGACCAGGGGAATGAAC	59.960	50.000	0.00	0.00	0.00	3.18
1743	3456	9.554395	AACAATACCAATTTTGAAACCTAAAGG	57.446	29.630	0.00	0.00	42.17	3.11
1813	3535	2.982470	CGCACTTTGAAATGAAGAAGGC	59.018	45.455	0.00	0.00	0.00	4.35
2063	3798	6.015603	CCCCATTGTATTTTGTGCCAAATTTT	60.016	34.615	1.89	0.00	0.00	1.82
2066	3801	4.587891	CCCCATTGTATTTTGTGCCAAAT	58.412	39.130	1.89	0.00	0.00	2.32
2071	3806	1.277557	TGGCCCCATTGTATTTTGTGC	59.722	47.619	0.00	0.00	0.00	4.57
2079	3814	3.108376	GGGTTTATTTGGCCCCATTGTA	58.892	45.455	0.00	0.00	37.09	2.41
2080	3815	1.912731	GGGTTTATTTGGCCCCATTGT	59.087	47.619	0.00	0.00	37.09	2.71
2081	3816	2.708216	GGGTTTATTTGGCCCCATTG	57.292	50.000	0.00	0.00	37.09	2.82
2126	3862	1.302993	GAACCCCTAACGCTGGCAA	60.303	57.895	0.00	0.00	0.00	4.52
2129	3865	0.529992	GATCGAACCCCTAACGCTGG	60.530	60.000	0.00	0.00	0.00	4.85
2130	3866	0.870307	CGATCGAACCCCTAACGCTG	60.870	60.000	10.26	0.00	0.00	5.18
2150	3886	2.216046	CCATCTACGTACGCTAGTGGA	58.784	52.381	16.72	3.45	32.60	4.02
2205	3941	2.026542	TCAAATCAGTCTCAGCAGCCAT	60.027	45.455	0.00	0.00	0.00	4.40
2206	3942	1.348696	TCAAATCAGTCTCAGCAGCCA	59.651	47.619	0.00	0.00	0.00	4.75
2210	3946	3.867600	GCTTCCTCAAATCAGTCTCAGCA	60.868	47.826	0.00	0.00	0.00	4.41
2219	3955	4.330250	CTTCCAGAAGCTTCCTCAAATCA	58.670	43.478	22.81	0.00	0.00	2.57
2261	3997	7.707035	AGCGATTCTGTAACCTTCTATAAAGTG	59.293	37.037	0.00	0.00	0.00	3.16
2264	4000	9.444600	AAAAGCGATTCTGTAACCTTCTATAAA	57.555	29.630	0.00	0.00	0.00	1.40
2267	4003	7.923414	AAAAAGCGATTCTGTAACCTTCTAT	57.077	32.000	0.00	0.00	0.00	1.98
2294	4030	9.853177	ACTCAAATATCCCGAAAAGATATTTCT	57.147	29.630	13.24	1.18	46.55	2.52
2345	4081	6.983474	ACTGAAAAGGACCACAAAATTTTG	57.017	33.333	25.73	25.73	43.62	2.44
2416	4157	8.266392	TGCAAACAGTTTTTGAAGATTTTGAT	57.734	26.923	5.94	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.