AutoCloner

Multiple sequence alignment - TraesCS1D01G055100

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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	TraesCS1D01G055100	chr1D	100.000	5486	0	0	667	6152	36533210	36538695	0.000000e+00	10131.0
1	TraesCS1D01G055100	chr1D	100.000	361	0	0	1	361	36532544	36532904	0.000000e+00	667.0
2	TraesCS1D01G055100	chr1D	96.296	135	2	1	4890	5024	36537370	36537501	1.040000e-52	219.0
3	TraesCS1D01G055100	chr1D	96.296	135	2	1	4827	4958	36537433	36537567	1.040000e-52	219.0
4	TraesCS1D01G055100	chr1A	97.333	5474	104	18	708	6152	35931662	35937122	0.000000e+00	9262.0
5	TraesCS1D01G055100	chr1A	94.949	297	5	7	66	361	35931142	35931429	2.020000e-124	457.0
6	TraesCS1D01G055100	chr1A	96.377	138	2	1	4890	5024	35935796	35935933	2.230000e-54	224.0
7	TraesCS1D01G055100	chr1A	92.254	142	4	3	4827	4961	35935862	35936003	1.750000e-45	195.0
8	TraesCS1D01G055100	chr1A	100.000	72	0	0	4953	5024	35935796	35935867	3.870000e-27	134.0
9	TraesCS1D01G055100	chr1A	91.892	74	6	0	3404	3477	35934409	35934482	3.030000e-18	104.0
10	TraesCS1D01G055100	chr1B	96.114	4375	95	29	667	5024	56310322	56314638	0.000000e+00	7068.0
11	TraesCS1D01G055100	chr1B	97.234	687	18	1	4827	5513	56314507	56315192	0.000000e+00	1162.0
12	TraesCS1D01G055100	chr1B	92.492	333	11	9	5823	6152	56315341	56315662	1.210000e-126	464.0
13	TraesCS1D01G055100	chr1B	90.332	331	24	6	11	336	56309556	56309883	1.580000e-115	427.0
14	TraesCS1D01G055100	chr1B	94.853	136	4	1	4889	5024	56314443	56314575	6.250000e-50	209.0
15	TraesCS1D01G055100	chr1B	92.806	139	6	2	4827	4961	56314570	56314708	1.350000e-46	198.0
16	TraesCS1D01G055100	chr1B	93.333	135	7	2	5703	5837	56315186	56315318	1.350000e-46	198.0
17	TraesCS1D01G055100	chr1B	94.521	73	1	1	4952	5024	56314443	56314512	6.520000e-20	110.0
18	TraesCS1D01G055100	chr1B	90.625	64	6	0	3414	3477	56313085	56313148	1.100000e-12	86.1
19	TraesCS1D01G055100	chr2D	92.904	606	19	4	5212	5817	90783997	90783416	0.000000e+00	859.0
20	TraesCS1D01G055100	chr2D	93.243	296	12	7	5860	6152	90783425	90783135	4.410000e-116	429.0
21	TraesCS1D01G055100	chr7B	94.949	198	5	3	4460	4656	159181692	159181885	7.750000e-79	305.0
22	TraesCS1D01G055100	chr7B	99.020	102	1	0	4319	4420	159181591	159181692	3.790000e-42	183.0
23	TraesCS1D01G055100	chr5B	89.000	100	11	0	1013	1112	465051171	465051072	2.330000e-24	124.0

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	TraesCS1D01G055100	chr1D	36532544	36538695	6151	False	2809.000000	10131	98.1480	1	6152	4	chr1D.!!$F1	6151
1	TraesCS1D01G055100	chr1A	35931142	35937122	5980	False	1729.333333	9262	95.4675	66	6152	6	chr1A.!!$F1	6086
2	TraesCS1D01G055100	chr1B	56309556	56315662	6106	False	1102.455556	7068	93.5900	11	6152	9	chr1B.!!$F1	6141
3	TraesCS1D01G055100	chr2D	90783135	90783997	862	True	644.000000	859	93.0735	5212	6152	2	chr2D.!!$R1	940

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	Hairpin	End Stability	Orientation
975	1270	0.032615	TTGCTGAGGGTTGGTTTGGT	60.033	50.000	0.00	0.00	3.67	F
977	1272	0.389025	GCTGAGGGTTGGTTTGGTTG	59.611	55.000	0.00	0.00	3.77	F
2229	2530	1.019673	CAGCATCATTTGACCCTCCG	58.980	55.000	0.00	0.00	4.63	F
3479	3780	1.486726	GGTTACTCCAGTGGCAGCTAT	59.513	52.381	3.51	35.97	2.97	F
4728	5029	1.556911	TCAGGAGAAGACAAGGATGGC	59.443	52.381	0.00	33.34	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2044	2345	0.819666	GACCGGATCCTGGGCAAATC	60.820	60.000	19.87	8.41	33.37	2.17	R
2488	2789	2.233431	CCTGTGATATCCTGCCTCTAGC	59.767	54.545	0.00	0.00	44.14	3.42	R
3639	3940	2.653115	CTCTGTGCGGTCTGCTCA	59.347	61.111	5.01	6.72	46.63	4.26	R
4822	5123	0.543277	TCTGGCCTTGCATCAGTAGG	59.457	55.000	3.32	0.00	0.00	3.18	R
5595	5962	2.310779	ACTCCTAGGTCACAGCTTGA	57.689	50.000	9.08	0.00	0.00	3.02	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
125	127	4.159857	CGAAGAGAGTGAAGTTAACCTCG	58.840	47.826	0.88	0.00	0.00	4.63
166	168	2.548295	TTCCCGCGCAAAACCAGAC	61.548	57.895	8.75	0.00	0.00	3.51
170	172	2.597510	GCGCAAAACCAGACCCCT	60.598	61.111	0.30	0.00	0.00	4.79
272	274	2.685380	CCTTCCTCCCACCTCGCT	60.685	66.667	0.00	0.00	0.00	4.93
707	818	3.735029	GCCACGTCTCCGTCGTCT	61.735	66.667	0.00	0.00	46.28	4.18
708	819	2.952245	CCACGTCTCCGTCGTCTT	59.048	61.111	0.00	0.00	46.28	3.01
709	820	1.154263	CCACGTCTCCGTCGTCTTC	60.154	63.158	0.00	0.00	46.28	2.87
710	821	1.154263	CACGTCTCCGTCGTCTTCC	60.154	63.158	0.00	0.00	46.28	3.46
711	822	1.302351	ACGTCTCCGTCGTCTTCCT	60.302	57.895	0.00	0.00	46.28	3.36
712	823	1.297456	ACGTCTCCGTCGTCTTCCTC	61.297	60.000	0.00	0.00	46.28	3.71
713	824	1.424635	GTCTCCGTCGTCTTCCTCG	59.575	63.158	0.00	0.00	0.00	4.63
714	825	2.100603	CTCCGTCGTCTTCCTCGC	59.899	66.667	0.00	0.00	0.00	5.03
718	982	3.379445	GTCGTCTTCCTCGCCCCA	61.379	66.667	0.00	0.00	0.00	4.96
850	1116	1.066143	TGCTTTCCTCCGGTGAGATTC	60.066	52.381	4.76	0.00	41.42	2.52
975	1270	0.032615	TTGCTGAGGGTTGGTTTGGT	60.033	50.000	0.00	0.00	0.00	3.67
976	1271	0.032615	TGCTGAGGGTTGGTTTGGTT	60.033	50.000	0.00	0.00	0.00	3.67
977	1272	0.389025	GCTGAGGGTTGGTTTGGTTG	59.611	55.000	0.00	0.00	0.00	3.77
978	1273	1.039856	CTGAGGGTTGGTTTGGTTGG	58.960	55.000	0.00	0.00	0.00	3.77
1335	1636	4.193334	CTCGGCGGCGTGATCTCA	62.193	66.667	31.06	8.99	0.00	3.27
1611	1912	1.315257	ACAATTCGATGGTGCTGGGC	61.315	55.000	0.00	0.00	0.00	5.36
1922	2223	2.743538	TGGTCGTGATGCTGCAGC	60.744	61.111	31.89	31.89	42.50	5.25
1946	2247	3.127895	GCTCTCTCTAAGCTTTCTCGTCA	59.872	47.826	3.20	0.00	36.80	4.35
1961	2262	6.530913	TTCTCGTCAAGATAATGCTTATGC	57.469	37.500	0.00	0.00	35.04	3.14
1997	2298	4.040068	GCATAGAGGGAAGCTGCG	57.960	61.111	0.00	0.00	0.00	5.18
2102	2403	1.821136	GCCAGTGAAGAAGGAATTGGG	59.179	52.381	0.00	0.00	0.00	4.12
2229	2530	1.019673	CAGCATCATTTGACCCTCCG	58.980	55.000	0.00	0.00	0.00	4.63
2488	2789	2.617308	GGTGCACATTCTGGATCTGATG	59.383	50.000	20.43	0.00	0.00	3.07
2838	3139	3.182572	CAGAGCCTGATTATTTACGCGAC	59.817	47.826	15.93	0.00	32.44	5.19
3378	3679	2.813754	TGGCTTTTCTTTCTCCATCGTG	59.186	45.455	0.00	0.00	0.00	4.35
3479	3780	1.486726	GGTTACTCCAGTGGCAGCTAT	59.513	52.381	3.51	0.00	35.97	2.97
3630	3931	3.682718	CGGGCAATGAAGTTGGAGATACT	60.683	47.826	0.00	0.00	38.29	2.12
3639	3940	3.370104	AGTTGGAGATACTAGTGCTGCT	58.630	45.455	5.39	0.00	0.00	4.24
4728	5029	1.556911	TCAGGAGAAGACAAGGATGGC	59.443	52.381	0.00	0.00	33.34	4.40
4822	5123	3.443099	AAGAAACCAGCAAGCTTGTTC	57.557	42.857	26.55	20.34	31.85	3.18
5025	5392	2.311854	AAGGGGGACAGCTGATGGG	61.312	63.158	23.35	0.00	0.00	4.00
5070	5437	0.106519	AGCACAATATGGCACTCCCC	60.107	55.000	0.00	0.00	0.00	4.81
5210	5577	7.829211	AGATTAGGTAATTGCTGCAGAAACTTA	59.171	33.333	20.43	11.04	0.00	2.24
5326	5693	2.027192	TGGAAACTGCTAGGTGGTCATC	60.027	50.000	0.00	0.00	0.00	2.92
5462	5829	7.594015	TCACTTTCTGTGTCTTAGTCGTAATTC	59.406	37.037	0.00	0.00	46.27	2.17
5572	5939	5.239306	TGTTTGTTCAGGCTGATTAAGACAG	59.761	40.000	19.50	7.74	35.71	3.51
5577	5944	5.078411	TCAGGCTGATTAAGACAGTTCTC	57.922	43.478	14.43	3.45	35.71	2.87
5595	5962	2.300152	TCTCGGCTTGAATCTGTCTGTT	59.700	45.455	0.00	0.00	0.00	3.16
5596	5963	2.670414	CTCGGCTTGAATCTGTCTGTTC	59.330	50.000	0.00	0.00	0.00	3.18
5630	5997	6.127310	ACCTAGGAGTAGTTTGCAGTTATCTG	60.127	42.308	17.98	0.00	43.87	2.90
5665	6034	6.005198	AGGTCTTATATCTCTAGTTCACCGG	58.995	44.000	0.00	0.00	0.00	5.28
5666	6035	5.183522	GGTCTTATATCTCTAGTTCACCGGG	59.816	48.000	6.32	0.00	0.00	5.73
5713	6082	4.794311	TCAGGAATCCCTTATCATGCAA	57.206	40.909	0.00	0.00	42.02	4.08
5717	6086	5.773680	CAGGAATCCCTTATCATGCAATCTT	59.226	40.000	0.00	0.00	42.02	2.40
5741	6110	4.469883	CCTCAGGCATAGCGCATT	57.530	55.556	11.47	0.00	45.17	3.56
5822	6191	3.680937	TGTACAGTAATTGTTAGCGTGGC	59.319	43.478	0.00	0.00	41.29	5.01
5913	6314	9.546909	CAATTATCCTAATTATGTCGTGCATTC	57.453	33.333	0.00	0.00	38.94	2.67
5916	6317	4.133820	CCTAATTATGTCGTGCATTCCCA	58.866	43.478	0.00	0.00	38.94	4.37
5968	6370	6.830324	CGTTCATTCATCCATAATCCCCATAT	59.170	38.462	0.00	0.00	0.00	1.78
5969	6371	7.992608	CGTTCATTCATCCATAATCCCCATATA	59.007	37.037	0.00	0.00	0.00	0.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	8.475639	ACTTCGTCCATAATAAGTACAAGATGT	58.524	33.333	0.00	0.00	30.62	3.06
30	31	7.590689	GCTACTCACTTCGTCCATAATAAGTAC	59.409	40.741	0.00	0.00	31.20	2.73
33	34	6.740110	AGCTACTCACTTCGTCCATAATAAG	58.260	40.000	0.00	0.00	0.00	1.73
38	39	3.130516	CCAAGCTACTCACTTCGTCCATA	59.869	47.826	0.00	0.00	0.00	2.74
39	40	2.093973	CCAAGCTACTCACTTCGTCCAT	60.094	50.000	0.00	0.00	0.00	3.41
41	42	1.544691	TCCAAGCTACTCACTTCGTCC	59.455	52.381	0.00	0.00	0.00	4.79
42	43	3.182967	CATCCAAGCTACTCACTTCGTC	58.817	50.000	0.00	0.00	0.00	4.20
43	44	2.675317	GCATCCAAGCTACTCACTTCGT	60.675	50.000	0.00	0.00	0.00	3.85
44	45	1.929836	GCATCCAAGCTACTCACTTCG	59.070	52.381	0.00	0.00	0.00	3.79
45	46	2.935201	CTGCATCCAAGCTACTCACTTC	59.065	50.000	0.00	0.00	34.99	3.01
59	61	1.134946	CCCGTGGATTTTTCTGCATCC	59.865	52.381	0.00	0.00	39.72	3.51
106	108	3.158676	AGCGAGGTTAACTTCACTCTCT	58.841	45.455	16.89	7.27	0.00	3.10
125	127	1.817099	CTGGGATTGCGGAGTGAGC	60.817	63.158	0.00	0.00	0.00	4.26
166	168	3.787001	GGGACTGGCGAGAAGGGG	61.787	72.222	1.44	0.00	0.00	4.79
170	172	3.706373	GCTGGGGACTGGCGAGAA	61.706	66.667	1.44	0.00	0.00	2.87
272	274	1.749638	GGGAGAAGAGACGAGGCGA	60.750	63.158	0.00	0.00	0.00	5.54
707	818	2.833151	ATAGTGGGTGGGGCGAGGAA	62.833	60.000	0.00	0.00	0.00	3.36
708	819	2.833151	AATAGTGGGTGGGGCGAGGA	62.833	60.000	0.00	0.00	0.00	3.71
709	820	1.921869	AAATAGTGGGTGGGGCGAGG	61.922	60.000	0.00	0.00	0.00	4.63
710	821	0.834612	TAAATAGTGGGTGGGGCGAG	59.165	55.000	0.00	0.00	0.00	5.03
711	822	1.418637	GATAAATAGTGGGTGGGGCGA	59.581	52.381	0.00	0.00	0.00	5.54
712	823	1.544759	GGATAAATAGTGGGTGGGGCG	60.545	57.143	0.00	0.00	0.00	6.13
713	824	1.544759	CGGATAAATAGTGGGTGGGGC	60.545	57.143	0.00	0.00	0.00	5.80
714	825	1.544759	GCGGATAAATAGTGGGTGGGG	60.545	57.143	0.00	0.00	0.00	4.96
718	982	1.697982	GGAGGCGGATAAATAGTGGGT	59.302	52.381	0.00	0.00	0.00	4.51
837	1103	2.128729	GGGAGGAATCTCACCGGAG	58.871	63.158	9.46	0.00	41.69	4.63
850	1116	2.092323	GAATCAAACGGAAAGGGGAGG	58.908	52.381	0.00	0.00	0.00	4.30
949	1233	1.001378	CCAACCCTCAGCAAAAAGACG	60.001	52.381	0.00	0.00	0.00	4.18
952	1236	3.197265	CAAACCAACCCTCAGCAAAAAG	58.803	45.455	0.00	0.00	0.00	2.27
978	1273	4.927782	TCACACCACCACCTGCGC	62.928	66.667	0.00	0.00	0.00	6.09
1158	1453	1.685077	CTCTGCCTCCTGCTCCTCA	60.685	63.158	0.00	0.00	42.00	3.86
1173	1474	1.620259	CTCCTCCTCTGCCTCCTCT	59.380	63.158	0.00	0.00	0.00	3.69
1251	1552	4.457496	ACCTGGCACATCTCCGCG	62.457	66.667	0.00	0.00	38.20	6.46
1335	1636	4.003788	CCGTTCCAGGCGTCCAGT	62.004	66.667	0.00	0.00	0.00	4.00
1506	1807	1.758514	GATCCTGGGGTCGCAGAGA	60.759	63.158	15.27	11.16	36.95	3.10
1611	1912	1.073199	GTCCTTGGTGTCCCACAGG	59.927	63.158	0.00	0.00	41.67	4.00
1773	2074	0.596600	TCGACCGTGTCAAGAACTGC	60.597	55.000	5.15	0.00	32.09	4.40
1922	2223	2.540769	CGAGAAAGCTTAGAGAGAGCCG	60.541	54.545	0.00	0.00	41.03	5.52
1946	2247	6.183360	GGCATCATACGCATAAGCATTATCTT	60.183	38.462	0.00	0.00	39.78	2.40
1961	2262	2.016704	GCGACTCCGGCATCATACG	61.017	63.158	0.00	0.00	36.06	3.06
1997	2298	1.878734	GAAGGCCATCTATGCTTCTGC	59.121	52.381	5.01	0.00	40.20	4.26
2044	2345	0.819666	GACCGGATCCTGGGCAAATC	60.820	60.000	19.87	8.41	33.37	2.17
2073	2374	3.558746	CCTTCTTCACTGGCTTCATCAGT	60.559	47.826	0.00	0.00	45.29	3.41
2102	2403	2.939103	GGATTGATATCATAGCCCGTGC	59.061	50.000	6.17	0.00	32.96	5.34
2229	2530	5.731599	CACTCCTTGCATTCTCAGAATAC	57.268	43.478	0.00	0.00	0.00	1.89
2488	2789	2.233431	CCTGTGATATCCTGCCTCTAGC	59.767	54.545	0.00	0.00	44.14	3.42
2838	3139	3.434319	GCCACCTCCACATGCACG	61.434	66.667	0.00	0.00	0.00	5.34
3378	3679	4.181578	TCTTAACAGCGGTTAGAAGATGC	58.818	43.478	9.40	0.00	40.40	3.91
3639	3940	2.653115	CTCTGTGCGGTCTGCTCA	59.347	61.111	5.01	6.72	46.63	4.26
4254	4555	3.584733	GGATGTCCCCTAGCTTTTGAT	57.415	47.619	0.00	0.00	0.00	2.57
4728	5029	3.126831	GCTGTTAGATGGATCCTGAACG	58.873	50.000	14.23	8.91	0.00	3.95
4822	5123	0.543277	TCTGGCCTTGCATCAGTAGG	59.457	55.000	3.32	0.00	0.00	3.18
4853	5154	2.167281	GCTGCATCTACTGAAGGTCTCA	59.833	50.000	0.00	0.00	30.11	3.27
4854	5155	2.167281	TGCTGCATCTACTGAAGGTCTC	59.833	50.000	0.00	0.00	30.11	3.36
4916	5220	2.167281	GCTGCATCTACTGAAGGTCTCA	59.833	50.000	0.00	0.00	30.11	3.27
4917	5221	2.167281	TGCTGCATCTACTGAAGGTCTC	59.833	50.000	0.00	0.00	30.11	3.36
5025	5392	3.287867	TCTGGGGCTCTTGATGAATTC	57.712	47.619	0.00	0.00	0.00	2.17
5326	5693	6.808008	AGATCAACAGGTTTCATACAACAG	57.192	37.500	0.00	0.00	0.00	3.16
5462	5829	9.698309	TTGTGAGAAGTAAGAAATAGACAAGAG	57.302	33.333	0.00	0.00	0.00	2.85
5572	5939	2.670414	CAGACAGATTCAAGCCGAGAAC	59.330	50.000	0.00	0.00	0.00	3.01
5577	5944	2.416747	TGAACAGACAGATTCAAGCCG	58.583	47.619	0.00	0.00	31.95	5.52
5595	5962	2.310779	ACTCCTAGGTCACAGCTTGA	57.689	50.000	9.08	0.00	0.00	3.02
5596	5963	3.093057	ACTACTCCTAGGTCACAGCTTG	58.907	50.000	9.08	0.00	0.00	4.01
5665	6034	2.554563	TCTAAACAACCCCTCCTACCC	58.445	52.381	0.00	0.00	0.00	3.69
5666	6035	3.328637	TGTTCTAAACAACCCCTCCTACC	59.671	47.826	0.00	0.00	38.72	3.18
5942	6344	3.758554	GGGGATTATGGATGAATGAACGG	59.241	47.826	0.00	0.00	0.00	4.44
5943	6345	4.397420	TGGGGATTATGGATGAATGAACG	58.603	43.478	0.00	0.00	0.00	3.95
5948	6350	8.642964	TCAGTATATGGGGATTATGGATGAAT	57.357	34.615	0.00	0.00	0.00	2.57
5968	6370	5.869579	AGCAAAAACAAGAGATCCTCAGTA	58.130	37.500	0.00	0.00	32.06	2.74
5969	6371	4.723309	AGCAAAAACAAGAGATCCTCAGT	58.277	39.130	0.00	0.00	32.06	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.