AutoCloner

Multiple sequence alignment - TraesCS6B01G212800

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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	TraesCS6B01G212800	chr6B	100.000	2357	0	0	1	2357	281828590	281826234	0.000000e+00	4353
1	TraesCS6B01G212800	chr6B	94.279	2377	91	8	1	2357	460300398	460298047	0.000000e+00	3594
2	TraesCS6B01G212800	chr6B	84.591	1285	129	28	2	1260	327557454	327558695	0.000000e+00	1212
3	TraesCS6B01G212800	chr6B	82.005	1117	119	45	1290	2357	327558695	327559778	0.000000e+00	874
4	TraesCS6B01G212800	chr3B	94.579	1605	63	6	1	1603	257549135	257547553	0.000000e+00	2460
5	TraesCS6B01G212800	chr3B	92.692	780	29	6	1598	2357	257538475	257537704	0.000000e+00	1099
6	TraesCS6B01G212800	chr6A	88.862	2065	139	22	1	2021	39927646	39925629	0.000000e+00	2455
7	TraesCS6B01G212800	chr6A	91.781	146	6	4	2216	2357	39925404	39925261	5.140000e-47	198
8	TraesCS6B01G212800	chr6A	96.296	81	3	0	2032	2112	39925502	39925422	1.470000e-27	134
9	TraesCS6B01G212800	chr7D	95.099	1510	42	10	1	1506	213609593	213608112	0.000000e+00	2350
10	TraesCS6B01G212800	chr7D	92.479	851	31	15	1532	2357	213608112	213607270	0.000000e+00	1186
11	TraesCS6B01G212800	chr7D	80.135	443	61	21	1729	2147	155888156	155887717	2.940000e-79	305
12	TraesCS6B01G212800	chr4D	87.800	1836	127	31	571	2357	239764364	239766151	0.000000e+00	2060
13	TraesCS6B01G212800	chr4D	89.087	504	46	3	1	498	239763861	239764361	3.330000e-173	617
14	TraesCS6B01G212800	chr4D	88.859	368	23	8	2000	2357	58930453	58930094	1.000000e-118	436
15	TraesCS6B01G212800	chr4D	93.200	250	16	1	1752	2000	58935845	58935596	1.330000e-97	366
16	TraesCS6B01G212800	chr4B	81.286	2426	260	69	2	2357	300483880	300481579	0.000000e+00	1786
17	TraesCS6B01G212800	chr4A	87.811	1206	99	23	1149	2322	228657844	228659033	0.000000e+00	1369
18	TraesCS6B01G212800	chr4A	90.364	934	75	5	38	959	228656700	228657630	0.000000e+00	1212
19	TraesCS6B01G212800	chr4A	84.024	820	95	22	2	803	334265549	334266350	0.000000e+00	756
20	TraesCS6B01G212800	chr4A	80.089	1125	117	51	1290	2357	334267608	334268682	0.000000e+00	737
21	TraesCS6B01G212800	chr4A	82.974	464	44	11	800	1260	334267177	334267608	1.020000e-103	387
22	TraesCS6B01G212800	chr4A	98.276	58	0	1	2301	2357	228659065	228659122	1.490000e-17	100
23	TraesCS6B01G212800	chr3D	80.370	433	58	21	1730	2138	225685033	225685462	1.060000e-78	303
24	TraesCS6B01G212800	chr2D	76.370	584	95	27	885	1461	413281315	413280768	8.300000e-70	274
25	TraesCS6B01G212800	chr7B	81.073	354	49	12	1119	1461	192740067	192740413	1.390000e-67	267
26	TraesCS6B01G212800	chr5B	89.844	128	13	0	457	584	330122381	330122508	5.210000e-37	165
27	TraesCS6B01G212800	chr5B	89.062	128	14	0	457	584	330431937	330432064	2.420000e-35	159

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	TraesCS6B01G212800	chr6B	281826234	281828590	2356	True	4353.000000	4353	100.000000	1	2357	1	chr6B.!!$R1	2356
1	TraesCS6B01G212800	chr6B	460298047	460300398	2351	True	3594.000000	3594	94.279000	1	2357	1	chr6B.!!$R2	2356
2	TraesCS6B01G212800	chr6B	327557454	327559778	2324	False	1043.000000	1212	83.298000	2	2357	2	chr6B.!!$F1	2355
3	TraesCS6B01G212800	chr3B	257547553	257549135	1582	True	2460.000000	2460	94.579000	1	1603	1	chr3B.!!$R2	1602
4	TraesCS6B01G212800	chr3B	257537704	257538475	771	True	1099.000000	1099	92.692000	1598	2357	1	chr3B.!!$R1	759
5	TraesCS6B01G212800	chr6A	39925261	39927646	2385	True	929.000000	2455	92.313000	1	2357	3	chr6A.!!$R1	2356
6	TraesCS6B01G212800	chr7D	213607270	213609593	2323	True	1768.000000	2350	93.789000	1	2357	2	chr7D.!!$R2	2356
7	TraesCS6B01G212800	chr4D	239763861	239766151	2290	False	1338.500000	2060	88.443500	1	2357	2	chr4D.!!$F1	2356
8	TraesCS6B01G212800	chr4B	300481579	300483880	2301	True	1786.000000	1786	81.286000	2	2357	1	chr4B.!!$R1	2355
9	TraesCS6B01G212800	chr4A	228656700	228659122	2422	False	893.666667	1369	92.150333	38	2357	3	chr4A.!!$F1	2319
10	TraesCS6B01G212800	chr4A	334265549	334268682	3133	False	626.666667	756	82.362333	2	2357	3	chr4A.!!$F2	2355
11	TraesCS6B01G212800	chr2D	413280768	413281315	547	True	274.000000	274	76.370000	885	1461	1	chr2D.!!$R1	576

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
934	1808	4.652822	AGGGGAGAGTTTAATTGACACAC	58.347	43.478	0.0	0.0	0.0	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2106	3365	1.39944	CCAATCAGATGTGGCTGTTCG	59.601	52.381	0.0	0.0	37.2	3.95	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
350	367	9.182214	AGTGCTCATATGTCTTGATAAAATTGT	57.818	29.630	1.90	0.0	0.00	2.71
382	401	8.651391	TCATGGACATTATTTTCAATTGATGC	57.349	30.769	9.40	0.0	0.00	3.91
427	449	7.060383	AGAGATTTCCAGGTGTAGTGATATG	57.940	40.000	0.00	0.0	0.00	1.78
494	525	9.578439	CAGGTAATTTCCTTTGATTCTTTCATC	57.422	33.333	0.00	0.0	35.37	2.92
521	561	7.446013	TCCCTAAATTTCACTTACAACATCGTT	59.554	33.333	0.00	0.0	0.00	3.85
934	1808	4.652822	AGGGGAGAGTTTAATTGACACAC	58.347	43.478	0.00	0.0	0.00	3.82
1040	2001	4.212004	ACGTCAAGTTGATGAACATGTCAG	59.788	41.667	27.85	4.1	40.43	3.51
1054	2015	8.620116	TGAACATGTCAGTAAGATCATTGAAA	57.380	30.769	0.00	0.0	0.00	2.69
1095	2057	2.310779	TAGTGTGTCCCTTGCTCTCT	57.689	50.000	0.00	0.0	0.00	3.10
1096	2058	0.972883	AGTGTGTCCCTTGCTCTCTC	59.027	55.000	0.00	0.0	0.00	3.20
1097	2059	0.972883	GTGTGTCCCTTGCTCTCTCT	59.027	55.000	0.00	0.0	0.00	3.10
1098	2060	1.067213	GTGTGTCCCTTGCTCTCTCTC	60.067	57.143	0.00	0.0	0.00	3.20
1099	2061	1.203112	TGTGTCCCTTGCTCTCTCTCT	60.203	52.381	0.00	0.0	0.00	3.10
1100	2062	1.476488	GTGTCCCTTGCTCTCTCTCTC	59.524	57.143	0.00	0.0	0.00	3.20
1101	2063	1.357420	TGTCCCTTGCTCTCTCTCTCT	59.643	52.381	0.00	0.0	0.00	3.10
1102	2064	2.024414	GTCCCTTGCTCTCTCTCTCTC	58.976	57.143	0.00	0.0	0.00	3.20
1103	2065	1.922447	TCCCTTGCTCTCTCTCTCTCT	59.078	52.381	0.00	0.0	0.00	3.10
1104	2066	2.092429	TCCCTTGCTCTCTCTCTCTCTC	60.092	54.545	0.00	0.0	0.00	3.20
1105	2067	2.092212	CCCTTGCTCTCTCTCTCTCTCT	60.092	54.545	0.00	0.0	0.00	3.10
1106	2068	3.209410	CCTTGCTCTCTCTCTCTCTCTC	58.791	54.545	0.00	0.0	0.00	3.20
1107	2069	3.118112	CCTTGCTCTCTCTCTCTCTCTCT	60.118	52.174	0.00	0.0	0.00	3.10
1108	2070	3.827008	TGCTCTCTCTCTCTCTCTCTC	57.173	52.381	0.00	0.0	0.00	3.20
1109	2071	3.378512	TGCTCTCTCTCTCTCTCTCTCT	58.621	50.000	0.00	0.0	0.00	3.10
1110	2072	3.386078	TGCTCTCTCTCTCTCTCTCTCTC	59.614	52.174	0.00	0.0	0.00	3.20
1156	2141	0.660005	GATTGTGCTTGCGCGTTTCA	60.660	50.000	8.43	0.0	39.65	2.69
1190	2176	7.550906	GCAGTTTCTCTCAGGAAGTTACAATAT	59.449	37.037	0.00	0.0	0.00	1.28
1395	2395	5.004922	TGGAACATGAAAGTTGTTTGACC	57.995	39.130	0.00	0.0	37.43	4.02
1652	2735	8.997621	ATTAGATAGTTCGTAGTTTTCTTGCA	57.002	30.769	0.00	0.0	0.00	4.08
1653	2736	6.707599	AGATAGTTCGTAGTTTTCTTGCAC	57.292	37.500	0.00	0.0	0.00	4.57
1654	2737	6.456501	AGATAGTTCGTAGTTTTCTTGCACT	58.543	36.000	0.00	0.0	0.00	4.40
1655	2738	6.586844	AGATAGTTCGTAGTTTTCTTGCACTC	59.413	38.462	0.00	0.0	0.00	3.51
1656	2739	3.808174	AGTTCGTAGTTTTCTTGCACTCC	59.192	43.478	0.00	0.0	0.00	3.85
1657	2740	2.762745	TCGTAGTTTTCTTGCACTCCC	58.237	47.619	0.00	0.0	0.00	4.30
1658	2741	1.804748	CGTAGTTTTCTTGCACTCCCC	59.195	52.381	0.00	0.0	0.00	4.81
1659	2742	2.160205	GTAGTTTTCTTGCACTCCCCC	58.840	52.381	0.00	0.0	0.00	5.40
1724	2830	2.372264	CTGTCCCAAATCTGGTGATGG	58.628	52.381	0.00	0.0	41.72	3.51
1726	2832	2.109834	TGTCCCAAATCTGGTGATGGTT	59.890	45.455	0.00	0.0	41.72	3.67
2235	3501	3.367395	GCCCTCAGTTTACAAAGAATGGC	60.367	47.826	0.00	0.0	0.00	4.40
2283	3559	9.489084	TTTGTACTCCATATAACATAGTGATGC	57.511	33.333	0.00	0.0	36.43	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
372	391	2.703416	AGCAAGACTCGCATCAATTGA	58.297	42.857	11.26	11.26	0.00	2.57
411	433	5.508153	GCAGTACTCATATCACTACACCTGG	60.508	48.000	0.00	0.00	0.00	4.45
427	449	2.667470	TCCCCTCATGTAGCAGTACTC	58.333	52.381	0.00	0.00	0.00	2.59
494	525	7.119262	ACGATGTTGTAAGTGAAATTTAGGGAG	59.881	37.037	0.00	0.00	0.00	4.30
574	614	4.396166	GTCATGCTAACCAGTGCTAACAAT	59.604	41.667	0.00	0.00	0.00	2.71
819	1692	9.563898	GGAAAATACCGTGGTTTCTAAAAATAG	57.436	33.333	0.00	0.00	32.89	1.73
1065	2027	4.980573	AGGGACACACTAAGCAAAATACA	58.019	39.130	0.00	0.00	0.00	2.29
1095	2057	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1096	2058	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1097	2059	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1098	2060	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1099	2061	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1100	2062	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1101	2063	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1102	2064	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1103	2065	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1104	2066	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1105	2067	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1106	2068	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1107	2069	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1108	2070	5.009911	CAGAGAGAGAGAGAGAGAGAGAGAG	59.990	52.000	0.00	0.00	0.00	3.20
1109	2071	4.892345	CAGAGAGAGAGAGAGAGAGAGAGA	59.108	50.000	0.00	0.00	0.00	3.10
1110	2072	4.892345	TCAGAGAGAGAGAGAGAGAGAGAG	59.108	50.000	0.00	0.00	0.00	3.20
1156	2141	4.008330	CCTGAGAGAAACTGCATGTCATT	58.992	43.478	0.00	0.00	0.00	2.57
1420	2420	5.470098	GTCTTAAACTCTGGCTGTTTCATGA	59.530	40.000	0.00	0.00	38.41	3.07
1656	2739	0.551624	TAAGAAACAGGGGGAGGGGG	60.552	60.000	0.00	0.00	0.00	5.40
1657	2740	0.919710	CTAAGAAACAGGGGGAGGGG	59.080	60.000	0.00	0.00	0.00	4.79
1658	2741	1.670059	ACTAAGAAACAGGGGGAGGG	58.330	55.000	0.00	0.00	0.00	4.30
1659	2742	2.642807	TGAACTAAGAAACAGGGGGAGG	59.357	50.000	0.00	0.00	0.00	4.30
1660	2743	4.576330	ATGAACTAAGAAACAGGGGGAG	57.424	45.455	0.00	0.00	0.00	4.30
1661	2744	6.423182	CATAATGAACTAAGAAACAGGGGGA	58.577	40.000	0.00	0.00	0.00	4.81
2106	3365	1.399440	CCAATCAGATGTGGCTGTTCG	59.601	52.381	0.00	0.00	37.20	3.95
2163	3427	6.698766	CACATGTTCTGAATATCGATGTCTCA	59.301	38.462	8.54	6.93	0.00	3.27
2167	3431	5.118286	TGCACATGTTCTGAATATCGATGT	58.882	37.500	8.54	0.00	0.00	3.06
2270	3546	3.699038	GCAAAAGGGGCATCACTATGTTA	59.301	43.478	0.00	0.00	35.38	2.41
2271	3547	2.497273	GCAAAAGGGGCATCACTATGTT	59.503	45.455	0.00	0.00	35.38	2.71
2272	3548	2.102578	GCAAAAGGGGCATCACTATGT	58.897	47.619	0.00	0.00	35.38	2.29
2283	3559	2.038387	ATACACGCTAGCAAAAGGGG	57.962	50.000	16.45	0.86	33.91	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.