AutoCloner

Multiple sequence alignment - TraesCS6D01G040700

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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	TraesCS6D01G040700	chr6D	100.000	2537	0	0	1	2537	16524174	16521638	0.000000e+00	4686.0
1	TraesCS6D01G040700	chr6D	88.631	818	68	14	724	1537	16502654	16503450	0.000000e+00	972.0
2	TraesCS6D01G040700	chr6A	93.889	1849	82	17	1	1829	16721182	16719345	0.000000e+00	2760.0
3	TraesCS6D01G040700	chr6A	88.067	771	56	21	796	1553	16593976	16593229	0.000000e+00	881.0
4	TraesCS6D01G040700	chr6A	87.419	771	54	23	789	1540	16658886	16658140	0.000000e+00	846.0
5	TraesCS6D01G040700	chr6A	87.302	378	38	6	2168	2537	16716651	16716276	8.390000e-115	424.0
6	TraesCS6D01G040700	chr6B	85.583	2178	169	57	1	2113	29061594	29059497	0.000000e+00	2148.0
7	TraesCS6D01G040700	chr6B	91.002	1467	95	20	454	1893	28980779	28979323	0.000000e+00	1943.0
8	TraesCS6D01G040700	chr6B	90.339	766	52	16	796	1553	28925846	28926597	0.000000e+00	985.0
9	TraesCS6D01G040700	chr6B	91.870	369	23	5	2174	2537	28978601	28978235	2.250000e-140	508.0
10	TraesCS6D01G040700	chr6B	87.027	370	38	5	1	365	28981151	28980787	2.350000e-110	409.0
11	TraesCS6D01G040700	chr6B	91.469	211	13	4	2165	2373	29059377	29059170	4.130000e-73	285.0
12	TraesCS6D01G040700	chr1B	85.107	2095	160	70	537	2532	587472429	587474470	0.000000e+00	2001.0
13	TraesCS6D01G040700	chr5D	87.337	845	65	25	723	1553	514924351	514923535	0.000000e+00	929.0
14	TraesCS6D01G040700	chr5D	87.273	55	7	0	1609	1663	514923487	514923433	2.110000e-06	63.9
15	TraesCS6D01G040700	chr5B	86.337	849	77	22	723	1553	647387587	647386760	0.000000e+00	889.0

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	TraesCS6D01G040700	chr6D	16521638	16524174	2536	True	4686.000000	4686	100.000000	1	2537	1	chr6D.!!$R1	2536
1	TraesCS6D01G040700	chr6D	16502654	16503450	796	False	972.000000	972	88.631000	724	1537	1	chr6D.!!$F1	813
2	TraesCS6D01G040700	chr6A	16716276	16721182	4906	True	1592.000000	2760	90.595500	1	2537	2	chr6A.!!$R3	2536
3	TraesCS6D01G040700	chr6A	16593229	16593976	747	True	881.000000	881	88.067000	796	1553	1	chr6A.!!$R1	757
4	TraesCS6D01G040700	chr6A	16658140	16658886	746	True	846.000000	846	87.419000	789	1540	1	chr6A.!!$R2	751
5	TraesCS6D01G040700	chr6B	29059170	29061594	2424	True	1216.500000	2148	88.526000	1	2373	2	chr6B.!!$R2	2372
6	TraesCS6D01G040700	chr6B	28925846	28926597	751	False	985.000000	985	90.339000	796	1553	1	chr6B.!!$F1	757
7	TraesCS6D01G040700	chr6B	28978235	28981151	2916	True	953.333333	1943	89.966333	1	2537	3	chr6B.!!$R1	2536
8	TraesCS6D01G040700	chr1B	587472429	587474470	2041	False	2001.000000	2001	85.107000	537	2532	1	chr1B.!!$F1	1995
9	TraesCS6D01G040700	chr5D	514923433	514924351	918	True	496.450000	929	87.305000	723	1663	2	chr5D.!!$R1	940
10	TraesCS6D01G040700	chr5B	647386760	647387587	827	True	889.000000	889	86.337000	723	1553	1	chr5B.!!$R1	830

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
117	120	0.387202	TCGTTGCCAATTTGTGTGGG	59.613	50.0	0.0	0.0	36.58	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1564	1652	0.039074	CCTGCTATCGACCTAAGCGG	60.039	60.0	11.02	11.02	41.38	5.52	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
112	114	3.119990	CCGTTCTATCGTTGCCAATTTGT	60.120	43.478	0.00	0.00	0.00	2.83
117	120	0.387202	TCGTTGCCAATTTGTGTGGG	59.613	50.000	0.00	0.00	36.58	4.61
167	170	7.100409	TCATCAACATCATGTACCTTTCGTAA	58.900	34.615	0.00	0.00	0.00	3.18
199	202	2.258591	GAGAAGCGGCGACAGACA	59.741	61.111	12.98	0.00	0.00	3.41
267	270	2.366972	ATGGGAGGAGGGGAACGG	60.367	66.667	0.00	0.00	0.00	4.44
340	347	1.259840	GGAGGTTACTGGGTGCCGTA	61.260	60.000	0.00	0.00	0.00	4.02
493	501	5.106869	CGTTCCATTTCGGACAACTATTTCA	60.107	40.000	0.00	0.00	46.36	2.69
500	508	3.435327	TCGGACAACTATTTCATGTGCAC	59.565	43.478	10.75	10.75	35.43	4.57
555	567	3.912496	AATCTAATTTGGGGCCTTTGC	57.088	42.857	0.84	0.00	0.00	3.68
635	657	8.565416	AGTAAATACTACAGCTGAAAAACCAAC	58.435	33.333	23.35	9.94	34.13	3.77
691	721	3.870419	TGATGCACAAAAAGAAAACCAGC	59.130	39.130	0.00	0.00	0.00	4.85
791	825	1.228737	CCAAACCAATCCCCACCGT	60.229	57.895	0.00	0.00	0.00	4.83
1231	1299	0.520404	TACTCTGTTCTCGTCGTGCC	59.480	55.000	0.00	0.00	0.00	5.01
1232	1300	1.797933	CTCTGTTCTCGTCGTGCCG	60.798	63.158	0.00	0.00	0.00	5.69
1559	1647	2.414293	CGCCACCATAGACTACTATCGC	60.414	54.545	0.00	0.00	37.24	4.58
1564	1652	3.497640	ACCATAGACTACTATCGCGACAC	59.502	47.826	12.93	0.00	37.24	3.67
1565	1653	3.120269	CCATAGACTACTATCGCGACACC	60.120	52.174	12.93	0.00	37.24	4.16
1598	1695	1.685355	GCAGGGAGAGGAAGAGGAGC	61.685	65.000	0.00	0.00	0.00	4.70
1614	1711	1.970640	GGAGCTTTGGTTGGTTGGATT	59.029	47.619	0.00	0.00	0.00	3.01
1751	1870	1.745087	CTTGTTTATCCATGGCTGCGT	59.255	47.619	6.96	0.00	0.00	5.24
1808	1927	3.470709	TCAGAGACAGTCAGCTTTTTGG	58.529	45.455	2.66	0.00	0.00	3.28
1839	1960	5.699458	ACATCTTGTACCTTGTCCGTTTAAG	59.301	40.000	0.00	0.00	0.00	1.85
1877	2477	8.200792	ACTAAATTAGATACTCCTGAGTTGCTG	58.799	37.037	7.06	0.00	42.54	4.41
1887	2488	2.945008	CCTGAGTTGCTGTCAGACAAAA	59.055	45.455	4.41	0.00	43.65	2.44
1896	2497	3.054878	CTGTCAGACAAAAATGGCAAGC	58.945	45.455	4.41	0.00	29.16	4.01
1912	2513	3.187022	GGCAAGCCAAATGACAAAATCAC	59.813	43.478	6.14	0.00	36.66	3.06
1918	2523	3.995705	CCAAATGACAAAATCACGGCAAT	59.004	39.130	0.00	0.00	41.24	3.56
1924	2529	2.292016	ACAAAATCACGGCAATCGAACA	59.708	40.909	0.00	0.00	42.43	3.18
1934	2539	3.453424	GGCAATCGAACAAAACTTTGGT	58.547	40.909	7.09	0.00	41.61	3.67
1959	2669	9.937175	GTAAATGAGATACCAGCATTAGTTTTC	57.063	33.333	0.00	0.00	32.39	2.29
1994	2713	5.702670	CAGGTACTTGCTGAGAAATCAAGAA	59.297	40.000	8.03	0.00	39.48	2.52
2070	2796	0.103026	AGTCGATGCTGCGCTTCATA	59.897	50.000	9.73	0.00	33.20	2.15
2071	2797	1.143305	GTCGATGCTGCGCTTCATAT	58.857	50.000	9.73	0.00	33.20	1.78
2072	2798	1.136419	GTCGATGCTGCGCTTCATATG	60.136	52.381	9.73	8.16	33.20	1.78
2073	2799	0.863799	CGATGCTGCGCTTCATATGT	59.136	50.000	9.73	0.00	33.20	2.29
2074	2800	2.061028	CGATGCTGCGCTTCATATGTA	58.939	47.619	9.73	0.00	33.20	2.29
2075	2801	2.669924	CGATGCTGCGCTTCATATGTAT	59.330	45.455	9.73	0.00	33.20	2.29
2121	2867	7.925043	TTCAGAAAACAAAGTTACCACTGTA	57.075	32.000	0.00	0.00	31.60	2.74
2122	2868	8.514330	TTCAGAAAACAAAGTTACCACTGTAT	57.486	30.769	0.00	0.00	31.60	2.29
2230	5178	4.782019	ACTGTAACTCTCTGCTCTCAAG	57.218	45.455	0.00	0.00	0.00	3.02
2343	5295	6.515512	AGGGGACATTAGTTGCTAATATGT	57.484	37.500	1.62	0.00	34.83	2.29
2382	5337	7.088905	TCGTGAATTTTCTTCTAGTAGTGTCC	58.911	38.462	0.00	0.00	0.00	4.02
2422	5377	5.419760	ACTTCATGATGCGATTGAATCAG	57.580	39.130	9.60	2.65	43.51	2.90
2505	5463	6.227522	ACCTGTTTTTGCTTACTTTTGTGTT	58.772	32.000	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
134	137	9.113838	AGGTACATGATGTTGATGAAAGTAATC	57.886	33.333	2.29	0.00	0.00	1.75
167	170	5.799213	CCGCTTCTCCTCCAATATTAGAAT	58.201	41.667	0.00	0.00	0.00	2.40
246	249	4.843331	TCCCCTCCTCCCATGCCC	62.843	72.222	0.00	0.00	0.00	5.36
247	250	2.696125	TTCCCCTCCTCCCATGCC	60.696	66.667	0.00	0.00	0.00	4.40
248	251	2.597903	GTTCCCCTCCTCCCATGC	59.402	66.667	0.00	0.00	0.00	4.06
340	347	1.282157	CCCTTCTTTTCCCCATCGACT	59.718	52.381	0.00	0.00	0.00	4.18
405	412	4.072131	ACATTTTTGAGCTCTTCGGCTTA	58.928	39.130	16.19	0.00	43.20	3.09
493	501	0.689080	TGGTTGTTTGGGGTGCACAT	60.689	50.000	20.43	0.00	0.00	3.21
500	508	2.008242	TCCAATCTGGTTGTTTGGGG	57.992	50.000	0.00	0.00	42.75	4.96
555	567	2.327568	GTTTCGGTTTGGATGCATGTG	58.672	47.619	2.46	0.00	0.00	3.21
622	641	4.503741	TGCATCTAGTTGGTTTTTCAGC	57.496	40.909	3.05	0.00	0.00	4.26
691	721	7.812669	ACGAAGGGATTTTGCTTTAATTAACAG	59.187	33.333	0.00	0.91	0.00	3.16
791	825	0.178876	TTGGATCTGTGGGGAGTGGA	60.179	55.000	0.00	0.00	0.00	4.02
898	933	4.589675	TTGTGGGTTGGGACGCCC	62.590	66.667	7.87	7.87	45.71	6.13
1231	1299	4.498850	CCAGATCAGTCAGTTATCTGTCCG	60.499	50.000	9.88	0.00	43.28	4.79
1232	1300	4.404073	ACCAGATCAGTCAGTTATCTGTCC	59.596	45.833	9.88	0.00	43.28	4.02
1564	1652	0.039074	CCTGCTATCGACCTAAGCGG	60.039	60.000	11.02	11.02	41.38	5.52
1565	1653	0.039074	CCCTGCTATCGACCTAAGCG	60.039	60.000	0.00	0.00	39.14	4.68
1575	1663	2.158385	TCCTCTTCCTCTCCCTGCTATC	60.158	54.545	0.00	0.00	0.00	2.08
1598	1695	5.243730	ACATACAGAATCCAACCAACCAAAG	59.756	40.000	0.00	0.00	0.00	2.77
1614	1711	6.791867	ACAGACTAGGCAATTACATACAGA	57.208	37.500	0.00	0.00	0.00	3.41
1751	1870	4.148128	ACCAAACATGCACAAAATGGAA	57.852	36.364	12.69	0.00	29.34	3.53
1808	1927	7.332678	ACGGACAAGGTACAAGATGTTAATAAC	59.667	37.037	0.00	0.00	0.00	1.89
1839	1960	8.298140	AGTATCTAATTTAGTACTGTCATCGGC	58.702	37.037	5.39	0.00	0.00	5.54
1877	2477	2.224018	TGGCTTGCCATTTTTGTCTGAC	60.224	45.455	10.65	0.00	0.00	3.51
1887	2488	3.488778	TTTGTCATTTGGCTTGCCATT	57.511	38.095	15.58	3.57	0.00	3.16
1896	2497	3.023946	TGCCGTGATTTTGTCATTTGG	57.976	42.857	0.00	0.00	39.48	3.28
1912	2513	2.470999	CCAAAGTTTTGTTCGATTGCCG	59.529	45.455	4.12	0.00	36.45	5.69
1918	2523	7.323049	TCTCATTTACCAAAGTTTTGTTCGA	57.677	32.000	0.00	0.00	36.45	3.71
1924	2529	7.232534	TGCTGGTATCTCATTTACCAAAGTTTT	59.767	33.333	4.31	0.00	46.35	2.43
1934	2539	8.826710	CGAAAACTAATGCTGGTATCTCATTTA	58.173	33.333	0.62	0.00	33.13	1.40
1959	2669	1.531149	CAAGTACCTGTTTCACAGCCG	59.469	52.381	0.00	0.00	44.63	5.52
1979	2698	4.759183	ACAGGAGTTTCTTGATTTCTCAGC	59.241	41.667	0.00	0.00	31.68	4.26
1994	2713	5.221722	TGACAAGCATTCTTCTACAGGAGTT	60.222	40.000	0.00	0.00	0.00	3.01
2041	2764	4.206843	CGCAGCATCGACTTGATTATTTC	58.793	43.478	0.00	0.00	34.13	2.17
2121	2867	9.220767	GTGAAACCTCTGACTGTTATTTTCTAT	57.779	33.333	0.00	0.00	0.00	1.98
2122	2868	8.208224	TGTGAAACCTCTGACTGTTATTTTCTA	58.792	33.333	0.00	0.00	34.36	2.10
2230	5178	8.176365	GCTGTATTCTGATGATAGCATTTGATC	58.824	37.037	0.00	0.00	34.11	2.92
2382	5337	9.961265	TCATGAAGTACCAAGTTCTATATTACG	57.039	33.333	0.00	0.00	36.23	3.18
2422	5377	7.196331	GCAAACAAGAATATGAGAATACACCC	58.804	38.462	0.00	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.