AutoCloner

Multiple sequence alignment - TraesCS2A01G276500

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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	TraesCS2A01G276500	chr2A	100.000	2198	0	0	1	2198	457221109	457218912	0.000000e+00	4060.0
1	TraesCS2A01G276500	chr2A	90.558	233	21	1	2	233	606519085	606519317	7.620000e-80	307.0
2	TraesCS2A01G276500	chr2A	90.558	233	21	1	2	233	699241092	699240860	7.620000e-80	307.0
3	TraesCS2A01G276500	chr2A	89.157	83	7	2	2118	2198	603543276	603543194	3.860000e-18	102.0
4	TraesCS2A01G276500	chr2A	89.024	82	7	2	2118	2197	164926128	164926209	1.390000e-17	100.0
5	TraesCS2A01G276500	chr2B	90.222	1309	67	29	283	1535	410942291	410940988	0.000000e+00	1652.0
6	TraesCS2A01G276500	chr2B	93.598	328	13	6	1734	2058	410940712	410940390	1.180000e-132	483.0
7	TraesCS2A01G276500	chr2B	93.229	192	13	0	1548	1739	410940940	410940749	1.280000e-72	283.0
8	TraesCS2A01G276500	chr2B	79.279	111	20	3	1735	1844	154841299	154841191	8.420000e-10	75.0
9	TraesCS2A01G276500	chr2D	89.498	1314	56	30	283	1545	345247581	345246299	0.000000e+00	1587.0
10	TraesCS2A01G276500	chr2D	94.243	469	18	7	1734	2198	345225890	345225427	0.000000e+00	708.0
11	TraesCS2A01G276500	chr2D	91.667	228	18	1	2	228	455942247	455942474	4.560000e-82	315.0
12	TraesCS2A01G276500	chr2D	88.213	263	25	5	2	261	380694312	380694571	2.120000e-80	309.0
13	TraesCS2A01G276500	chr2D	91.150	113	6	2	1546	1658	345246265	345246157	1.360000e-32	150.0
14	TraesCS2A01G276500	chr2D	93.939	66	3	1	2133	2197	285901607	285901542	4.990000e-17	99.0
15	TraesCS2A01G276500	chr7A	92.208	231	16	2	2	230	60605000	60605230	2.100000e-85	326.0
16	TraesCS2A01G276500	chr7A	90.558	233	21	1	2	233	669666379	669666611	7.620000e-80	307.0
17	TraesCS2A01G276500	chr3D	92.070	227	16	2	8	233	305497383	305497158	3.520000e-83	318.0
18	TraesCS2A01G276500	chr4B	90.948	232	20	1	3	233	22857380	22857611	5.890000e-81	311.0
19	TraesCS2A01G276500	chr4B	79.279	111	20	3	1735	1843	78503023	78503132	8.420000e-10	75.0
20	TraesCS2A01G276500	chr5A	91.228	228	19	1	2	228	336841673	336841446	2.120000e-80	309.0
21	TraesCS2A01G276500	chr6B	91.566	83	4	3	2118	2198	648802241	648802160	6.410000e-21	111.0
22	TraesCS2A01G276500	chr1B	88.636	88	6	1	487	574	655858109	655858026	1.070000e-18	104.0
23	TraesCS2A01G276500	chr4D	91.667	72	6	0	2123	2194	97693380	97693451	1.390000e-17	100.0
24	TraesCS2A01G276500	chr4D	94.737	38	2	0	1735	1772	48713668	48713705	2.360000e-05	60.2
25	TraesCS2A01G276500	chr3B	93.939	66	4	0	2133	2198	17582252	17582317	1.390000e-17	100.0
26	TraesCS2A01G276500	chr3B	88.608	79	8	1	2121	2198	253503469	253503547	6.460000e-16	95.3
27	TraesCS2A01G276500	chr6D	87.654	81	8	2	2117	2197	410203117	410203039	2.320000e-15	93.5
28	TraesCS2A01G276500	chr4A	82.955	88	12	3	1739	1824	635657500	635657586	2.340000e-10	76.8
29	TraesCS2A01G276500	chr4A	96.774	31	1	0	1739	1769	635848439	635848469	4.000000e-03	52.8
30	TraesCS2A01G276500	chr5D	77.692	130	23	5	1742	1869	536004470	536004345	8.420000e-10	75.0

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	TraesCS2A01G276500	chr2A	457218912	457221109	2197	True	4060.0	4060	100.000000	1	2198	1	chr2A.!!$R1	2197
1	TraesCS2A01G276500	chr2B	410940390	410942291	1901	True	806.0	1652	92.349667	283	2058	3	chr2B.!!$R2	1775
2	TraesCS2A01G276500	chr2D	345246157	345247581	1424	True	868.5	1587	90.324000	283	1658	2	chr2D.!!$R3	1375

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
991	1029	0.723981	GCGATCTTTCCTGCTGTGTC	59.276	55.0	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2098	2253	1.064946	CTCCCTGCTCTAGCGAACG	59.935	63.158	0.0	0.0	45.83	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	3.603158	TCCACGTATTAGCTTTGCTCA	57.397	42.857	0.00	0.00	40.44	4.26
22	23	3.932822	TCCACGTATTAGCTTTGCTCAA	58.067	40.909	0.00	0.00	40.44	3.02
23	24	3.932710	TCCACGTATTAGCTTTGCTCAAG	59.067	43.478	0.00	0.00	40.44	3.02
24	25	3.063997	CCACGTATTAGCTTTGCTCAAGG	59.936	47.826	0.00	0.00	40.44	3.61
25	26	3.684788	CACGTATTAGCTTTGCTCAAGGT	59.315	43.478	0.00	6.24	45.51	3.50
26	27	3.933332	ACGTATTAGCTTTGCTCAAGGTC	59.067	43.478	0.00	0.00	42.50	3.85
27	28	3.932710	CGTATTAGCTTTGCTCAAGGTCA	59.067	43.478	0.00	0.00	42.50	4.02
28	29	4.391830	CGTATTAGCTTTGCTCAAGGTCAA	59.608	41.667	0.00	0.70	42.50	3.18
29	30	5.106712	CGTATTAGCTTTGCTCAAGGTCAAA	60.107	40.000	0.00	0.00	42.50	2.69
30	31	4.568152	TTAGCTTTGCTCAAGGTCAAAC	57.432	40.909	0.00	0.00	42.50	2.93
31	32	2.659428	AGCTTTGCTCAAGGTCAAACT	58.341	42.857	0.00	0.00	39.06	2.66
32	33	3.026694	AGCTTTGCTCAAGGTCAAACTT	58.973	40.909	0.00	0.00	39.06	2.66
33	34	3.448660	AGCTTTGCTCAAGGTCAAACTTT	59.551	39.130	0.00	0.00	39.06	2.66
34	35	3.553105	GCTTTGCTCAAGGTCAAACTTTG	59.447	43.478	0.00	0.00	36.63	2.77
35	36	4.747810	CTTTGCTCAAGGTCAAACTTTGT	58.252	39.130	1.44	0.00	36.66	2.83
36	37	5.678616	GCTTTGCTCAAGGTCAAACTTTGTA	60.679	40.000	1.44	0.00	36.66	2.41
37	38	5.906113	TTGCTCAAGGTCAAACTTTGTAA	57.094	34.783	1.44	0.00	36.66	2.41
38	39	5.906113	TGCTCAAGGTCAAACTTTGTAAA	57.094	34.783	1.44	0.00	36.66	2.01
39	40	5.646606	TGCTCAAGGTCAAACTTTGTAAAC	58.353	37.500	1.44	0.00	36.66	2.01
40	41	5.417580	TGCTCAAGGTCAAACTTTGTAAACT	59.582	36.000	1.44	0.00	36.66	2.66
41	42	6.071616	TGCTCAAGGTCAAACTTTGTAAACTT	60.072	34.615	1.44	0.00	36.66	2.66
42	43	6.811665	GCTCAAGGTCAAACTTTGTAAACTTT	59.188	34.615	1.44	0.00	36.66	2.66
43	44	7.201435	GCTCAAGGTCAAACTTTGTAAACTTTG	60.201	37.037	8.97	8.97	36.66	2.77
44	45	6.588373	TCAAGGTCAAACTTTGTAAACTTTGC	59.412	34.615	9.85	0.00	36.66	3.68
45	46	6.031751	AGGTCAAACTTTGTAAACTTTGCA	57.968	33.333	1.44	0.00	0.00	4.08

Showing 1 to 25 of 180 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.137116	TGAGCAAAGCTAATACGTGGAT	57.863	40.909	0.00	0.00	39.88	3.41
2	3	3.063997	CCTTGAGCAAAGCTAATACGTGG	59.936	47.826	0.00	0.00	39.88	4.94
4	5	3.933332	GACCTTGAGCAAAGCTAATACGT	59.067	43.478	0.00	0.00	39.88	3.57
5	6	3.932710	TGACCTTGAGCAAAGCTAATACG	59.067	43.478	0.00	0.00	39.88	3.06
6	7	5.880054	TTGACCTTGAGCAAAGCTAATAC	57.120	39.130	0.00	0.00	39.88	1.89
7	8	6.003950	AGTTTGACCTTGAGCAAAGCTAATA	58.996	36.000	0.00	0.00	39.88	0.98
8	9	4.829492	AGTTTGACCTTGAGCAAAGCTAAT	59.171	37.500	0.00	0.00	39.88	1.73
9	10	4.207165	AGTTTGACCTTGAGCAAAGCTAA	58.793	39.130	0.00	0.00	39.88	3.09
10	11	3.820557	AGTTTGACCTTGAGCAAAGCTA	58.179	40.909	0.00	0.00	39.88	3.32
11	12	2.659428	AGTTTGACCTTGAGCAAAGCT	58.341	42.857	0.00	0.00	43.88	3.74
12	13	3.443099	AAGTTTGACCTTGAGCAAAGC	57.557	42.857	0.00	0.00	34.95	3.51
13	14	4.747810	ACAAAGTTTGACCTTGAGCAAAG	58.252	39.130	22.23	0.00	34.95	2.77
14	15	4.799564	ACAAAGTTTGACCTTGAGCAAA	57.200	36.364	22.23	0.00	0.00	3.68
15	16	5.906113	TTACAAAGTTTGACCTTGAGCAA	57.094	34.783	22.23	0.00	0.00	3.91
16	17	5.417580	AGTTTACAAAGTTTGACCTTGAGCA	59.582	36.000	22.23	0.00	0.00	4.26
17	18	5.891451	AGTTTACAAAGTTTGACCTTGAGC	58.109	37.500	22.23	0.00	0.00	4.26
100	101	8.541133	TGACGTGAAAGTACATTCAATAATGA	57.459	30.769	14.64	0.00	44.50	2.57
104	105	9.040939	CCATATGACGTGAAAGTACATTCAATA	57.959	33.333	14.64	9.55	40.76	1.90
105	106	7.768582	TCCATATGACGTGAAAGTACATTCAAT	59.231	33.333	14.64	6.81	40.76	2.57
106	107	7.100409	TCCATATGACGTGAAAGTACATTCAA	58.900	34.615	14.64	0.60	40.76	2.69
107	108	6.635755	TCCATATGACGTGAAAGTACATTCA	58.364	36.000	9.38	9.38	36.99	2.57
108	109	7.715265	ATCCATATGACGTGAAAGTACATTC	57.285	36.000	3.65	3.88	0.00	2.67
109	110	8.397906	CAAATCCATATGACGTGAAAGTACATT	58.602	33.333	3.65	0.00	0.00	2.71
110	111	7.552687	ACAAATCCATATGACGTGAAAGTACAT	59.447	33.333	3.65	0.00	0.00	2.29
111	112	6.876789	ACAAATCCATATGACGTGAAAGTACA	59.123	34.615	3.65	0.00	0.00	2.90

Showing 1 to 25 of 179 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.