AutoCloner

Multiple sequence alignment - TraesCS7A01G492100

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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	TraesCS7A01G492100	chr7A	100.000	3437	0	0	1	3437	680681703	680678267	0.000000e+00	6348.0
1	TraesCS7A01G492100	chr7B	94.359	2588	109	20	548	3126	663751620	663749061	0.000000e+00	3936.0
2	TraesCS7A01G492100	chr7B	95.679	1967	79	4	546	2509	663842857	663844820	0.000000e+00	3157.0
3	TraesCS7A01G492100	chr7B	89.051	411	31	10	2722	3126	663846258	663846660	6.620000e-137	497.0
4	TraesCS7A01G492100	chr7B	92.636	258	16	1	3	260	663842621	663842875	5.420000e-98	368.0
5	TraesCS7A01G492100	chr7B	84.848	66	8	2	3373	3437	643329671	643329735	7.960000e-07	65.8
6	TraesCS7A01G492100	chr7D	94.192	2600	100	22	563	3126	589391688	589389104	0.000000e+00	3917.0
7	TraesCS7A01G492100	chr7D	90.260	308	26	4	239	545	263324536	263324840	1.920000e-107	399.0
8	TraesCS7A01G492100	chr2B	83.141	1910	247	48	700	2554	138993596	138991707	0.000000e+00	1674.0
9	TraesCS7A01G492100	chr2B	80.653	1959	288	55	622	2515	12421937	12423869	0.000000e+00	1434.0
10	TraesCS7A01G492100	chr2B	80.935	1883	280	45	625	2446	11518691	11516827	0.000000e+00	1415.0
11	TraesCS7A01G492100	chr2B	82.829	1619	201	36	917	2480	12996047	12994451	0.000000e+00	1378.0
12	TraesCS7A01G492100	chr2B	82.403	1631	213	29	902	2480	11445348	11446956	0.000000e+00	1354.0
13	TraesCS7A01G492100	chr2B	77.612	134	21	5	2527	2657	13066996	13066869	4.760000e-09	73.1
14	TraesCS7A01G492100	chr2B	92.157	51	4	0	127	177	13342907	13342857	4.760000e-09	73.1
15	TraesCS7A01G492100	chr2D	82.661	1909	251	40	700	2554	85929887	85928005	0.000000e+00	1618.0
16	TraesCS7A01G492100	chr2D	81.622	1948	274	43	546	2433	19586562	19588485	0.000000e+00	1537.0
17	TraesCS7A01G492100	chr2D	83.119	1635	195	37	902	2480	9665345	9663736	0.000000e+00	1415.0
18	TraesCS7A01G492100	chr2D	80.640	1875	275	50	638	2446	9604386	9606238	0.000000e+00	1371.0
19	TraesCS7A01G492100	chr2D	81.990	1427	225	14	1000	2395	8659797	8661222	0.000000e+00	1182.0
20	TraesCS7A01G492100	chr2D	92.177	294	21	2	253	545	180879717	180879425	6.860000e-112	414.0
21	TraesCS7A01G492100	chr2A	81.583	1428	229	17	1000	2395	7727400	7728825	0.000000e+00	1149.0
22	TraesCS7A01G492100	chr2A	91.837	294	22	2	253	545	177014164	177014456	3.190000e-110	409.0
23	TraesCS7A01G492100	chr2A	92.157	51	4	0	127	177	9947604	9947654	4.760000e-09	73.1
24	TraesCS7A01G492100	chr2A	76.596	141	23	6	2527	2663	9092976	9092842	6.150000e-08	69.4
25	TraesCS7A01G492100	chr4B	92.177	294	21	2	253	545	322760395	322760103	6.860000e-112	414.0
26	TraesCS7A01G492100	chr5D	91.837	294	22	2	253	545	292148187	292147895	3.190000e-110	409.0
27	TraesCS7A01G492100	chr5D	84.211	76	12	0	3360	3435	357503054	357503129	1.320000e-09	75.0
28	TraesCS7A01G492100	chr5D	100.000	31	0	0	132	162	404501616	404501586	1.330000e-04	58.4
29	TraesCS7A01G492100	chr5A	91.837	294	22	2	253	545	366235117	366234825	3.190000e-110	409.0
30	TraesCS7A01G492100	chr4D	91.837	294	22	2	253	545	428568246	428568538	3.190000e-110	409.0
31	TraesCS7A01G492100	chr3A	91.837	294	22	2	253	545	308688838	308688546	3.190000e-110	409.0
32	TraesCS7A01G492100	chr4A	91.554	296	23	2	253	547	588567678	588567384	1.150000e-109	407.0
33	TraesCS7A01G492100	chr3D	85.000	80	12	0	3358	3437	230778260	230778339	7.910000e-12	82.4

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	TraesCS7A01G492100	chr7A	680678267	680681703	3436	True	6348.000000	6348	100.000000	1	3437	1	chr7A.!!$R1	3436
1	TraesCS7A01G492100	chr7B	663749061	663751620	2559	True	3936.000000	3936	94.359000	548	3126	1	chr7B.!!$R1	2578
2	TraesCS7A01G492100	chr7B	663842621	663846660	4039	False	1340.666667	3157	92.455333	3	3126	3	chr7B.!!$F2	3123
3	TraesCS7A01G492100	chr7D	589389104	589391688	2584	True	3917.000000	3917	94.192000	563	3126	1	chr7D.!!$R1	2563
4	TraesCS7A01G492100	chr2B	138991707	138993596	1889	True	1674.000000	1674	83.141000	700	2554	1	chr2B.!!$R5	1854
5	TraesCS7A01G492100	chr2B	12421937	12423869	1932	False	1434.000000	1434	80.653000	622	2515	1	chr2B.!!$F2	1893
6	TraesCS7A01G492100	chr2B	11516827	11518691	1864	True	1415.000000	1415	80.935000	625	2446	1	chr2B.!!$R1	1821
7	TraesCS7A01G492100	chr2B	12994451	12996047	1596	True	1378.000000	1378	82.829000	917	2480	1	chr2B.!!$R2	1563
8	TraesCS7A01G492100	chr2B	11445348	11446956	1608	False	1354.000000	1354	82.403000	902	2480	1	chr2B.!!$F1	1578
9	TraesCS7A01G492100	chr2D	85928005	85929887	1882	True	1618.000000	1618	82.661000	700	2554	1	chr2D.!!$R2	1854
10	TraesCS7A01G492100	chr2D	19586562	19588485	1923	False	1537.000000	1537	81.622000	546	2433	1	chr2D.!!$F3	1887
11	TraesCS7A01G492100	chr2D	9663736	9665345	1609	True	1415.000000	1415	83.119000	902	2480	1	chr2D.!!$R1	1578
12	TraesCS7A01G492100	chr2D	9604386	9606238	1852	False	1371.000000	1371	80.640000	638	2446	1	chr2D.!!$F2	1808
13	TraesCS7A01G492100	chr2D	8659797	8661222	1425	False	1182.000000	1182	81.990000	1000	2395	1	chr2D.!!$F1	1395
14	TraesCS7A01G492100	chr2A	7727400	7728825	1425	False	1149.000000	1149	81.583000	1000	2395	1	chr2A.!!$F1	1395

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
65	66	0.040351	CACCTCCTCCTCTCACCTGA	59.960	60.0	0.00	0.00	3.86	F
108	109	0.178955	TTGACCCACGGTGTCCTCTA	60.179	55.0	7.45	35.25	2.43	F
439	440	0.179004	ATGGACAAGGGTGCGTGAAA	60.179	50.0	0.00	38.35	2.69	F
440	441	0.817634	TGGACAAGGGTGCGTGAAAG	60.818	55.0	0.00	38.35	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1992	2086	1.270625	TGCAACTCCCTGGTAAACTCG	60.271	52.381	4.18	R
2185	2279	2.030274	GCAAAGCAAGGTCCGTTATGTT	60.030	45.455	2.71	R
2408	2523	2.100603	GTCCTCGTCGCTTCCTCG	59.899	66.667	4.63	R
2494	2611	4.516323	CCACATGAACACATCCATCTGTA	58.484	43.478	2.74	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
33	34	1.250328	TCGAAGGAAGTAGGTCGCAA	58.750	50.000	0.00	0.00	33.58	4.85
47	48	4.980805	GCAACACCTCCGTCGCCA	62.981	66.667	0.00	0.00	0.00	5.69
65	66	0.040351	CACCTCCTCCTCTCACCTGA	59.960	60.000	0.00	0.00	0.00	3.86
98	99	0.871722	TTGCGAGATTTTGACCCACG	59.128	50.000	0.00	0.00	0.00	4.94
108	109	0.178955	TTGACCCACGGTGTCCTCTA	60.179	55.000	7.45	0.00	35.25	2.43
122	123	8.889717	ACGGTGTCCTCTAAAACAATATTATTG	58.110	33.333	13.64	13.64	0.00	1.90
125	126	9.503427	GTGTCCTCTAAAACAATATTATTGCAC	57.497	33.333	14.88	8.01	0.00	4.57
146	147	6.014925	TGCACTACTAAAGTATGGAGTTGTGA	60.015	38.462	16.36	3.34	44.48	3.58
177	178	5.546499	TCATCACTGAGTAAGGTAAAAGGGT	59.454	40.000	0.00	0.00	0.00	4.34
212	213	7.931578	ATCATGCCAATGAATTTTGTTCATT	57.068	28.000	9.53	9.53	45.81	2.57
241	242	4.658063	ACCTCAAATAATTTCCACCGTCA	58.342	39.130	0.00	0.00	0.00	4.35
242	243	5.074115	ACCTCAAATAATTTCCACCGTCAA	58.926	37.500	0.00	0.00	0.00	3.18
243	244	5.536916	ACCTCAAATAATTTCCACCGTCAAA	59.463	36.000	0.00	0.00	0.00	2.69
244	245	5.861787	CCTCAAATAATTTCCACCGTCAAAC	59.138	40.000	0.00	0.00	0.00	2.93
245	246	6.294508	CCTCAAATAATTTCCACCGTCAAACT	60.295	38.462	0.00	0.00	0.00	2.66
246	247	7.045126	TCAAATAATTTCCACCGTCAAACTT	57.955	32.000	0.00	0.00	0.00	2.66
247	248	7.493367	TCAAATAATTTCCACCGTCAAACTTT	58.507	30.769	0.00	0.00	0.00	2.66
248	249	7.436673	TCAAATAATTTCCACCGTCAAACTTTG	59.563	33.333	0.00	0.00	0.00	2.77
249	250	3.726291	ATTTCCACCGTCAAACTTTGG	57.274	42.857	1.62	0.00	0.00	3.28
250	251	2.131776	TTCCACCGTCAAACTTTGGT	57.868	45.000	1.62	0.00	34.29	3.67
251	252	3.278668	TTCCACCGTCAAACTTTGGTA	57.721	42.857	1.62	0.00	32.29	3.25
252	253	2.563702	TCCACCGTCAAACTTTGGTAC	58.436	47.619	1.62	0.00	32.29	3.34
253	254	2.171027	TCCACCGTCAAACTTTGGTACT	59.829	45.455	1.62	0.00	32.29	2.73
254	255	2.289547	CCACCGTCAAACTTTGGTACTG	59.710	50.000	1.62	0.00	32.29	2.74
255	256	1.944709	ACCGTCAAACTTTGGTACTGC	59.055	47.619	1.62	0.00	31.60	4.40

Showing 1 to 25 of 570 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	6.238648	ACTTCCTTCGATCCAAAATAAGTGT	58.761	36.000	0.00	0.00	0.00	3.55
1	2	6.743575	ACTTCCTTCGATCCAAAATAAGTG	57.256	37.500	0.00	0.00	0.00	3.16
17	18	1.270678	GGTGTTGCGACCTACTTCCTT	60.271	52.381	0.45	0.00	32.69	3.36
47	48	0.040499	GTCAGGTGAGAGGAGGAGGT	59.960	60.000	0.00	0.00	0.00	3.85
65	66	1.066257	CGCAAACAAAGCAGCTGGT	59.934	52.632	13.85	13.85	0.00	4.00
98	99	8.682710	TGCAATAATATTGTTTTAGAGGACACC	58.317	33.333	13.77	0.00	0.00	4.16
122	123	6.395629	TCACAACTCCATACTTTAGTAGTGC	58.604	40.000	0.00	0.00	37.73	4.40
125	126	9.522804	GAGAATCACAACTCCATACTTTAGTAG	57.477	37.037	0.00	0.00	31.63	2.57
146	147	6.805016	ACCTTACTCAGTGATGATGAGAAT	57.195	37.500	9.78	0.00	45.80	2.40
160	161	4.650972	ATGCACCCTTTTACCTTACTCA	57.349	40.909	0.00	0.00	0.00	3.41
161	162	4.575236	GCTATGCACCCTTTTACCTTACTC	59.425	45.833	0.00	0.00	0.00	2.59
162	163	4.524053	GCTATGCACCCTTTTACCTTACT	58.476	43.478	0.00	0.00	0.00	2.24
163	164	3.311596	CGCTATGCACCCTTTTACCTTAC	59.688	47.826	0.00	0.00	0.00	2.34
164	165	3.054948	ACGCTATGCACCCTTTTACCTTA	60.055	43.478	0.00	0.00	0.00	2.69
165	166	2.290705	ACGCTATGCACCCTTTTACCTT	60.291	45.455	0.00	0.00	0.00	3.50
177	178	2.252976	TGGCATGATAACGCTATGCA	57.747	45.000	10.16	0.00	46.74	3.96
212	213	7.439655	CGGTGGAAATTATTTGAGGTTTTTCAA	59.560	33.333	0.00	0.00	35.38	2.69
241	242	3.577805	ACCTCTGCAGTACCAAAGTTT	57.422	42.857	14.67	0.00	0.00	2.66
242	243	3.577805	AACCTCTGCAGTACCAAAGTT	57.422	42.857	14.67	5.42	0.00	2.66
243	244	3.214328	CAAACCTCTGCAGTACCAAAGT	58.786	45.455	14.67	0.00	0.00	2.66
244	245	2.554032	CCAAACCTCTGCAGTACCAAAG	59.446	50.000	14.67	1.93	0.00	2.77
245	246	2.582052	CCAAACCTCTGCAGTACCAAA	58.418	47.619	14.67	0.00	0.00	3.28
246	247	1.202879	CCCAAACCTCTGCAGTACCAA	60.203	52.381	14.67	0.00	0.00	3.67
247	248	0.400213	CCCAAACCTCTGCAGTACCA	59.600	55.000	14.67	0.00	0.00	3.25
248	249	0.960861	GCCCAAACCTCTGCAGTACC	60.961	60.000	14.67	0.00	0.00	3.34

Showing 1 to 25 of 575 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.