AutoCloner

Multiple sequence alignment - TraesCS5B01G036200

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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	TraesCS5B01G036200	chr5B	100.000	3056	0	0	1	3056	39743140	39740085	0.000000e+00	5644.0
1	TraesCS5B01G036200	chr5B	96.707	2126	66	4	1	2124	39545364	39543241	0.000000e+00	3535.0
2	TraesCS5B01G036200	chr5B	96.439	674	22	2	2359	3030	39543242	39542569	0.000000e+00	1110.0
3	TraesCS5B01G036200	chr5B	94.374	711	34	3	2344	3052	713054565	713053859	0.000000e+00	1086.0
4	TraesCS5B01G036200	chr7D	94.545	715	33	3	2344	3056	382021038	382020328	0.000000e+00	1099.0
5	TraesCS5B01G036200	chr7D	86.072	718	62	18	1	692	630113388	630112683	0.000000e+00	737.0
6	TraesCS5B01G036200	chr7D	85.106	282	27	5	427	696	630180543	630180821	1.080000e-69	274.0
7	TraesCS5B01G036200	chr7D	72.214	673	155	25	1388	2044	629450433	629449777	8.710000e-41	178.0
8	TraesCS5B01G036200	chr4D	94.406	715	34	3	2344	3056	123359278	123359988	0.000000e+00	1094.0
9	TraesCS5B01G036200	chr4D	86.790	704	63	16	1	691	428622025	428621339	0.000000e+00	758.0
10	TraesCS5B01G036200	chr4D	100.000	50	0	0	2280	2329	123570188	123570237	3.240000e-15	93.5
11	TraesCS5B01G036200	chr3D	94.266	715	35	3	2344	3056	202603583	202604293	0.000000e+00	1088.0
12	TraesCS5B01G036200	chr3D	100.000	50	0	0	2280	2329	202603551	202603600	3.240000e-15	93.5
13	TraesCS5B01G036200	chr2D	94.266	715	35	3	2344	3056	635027169	635027879	0.000000e+00	1088.0
14	TraesCS5B01G036200	chr2D	87.482	703	56	8	1	691	81395201	81394519	0.000000e+00	782.0
15	TraesCS5B01G036200	chr2D	86.490	718	59	17	1	692	573364271	573363566	0.000000e+00	754.0
16	TraesCS5B01G036200	chr2D	85.714	280	25	5	427	694	573453103	573453379	6.450000e-72	281.0
17	TraesCS5B01G036200	chr1B	94.374	711	34	3	2344	3052	461443911	461444617	0.000000e+00	1086.0
18	TraesCS5B01G036200	chr1B	100.000	50	0	0	2280	2329	338920054	338920103	3.240000e-15	93.5
19	TraesCS5B01G036200	chr1B	100.000	50	0	0	2280	2329	338995232	338995281	3.240000e-15	93.5
20	TraesCS5B01G036200	chr1B	100.000	50	0	0	2280	2329	461443879	461443928	3.240000e-15	93.5
21	TraesCS5B01G036200	chr1B	100.000	50	0	0	2280	2329	583509145	583509096	3.240000e-15	93.5
22	TraesCS5B01G036200	chr7A	94.233	711	35	3	2344	3052	120934201	120933495	0.000000e+00	1081.0
23	TraesCS5B01G036200	chr7A	74.003	727	128	49	1	692	689937102	689936402	3.940000e-59	239.0
24	TraesCS5B01G036200	chr5A	94.233	711	35	3	2344	3052	300040228	300040934	0.000000e+00	1081.0
25	TraesCS5B01G036200	chr5D	87.764	711	50	15	1	688	391329073	391329769	0.000000e+00	797.0
26	TraesCS5B01G036200	chr5D	84.874	714	60	23	1	691	356118808	356119496	0.000000e+00	676.0
27	TraesCS5B01G036200	chr5D	83.520	716	46	23	1	691	305761519	305762187	1.210000e-168	603.0
28	TraesCS5B01G036200	chr5D	74.740	673	154	12	1377	2044	524250253	524250914	1.390000e-73	287.0
29	TraesCS5B01G036200	chr5D	84.249	273	30	6	427	691	305736455	305736188	1.410000e-63	254.0
30	TraesCS5B01G036200	chr4B	86.932	704	47	15	1	691	187439803	187439132	0.000000e+00	749.0
31	TraesCS5B01G036200	chr4B	87.451	255	19	5	437	679	187462130	187462383	6.450000e-72	281.0
32	TraesCS5B01G036200	chr4B	90.000	170	16	1	523	691	526746588	526746419	5.130000e-53	219.0
33	TraesCS5B01G036200	chr4B	100.000	50	0	0	2280	2329	209157973	209157924	3.240000e-15	93.5
34	TraesCS5B01G036200	chr3A	85.486	689	54	27	1	671	22037514	22038174	0.000000e+00	676.0
35	TraesCS5B01G036200	chr4A	84.658	717	61	36	1	691	616787997	616788690	0.000000e+00	669.0
36	TraesCS5B01G036200	chrUn	100.000	50	0	0	2280	2329	390053597	390053646	3.240000e-15	93.5
37	TraesCS5B01G036200	chr6D	100.000	50	0	0	2280	2329	83963243	83963194	3.240000e-15	93.5

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	TraesCS5B01G036200	chr5B	39740085	39743140	3055	True	5644.00	5644	100.000	1	3056	1	chr5B.!!$R1	3055
1	TraesCS5B01G036200	chr5B	39542569	39545364	2795	True	2322.50	3535	96.573	1	3030	2	chr5B.!!$R3	3029
2	TraesCS5B01G036200	chr5B	713053859	713054565	706	True	1086.00	1086	94.374	2344	3052	1	chr5B.!!$R2	708
3	TraesCS5B01G036200	chr7D	382020328	382021038	710	True	1099.00	1099	94.545	2344	3056	1	chr7D.!!$R1	712
4	TraesCS5B01G036200	chr7D	630112683	630113388	705	True	737.00	737	86.072	1	692	1	chr7D.!!$R3	691
5	TraesCS5B01G036200	chr4D	123359278	123359988	710	False	1094.00	1094	94.406	2344	3056	1	chr4D.!!$F1	712
6	TraesCS5B01G036200	chr4D	428621339	428622025	686	True	758.00	758	86.790	1	691	1	chr4D.!!$R1	690
7	TraesCS5B01G036200	chr3D	202603551	202604293	742	False	590.75	1088	97.133	2280	3056	2	chr3D.!!$F1	776
8	TraesCS5B01G036200	chr2D	635027169	635027879	710	False	1088.00	1088	94.266	2344	3056	1	chr2D.!!$F2	712
9	TraesCS5B01G036200	chr2D	81394519	81395201	682	True	782.00	782	87.482	1	691	1	chr2D.!!$R1	690
10	TraesCS5B01G036200	chr2D	573363566	573364271	705	True	754.00	754	86.490	1	692	1	chr2D.!!$R2	691
11	TraesCS5B01G036200	chr1B	461443879	461444617	738	False	589.75	1086	97.187	2280	3052	2	chr1B.!!$F3	772
12	TraesCS5B01G036200	chr7A	120933495	120934201	706	True	1081.00	1081	94.233	2344	3052	1	chr7A.!!$R1	708
13	TraesCS5B01G036200	chr7A	689936402	689937102	700	True	239.00	239	74.003	1	692	1	chr7A.!!$R2	691
14	TraesCS5B01G036200	chr5A	300040228	300040934	706	False	1081.00	1081	94.233	2344	3052	1	chr5A.!!$F1	708
15	TraesCS5B01G036200	chr5D	391329073	391329769	696	False	797.00	797	87.764	1	688	1	chr5D.!!$F3	687
16	TraesCS5B01G036200	chr5D	356118808	356119496	688	False	676.00	676	84.874	1	691	1	chr5D.!!$F2	690
17	TraesCS5B01G036200	chr5D	305761519	305762187	668	False	603.00	603	83.520	1	691	1	chr5D.!!$F1	690
18	TraesCS5B01G036200	chr5D	524250253	524250914	661	False	287.00	287	74.740	1377	2044	1	chr5D.!!$F4	667
19	TraesCS5B01G036200	chr4B	187439132	187439803	671	True	749.00	749	86.932	1	691	1	chr4B.!!$R1	690
20	TraesCS5B01G036200	chr3A	22037514	22038174	660	False	676.00	676	85.486	1	671	1	chr3A.!!$F1	670
21	TraesCS5B01G036200	chr4A	616787997	616788690	693	False	669.00	669	84.658	1	691	1	chr4A.!!$F1	690

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
768	858	1.453928	GGGTTGGCATGCCCTAGAC	60.454	63.158	33.44	23.74	41.63	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2139	2229	0.174389	TTAAGAGAGCGAGCAGGCAG	59.826	55.0	0.0	0.0	34.64	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
258	272	4.175489	CCATCTGCACGCTGCTGC	62.175	66.667	14.42	14.42	45.31	5.25
385	423	3.626930	ACAGAGGAAGAAGATAGCGAGT	58.373	45.455	0.00	0.00	0.00	4.18
400	438	1.608717	CGAGTTGGGGAGAGGAGTGG	61.609	65.000	0.00	0.00	0.00	4.00
511	585	2.507769	GCGCCGTTAGCCGTTAGT	60.508	61.111	0.00	0.00	38.78	2.24
549	635	3.057526	GCCATGTCAGGAAAGTGGTTAAC	60.058	47.826	0.00	0.00	32.56	2.01
655	742	2.803956	AGTGATAGTTCTGTGGGACGA	58.196	47.619	0.00	0.00	0.00	4.20
740	829	2.432628	GATATTCGGCCGGGAGCG	60.433	66.667	27.83	0.00	45.17	5.03
768	858	1.453928	GGGTTGGCATGCCCTAGAC	60.454	63.158	33.44	23.74	41.63	2.59
777	867	3.181450	GGCATGCCCTAGACTTGATACTT	60.181	47.826	27.24	0.00	0.00	2.24
778	868	4.455606	GCATGCCCTAGACTTGATACTTT	58.544	43.478	6.36	0.00	0.00	2.66
779	869	5.454755	GGCATGCCCTAGACTTGATACTTTA	60.455	44.000	27.24	0.00	0.00	1.85
916	1006	4.859304	TCTGATGTACCGTACAACAAGT	57.141	40.909	18.83	2.84	40.27	3.16
926	1016	9.787532	TGTACCGTACAACAAGTCTATAAATAC	57.212	33.333	8.99	0.00	35.38	1.89
934	1024	9.886132	ACAACAAGTCTATAAATACACCCTTAG	57.114	33.333	0.00	0.00	0.00	2.18
1005	1095	3.573967	AGCCCAATAATTAGGAAATGGCG	59.426	43.478	0.00	0.00	35.39	5.69
1051	1141	2.693762	TTGCAGCTCTCATTGGCGC	61.694	57.895	0.00	0.00	0.00	6.53
1079	1169	0.445436	CCAATGACACTCAAGAGCGC	59.555	55.000	0.00	0.00	0.00	5.92
1137	1227	2.892425	GGGAAGATGCTGTCGCCG	60.892	66.667	0.00	0.00	34.43	6.46
1342	1432	3.917760	CTTCCCTAGGCCCGCTCG	61.918	72.222	2.05	0.00	0.00	5.03
1490	1580	3.665848	CGATTCAACGGCGTGTTTAATGT	60.666	43.478	15.70	0.00	39.29	2.71
1693	1783	0.040067	CCAAGCGCCTTCTTTCACAC	60.040	55.000	2.29	0.00	0.00	3.82
1906	1996	1.260206	CGAGGTGAAGACGATGTTCG	58.740	55.000	0.00	0.00	46.93	3.95
2085	2175	0.110010	GTGCTTTCGAGCTTCCTTGC	60.110	55.000	0.00	0.00	35.49	4.01
2102	2192	3.061429	CCTTGCTTTCTCTCGATCGTTTC	59.939	47.826	15.94	0.00	0.00	2.78
2122	2212	2.942376	TCAGCGTGTGTCATGTCTTTTT	59.058	40.909	0.00	0.00	0.00	1.94

Showing 1 to 25 of 109 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	2.026262	GGGCTTCTGGTTGAACCTGATA	60.026	50.000	22.04	13.06	44.15	2.15
258	272	1.467342	TGACGAGTACATGGACGAGTG	59.533	52.381	14.73	3.72	0.00	3.51
385	423	1.538876	CACCCACTCCTCTCCCCAA	60.539	63.158	0.00	0.00	0.00	4.12
400	438	1.470890	CTCACTCCTCTTCGTCTCACC	59.529	57.143	0.00	0.00	0.00	4.02
466	540	1.672854	CGGATGTTAGTGCCTCGGGA	61.673	60.000	0.00	0.00	0.00	5.14
542	628	4.022416	TCGTCGTTTTAGCTAGGTTAACCA	60.022	41.667	26.26	11.41	38.89	3.67
549	635	4.031426	GTGTTGATCGTCGTTTTAGCTAGG	59.969	45.833	0.00	0.00	0.00	3.02
768	858	9.239002	CGGTTCTCTTACAGATAAAGTATCAAG	57.761	37.037	0.00	0.00	37.65	3.02
777	867	6.318144	CCACTCTACGGTTCTCTTACAGATAA	59.682	42.308	0.00	0.00	0.00	1.75
778	868	5.821470	CCACTCTACGGTTCTCTTACAGATA	59.179	44.000	0.00	0.00	0.00	1.98
779	869	4.641094	CCACTCTACGGTTCTCTTACAGAT	59.359	45.833	0.00	0.00	0.00	2.90
789	879	3.881937	ATTGGTACCACTCTACGGTTC	57.118	47.619	16.04	0.00	37.99	3.62
796	886	4.715297	AGGATAACGAATTGGTACCACTCT	59.285	41.667	16.04	1.01	0.00	3.24
797	887	5.019785	AGGATAACGAATTGGTACCACTC	57.980	43.478	16.04	13.35	0.00	3.51
916	1006	7.070696	TCTGCTTGCTAAGGGTGTATTTATAGA	59.929	37.037	0.00	0.00	0.00	1.98
926	1016	1.446907	CAGTCTGCTTGCTAAGGGTG	58.553	55.000	0.00	0.00	0.00	4.61
1005	1095	3.003763	AAGGCCTCCCTGTCGTCC	61.004	66.667	5.23	0.00	41.90	4.79
1051	1141	2.205074	GAGTGTCATTGGCACGATAGG	58.795	52.381	15.25	0.00	41.36	2.57
1210	1300	0.731514	ACGATGTTGTACGACGCCAG	60.732	55.000	8.73	3.08	0.00	4.85
1251	1341	3.741476	GCAAGCAGGCCGTCCTTG	61.741	66.667	21.39	21.39	41.93	3.61
1342	1432	2.417515	GGATCTTGTCGTTCAGGAGGAC	60.418	54.545	0.00	0.00	42.17	3.85
1467	1557	0.164217	TAAACACGCCGTTGAATCGC	59.836	50.000	0.00	0.00	38.07	4.58
1693	1783	4.806481	GCTCACATGCTGCACGCG	62.806	66.667	3.57	3.53	43.27	6.01
1773	1863	2.338620	CAGTGCTCGTCGGTCCAA	59.661	61.111	0.00	0.00	0.00	3.53
1869	1959	2.686816	GGGCGTGTCATCCGGTTTG	61.687	63.158	0.00	0.36	0.00	2.93

Showing 1 to 25 of 120 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.