AutoCloner

Multiple sequence alignment - TraesCS2D01G157400

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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	TraesCS2D01G157400	chr2D	100.000	3819	0	0	1	3819	100430260	100434078	0.000000e+00	7053.0
1	TraesCS2D01G157400	chr2D	89.577	710	54	11	759	1468	100947010	100946321	0.000000e+00	883.0
2	TraesCS2D01G157400	chr2D	86.387	191	14	5	542	721	100947282	100947093	8.370000e-47	198.0
3	TraesCS2D01G157400	chr2D	82.381	210	21	8	523	717	100948563	100948355	6.560000e-38	169.0
4	TraesCS2D01G157400	chr2D	91.057	123	10	1	3131	3252	100325599	100325477	8.490000e-37	165.0
5	TraesCS2D01G157400	chr2D	94.937	79	4	0	1464	1542	100943906	100943828	1.440000e-24	124.0
6	TraesCS2D01G157400	chr2D	89.189	74	6	2	3241	3312	100325523	100325450	1.460000e-14	91.6
7	TraesCS2D01G157400	chr2D	91.489	47	2	2	3241	3285	100433465	100433511	3.180000e-06	63.9
8	TraesCS2D01G157400	chr2D	91.489	47	2	2	3206	3252	100433500	100433544	3.180000e-06	63.9
9	TraesCS2D01G157400	chr2A	90.315	2127	104	36	759	2821	100629220	100627132	0.000000e+00	2693.0
10	TraesCS2D01G157400	chr2A	94.389	303	16	1	1	302	595240099	595240401	7.470000e-127	464.0
11	TraesCS2D01G157400	chr2A	94.198	293	9	3	1	292	585194869	585195154	1.260000e-119	440.0
12	TraesCS2D01G157400	chr2A	91.154	260	20	2	2993	3252	100199770	100199514	2.180000e-92	350.0
13	TraesCS2D01G157400	chr2A	92.000	125	9	1	2866	2989	100627134	100627010	1.410000e-39	174.0
14	TraesCS2D01G157400	chr2A	94.340	106	6	0	759	864	100543266	100543371	3.050000e-36	163.0
15	TraesCS2D01G157400	chr2A	89.333	75	6	2	3240	3312	100199561	100199487	4.060000e-15	93.5
16	TraesCS2D01G157400	chr2B	93.539	1331	59	13	1676	2987	152504014	152505336	0.000000e+00	1956.0
17	TraesCS2D01G157400	chr2B	90.105	859	61	10	759	1611	152503058	152503898	0.000000e+00	1094.0
18	TraesCS2D01G157400	chr2B	91.406	128	9	2	2991	3118	152506514	152506639	1.410000e-39	174.0
19	TraesCS2D01G157400	chr7D	95.927	491	17	3	3330	3819	568402843	568402355	0.000000e+00	793.0
20	TraesCS2D01G157400	chr7D	93.673	490	28	3	3331	3819	515235850	515235363	0.000000e+00	730.0
21	TraesCS2D01G157400	chr7D	93.469	490	29	3	3331	3819	515219645	515219158	0.000000e+00	725.0
22	TraesCS2D01G157400	chr7D	92.653	490	27	4	3331	3819	514094101	514094582	0.000000e+00	697.0
23	TraesCS2D01G157400	chr7D	83.562	73	9	1	3132	3201	392646368	392646296	8.860000e-07	65.8
24	TraesCS2D01G157400	chr7D	91.111	45	3	1	2544	2588	162789382	162789339	4.120000e-05	60.2
25	TraesCS2D01G157400	chr7A	94.373	391	18	4	3430	3819	588725075	588724688	7.060000e-167	597.0
26	TraesCS2D01G157400	chr7A	80.309	259	39	11	2102	2350	107916821	107916565	6.510000e-43	185.0
27	TraesCS2D01G157400	chr7A	98.113	106	2	0	3333	3438	587520228	587520333	6.510000e-43	185.0
28	TraesCS2D01G157400	chr7A	95.495	111	5	0	3331	3441	588738682	588738572	1.090000e-40	178.0
29	TraesCS2D01G157400	chr7A	91.111	45	3	1	2544	2588	163393303	163393260	4.120000e-05	60.2
30	TraesCS2D01G157400	chr6A	94.198	293	16	1	1	292	577016323	577016031	2.710000e-121	446.0
31	TraesCS2D01G157400	chr7B	92.808	292	21	0	1	292	626048907	626049198	1.270000e-114	424.0
32	TraesCS2D01G157400	chr7B	92.414	290	22	0	1	290	4921374	4921085	7.630000e-112	414.0
33	TraesCS2D01G157400	chr7B	80.695	259	38	11	2102	2350	61627955	61627699	1.400000e-44	191.0
34	TraesCS2D01G157400	chr7B	78.846	260	43	8	2101	2350	61746303	61746046	8.490000e-37	165.0
35	TraesCS2D01G157400	chr7B	80.342	117	14	8	2210	2321	425159131	425159243	3.160000e-11	80.5
36	TraesCS2D01G157400	chr7B	91.111	45	3	1	2544	2588	124743281	124743238	4.120000e-05	60.2
37	TraesCS2D01G157400	chr5D	92.833	293	20	1	1	292	553058473	553058765	1.270000e-114	424.0
38	TraesCS2D01G157400	chr5D	81.731	104	13	4	2212	2312	320873690	320873590	8.790000e-12	82.4
39	TraesCS2D01G157400	chr1B	92.833	293	20	1	1	292	357457110	357456818	1.270000e-114	424.0
40	TraesCS2D01G157400	chr1B	91.809	293	23	1	1	292	532683266	532683558	1.280000e-109	407.0
41	TraesCS2D01G157400	chr5B	91.809	293	23	1	1	292	605507133	605507425	1.280000e-109	407.0
42	TraesCS2D01G157400	chr5B	83.654	104	11	4	2212	2312	372081465	372081365	4.060000e-15	93.5
43	TraesCS2D01G157400	chr5A	82.692	104	12	3	2212	2312	413429635	413429735	1.890000e-13	87.9

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	TraesCS2D01G157400	chr2D	100430260	100434078	3818	False	2393.600000	7053	94.326000	1	3819	3	chr2D.!!$F1	3818
1	TraesCS2D01G157400	chr2D	100943828	100948563	4735	True	343.500000	883	88.320500	523	1542	4	chr2D.!!$R2	1019
2	TraesCS2D01G157400	chr2A	100627010	100629220	2210	True	1433.500000	2693	91.157500	759	2989	2	chr2A.!!$R2	2230
3	TraesCS2D01G157400	chr2B	152503058	152506639	3581	False	1074.666667	1956	91.683333	759	3118	3	chr2B.!!$F1	2359

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
76	77	0.031178	GCTCAAAGCACCCACAACAG	59.969	55.0	0.00	0.0	41.89	3.16	F
104	105	0.031585	CAACACCGGTCTCTCGTTGA	59.968	55.0	23.46	0.0	39.39	3.18	F
844	2166	0.032540	GGACAAGCAAGCAACCAAGG	59.967	55.0	0.00	0.0	0.00	3.61	F
1351	2696	0.179056	CAGTGTCGTGGTGTTCCCTT	60.179	55.0	0.00	0.0	0.00	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1743	5580	0.615331	TTCTTGCCCTGAGTAGCCAG	59.385	55.0	0.0	0.0	0.00	4.85	R
1763	5600	0.943359	GCTCGATCTCCTGGCAATCG	60.943	60.0	18.6	18.6	42.70	3.34	R
2192	6051	0.179089	ATCTCGTCCATGCTCAGCAC	60.179	55.0	0.0	0.0	43.04	4.40	R
3295	8344	0.034059	GCCATCTGGGACACCTATCG	59.966	60.0	0.0	0.0	40.01	2.92	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
17	18	3.821995	ACACAGGACAACAACGCC	58.178	55.556	0.00	0.00	0.00	5.68
18	19	1.223487	ACACAGGACAACAACGCCT	59.777	52.632	0.00	0.00	0.00	5.52
19	20	0.466543	ACACAGGACAACAACGCCTA	59.533	50.000	0.00	0.00	0.00	3.93
20	21	1.071699	ACACAGGACAACAACGCCTAT	59.928	47.619	0.00	0.00	0.00	2.57
21	22	1.732259	CACAGGACAACAACGCCTATC	59.268	52.381	0.00	0.00	0.00	2.08
22	23	1.346395	ACAGGACAACAACGCCTATCA	59.654	47.619	0.00	0.00	0.00	2.15
23	24	2.027192	ACAGGACAACAACGCCTATCAT	60.027	45.455	0.00	0.00	0.00	2.45
24	25	3.009723	CAGGACAACAACGCCTATCATT	58.990	45.455	0.00	0.00	0.00	2.57
25	26	3.009723	AGGACAACAACGCCTATCATTG	58.990	45.455	0.00	0.00	0.00	2.82
26	27	2.747446	GGACAACAACGCCTATCATTGT	59.253	45.455	0.00	0.00	38.18	2.71
27	28	3.190535	GGACAACAACGCCTATCATTGTT	59.809	43.478	0.00	0.00	45.13	2.83
30	31	4.685169	AACAACGCCTATCATTGTTGAG	57.315	40.909	10.54	0.00	43.19	3.02
31	32	3.937814	ACAACGCCTATCATTGTTGAGA	58.062	40.909	10.54	0.00	43.26	3.27
32	33	4.517285	ACAACGCCTATCATTGTTGAGAT	58.483	39.130	10.54	0.00	43.26	2.75
33	34	4.333649	ACAACGCCTATCATTGTTGAGATG	59.666	41.667	10.54	0.00	43.26	2.90
34	35	3.470709	ACGCCTATCATTGTTGAGATGG	58.529	45.455	0.00	0.00	34.73	3.51
35	36	3.134623	ACGCCTATCATTGTTGAGATGGA	59.865	43.478	0.00	0.00	34.73	3.41
36	37	4.202398	ACGCCTATCATTGTTGAGATGGAT	60.202	41.667	0.00	0.00	34.73	3.41
37	38	5.012046	ACGCCTATCATTGTTGAGATGGATA	59.988	40.000	0.00	0.00	34.73	2.59
38	39	5.579904	CGCCTATCATTGTTGAGATGGATAG	59.420	44.000	0.00	0.00	34.73	2.08
39	40	6.471146	GCCTATCATTGTTGAGATGGATAGT	58.529	40.000	0.00	0.00	34.73	2.12
40	41	6.370994	GCCTATCATTGTTGAGATGGATAGTG	59.629	42.308	0.00	0.00	34.73	2.74
41	42	6.370994	CCTATCATTGTTGAGATGGATAGTGC	59.629	42.308	0.00	0.00	34.73	4.40
42	43	4.122046	TCATTGTTGAGATGGATAGTGCG	58.878	43.478	0.00	0.00	0.00	5.34
43	44	2.602257	TGTTGAGATGGATAGTGCGG	57.398	50.000	0.00	0.00	0.00	5.69

Showing 1 to 25 of 867 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.732259	GATAGGCGTTGTTGTCCTGTG	59.268	52.381	0.00	0.00	0.00	3.66
2	3	1.346395	TGATAGGCGTTGTTGTCCTGT	59.654	47.619	0.00	0.00	0.00	4.00
4	5	3.009723	CAATGATAGGCGTTGTTGTCCT	58.990	45.455	0.00	0.00	38.44	3.85
5	6	3.405170	CAATGATAGGCGTTGTTGTCC	57.595	47.619	0.00	0.00	38.44	4.02
11	12	4.260907	CCATCTCAACAATGATAGGCGTTG	60.261	45.833	0.00	0.00	46.63	4.10
12	13	3.879295	CCATCTCAACAATGATAGGCGTT	59.121	43.478	0.00	0.00	34.37	4.84
13	14	3.134623	TCCATCTCAACAATGATAGGCGT	59.865	43.478	0.00	0.00	34.37	5.68
14	15	3.732212	TCCATCTCAACAATGATAGGCG	58.268	45.455	0.00	0.00	34.37	5.52
15	16	6.370994	CACTATCCATCTCAACAATGATAGGC	59.629	42.308	0.00	0.00	34.37	3.93
16	17	6.370994	GCACTATCCATCTCAACAATGATAGG	59.629	42.308	0.00	0.00	34.37	2.57
17	18	6.090493	CGCACTATCCATCTCAACAATGATAG	59.910	42.308	0.00	0.00	34.37	2.08
18	19	5.928264	CGCACTATCCATCTCAACAATGATA	59.072	40.000	0.00	0.00	34.37	2.15
19	20	4.753610	CGCACTATCCATCTCAACAATGAT	59.246	41.667	0.00	0.00	34.37	2.45
20	21	4.122046	CGCACTATCCATCTCAACAATGA	58.878	43.478	0.00	0.00	0.00	2.57
21	22	3.249320	CCGCACTATCCATCTCAACAATG	59.751	47.826	0.00	0.00	0.00	2.82
22	23	3.134623	TCCGCACTATCCATCTCAACAAT	59.865	43.478	0.00	0.00	0.00	2.71
23	24	2.499693	TCCGCACTATCCATCTCAACAA	59.500	45.455	0.00	0.00	0.00	2.83
24	25	2.101415	CTCCGCACTATCCATCTCAACA	59.899	50.000	0.00	0.00	0.00	3.33
25	26	2.546795	CCTCCGCACTATCCATCTCAAC	60.547	54.545	0.00	0.00	0.00	3.18
26	27	1.688735	CCTCCGCACTATCCATCTCAA	59.311	52.381	0.00	0.00	0.00	3.02
27	28	1.332195	CCTCCGCACTATCCATCTCA	58.668	55.000	0.00	0.00	0.00	3.27
28	29	0.037790	GCCTCCGCACTATCCATCTC	60.038	60.000	0.00	0.00	34.03	2.75
29	30	0.470833	AGCCTCCGCACTATCCATCT	60.471	55.000	0.00	0.00	37.52	2.90
30	31	0.320247	CAGCCTCCGCACTATCCATC	60.320	60.000	0.00	0.00	37.52	3.51
31	32	1.050988	ACAGCCTCCGCACTATCCAT	61.051	55.000	0.00	0.00	37.52	3.41

Showing 1 to 25 of 887 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.