AutoCloner

Multiple sequence alignment - TraesCS2D01G445000

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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	TraesCS2D01G445000	chr2D	100.000	5236	0	0	1	5236	555934189	555928954	0.000000e+00	9670.0
1	TraesCS2D01G445000	chr2D	82.680	791	107	17	976	1740	555916847	555916061	0.000000e+00	675.0
2	TraesCS2D01G445000	chr2D	80.330	666	94	18	1098	1740	154608562	154609213	2.210000e-128	470.0
3	TraesCS2D01G445000	chr2D	85.606	132	12	3	246	377	556020403	556020279	1.180000e-26	132.0
4	TraesCS2D01G445000	chr2D	83.333	132	14	3	246	377	555959846	555959723	1.190000e-21	115.0
5	TraesCS2D01G445000	chr2D	95.556	45	2	0	800	844	558960532	558960488	7.270000e-09	73.1
6	TraesCS2D01G445000	chr2B	95.717	4996	128	30	4	4962	662798420	662793474	0.000000e+00	7962.0
7	TraesCS2D01G445000	chr2B	82.828	792	104	19	976	1740	662688397	662687611	0.000000e+00	680.0
8	TraesCS2D01G445000	chr2B	83.333	132	15	3	246	377	662906804	662906680	1.190000e-21	115.0
9	TraesCS2D01G445000	chr2B	90.000	90	7	2	289	377	727499446	727499534	1.190000e-21	115.0
10	TraesCS2D01G445000	chr2B	100.000	40	0	0	798	837	448906729	448906768	2.020000e-09	75.0
11	TraesCS2D01G445000	chr2A	91.583	2495	140	23	1	2464	695352387	695349932	0.000000e+00	3380.0
12	TraesCS2D01G445000	chr2A	94.779	2107	80	9	2440	4529	695349750	695347657	0.000000e+00	3254.0
13	TraesCS2D01G445000	chr2A	92.449	437	19	6	4529	4962	695344938	695344513	3.470000e-171	612.0
14	TraesCS2D01G445000	chr2A	83.628	452	73	1	1290	1740	695318360	695317909	1.740000e-114	424.0
15	TraesCS2D01G445000	chr2A	80.580	448	56	14	1098	1526	146350514	146350079	3.040000e-82	316.0
16	TraesCS2D01G445000	chr2A	79.511	327	55	6	1416	1740	146350050	146349734	6.820000e-54	222.0
17	TraesCS2D01G445000	chr2A	82.963	135	16	3	246	380	695468768	695468641	1.190000e-21	115.0
18	TraesCS2D01G445000	chrUn	100.000	406	0	0	2545	2950	478141517	478141922	0.000000e+00	750.0
19	TraesCS2D01G445000	chrUn	93.878	49	2	1	799	847	108299102	108299055	7.270000e-09	73.1
20	TraesCS2D01G445000	chr3D	80.321	249	38	5	1416	1663	449730236	449729998	1.500000e-40	178.0
21	TraesCS2D01G445000	chr6D	79.920	249	39	4	1416	1663	428453285	428453047	6.970000e-39	172.0
22	TraesCS2D01G445000	chr5A	89.888	89	9	0	289	377	41643578	41643666	1.190000e-21	115.0
23	TraesCS2D01G445000	chr5A	93.333	45	3	0	5000	5044	601706396	601706440	3.380000e-07	67.6
24	TraesCS2D01G445000	chr1B	96.226	53	1	1	325	376	284212547	284212495	9.340000e-13	86.1
25	TraesCS2D01G445000	chr1B	95.556	45	2	0	798	842	668127135	668127091	7.270000e-09	73.1
26	TraesCS2D01G445000	chr4D	96.078	51	2	0	4966	5016	463410988	463410938	3.360000e-12	84.2
27	TraesCS2D01G445000	chr7D	87.879	66	4	2	779	841	34443183	34443247	2.020000e-09	75.0
28	TraesCS2D01G445000	chr6B	97.619	42	1	0	798	839	501066299	501066258	7.270000e-09	73.1
29	TraesCS2D01G445000	chr6B	100.000	38	0	0	4963	5000	552507158	552507121	2.620000e-08	71.3
30	TraesCS2D01G445000	chr1A	97.619	42	1	0	798	839	49963201	49963242	7.270000e-09	73.1
31	TraesCS2D01G445000	chr1A	100.000	38	0	0	4963	5000	512640235	512640272	2.620000e-08	71.3
32	TraesCS2D01G445000	chr1A	100.000	38	0	0	4963	5000	534530292	534530255	2.620000e-08	71.3
33	TraesCS2D01G445000	chr1A	100.000	38	0	0	4963	5000	548544033	548544070	2.620000e-08	71.3
34	TraesCS2D01G445000	chr6A	100.000	38	0	0	4963	5000	147454498	147454461	2.620000e-08	71.3
35	TraesCS2D01G445000	chr5B	100.000	38	0	0	4963	5000	465867803	465867840	2.620000e-08	71.3
36	TraesCS2D01G445000	chr5B	100.000	30	0	0	4999	5028	387906757	387906786	7.320000e-04	56.5
37	TraesCS2D01G445000	chr4A	100.000	38	0	0	4963	5000	499955913	499955876	2.620000e-08	71.3
38	TraesCS2D01G445000	chr4A	100.000	38	0	0	4963	5000	645948959	645948922	2.620000e-08	71.3
39	TraesCS2D01G445000	chr1D	93.023	43	1	1	4999	5041	329677081	329677121	1.570000e-05	62.1

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	TraesCS2D01G445000	chr2D	555928954	555934189	5235	True	9670.000000	9670	100.0000	1	5236	1	chr2D.!!$R2	5235
1	TraesCS2D01G445000	chr2D	555916061	555916847	786	True	675.000000	675	82.6800	976	1740	1	chr2D.!!$R1	764
2	TraesCS2D01G445000	chr2D	154608562	154609213	651	False	470.000000	470	80.3300	1098	1740	1	chr2D.!!$F1	642
3	TraesCS2D01G445000	chr2B	662793474	662798420	4946	True	7962.000000	7962	95.7170	4	4962	1	chr2B.!!$R2	4958
4	TraesCS2D01G445000	chr2B	662687611	662688397	786	True	680.000000	680	82.8280	976	1740	1	chr2B.!!$R1	764
5	TraesCS2D01G445000	chr2A	695344513	695352387	7874	True	2415.333333	3380	92.9370	1	4962	3	chr2A.!!$R4	4961
6	TraesCS2D01G445000	chr2A	146349734	146350514	780	True	269.000000	316	80.0455	1098	1740	2	chr2A.!!$R3	642

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
392	413	0.106167	TCCCACTGCTACCTCGCTAT	60.106	55.0	0.00	0.00	0.00	2.97	F
526	548	0.391661	CCATGGACACCCGTTCTCTG	60.392	60.0	5.56	0.00	34.29	3.35	F
1925	2122	0.253160	TACTGGGGCTCCATGGAGTT	60.253	55.0	36.32	19.13	43.11	3.01	F
1930	2127	0.694444	GGGCTCCATGGAGTTAGGGA	60.694	60.0	36.32	4.47	43.70	4.20	F
3006	3421	1.039068	CACACCTGGTTTTGATGCCA	58.961	50.0	0.00	0.00	0.00	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1925	2122	3.513515	GCATTTGAAACCATGGTTCCCTA	59.486	43.478	29.91	17.89	37.35	3.53	R
1930	2127	3.834489	TGTGCATTTGAAACCATGGTT	57.166	38.095	24.86	24.86	40.45	3.67	R
3008	3423	1.135527	CCAGGTTCGCTCGGTACATAA	59.864	52.381	0.00	0.00	0.00	1.90	R
3010	3425	1.255667	ACCAGGTTCGCTCGGTACAT	61.256	55.000	0.00	0.00	0.00	2.29	R
4667	7815	0.823769	GGGGGTGCTAGCAATTAGGC	60.824	60.000	21.29	5.51	0.00	3.93	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
43	44	5.010314	TCCGACTATACACATGGTTCCATAC	59.990	44.000	3.88	0.00	0.00	2.39
44	45	5.010719	CCGACTATACACATGGTTCCATACT	59.989	44.000	3.88	0.00	0.00	2.12
45	46	6.150318	CGACTATACACATGGTTCCATACTC	58.850	44.000	3.88	0.00	0.00	2.59
46	47	6.420913	ACTATACACATGGTTCCATACTCC	57.579	41.667	3.88	0.00	0.00	3.85
47	48	5.903010	ACTATACACATGGTTCCATACTCCA	59.097	40.000	3.88	0.00	35.64	3.86
48	49	5.912149	ATACACATGGTTCCATACTCCAT	57.088	39.130	3.88	0.00	41.88	3.41
49	50	7.733047	ACTATACACATGGTTCCATACTCCATA	59.267	37.037	3.88	0.00	39.57	2.74
82	83	3.191669	TCCGTTGCGATTCGTATTCAAT	58.808	40.909	8.03	0.00	0.00	2.57
283	304	3.260483	CTGCACGAGATGGCGCTC	61.260	66.667	7.64	0.00	33.86	5.03
284	305	4.819761	TGCACGAGATGGCGCTCC	62.820	66.667	7.64	0.00	33.86	4.70
392	413	0.106167	TCCCACTGCTACCTCGCTAT	60.106	55.000	0.00	0.00	0.00	2.97
393	414	1.144298	TCCCACTGCTACCTCGCTATA	59.856	52.381	0.00	0.00	0.00	1.31
526	548	0.391661	CCATGGACACCCGTTCTCTG	60.392	60.000	5.56	0.00	34.29	3.35
730	752	6.705381	TCACCTTTAGAATGCAAAAACAATGG	59.295	34.615	0.00	0.00	0.00	3.16
848	870	2.303311	AGAGGGAGTACTTTGTTCTGCC	59.697	50.000	0.00	6.75	40.54	4.85
870	892	7.051623	TGCCAGACTTAAACTGAAGAAAGTTA	58.948	34.615	9.88	0.00	39.48	2.24
887	909	1.843753	GTTATATGCCAAAACACGCGC	59.156	47.619	5.73	0.00	0.00	6.86
923	946	4.789012	TGAATGCAGATTGGTTTTCTCC	57.211	40.909	0.00	0.00	0.00	3.71
938	961	7.004086	TGGTTTTCTCCAAACTAGATGAATGT	58.996	34.615	0.00	0.00	43.95	2.71
939	962	7.040478	TGGTTTTCTCCAAACTAGATGAATGTG	60.040	37.037	0.00	0.00	43.95	3.21
1296	1358	6.934083	GTGTTGATGATTACCCAACCAAATTT	59.066	34.615	0.00	0.00	39.36	1.82
1527	1589	6.624423	CGCTCTCTCATTTTGGTTTTGATGAT	60.624	38.462	0.00	0.00	0.00	2.45
1617	1809	5.047731	TCTGTCTGTAGAGGATGTTGTTCAG	60.048	44.000	0.00	0.00	0.00	3.02
1883	2080	6.784969	ACAGTAAGGGAGAGTGCTAATGATAT	59.215	38.462	0.00	0.00	0.00	1.63
1886	2083	9.554053	AGTAAGGGAGAGTGCTAATGATATTAT	57.446	33.333	0.00	0.00	0.00	1.28

Showing 1 to 25 of 200 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	4.761227	TGGTGTGTCTAGTAATGTACACGA	59.239	41.667	0.00	0.00	44.03	4.35
464	486	4.148891	GTTCGTAATTTCCAGTTTGCGAG	58.851	43.478	0.00	0.00	40.19	5.03
526	548	4.142138	ACTCCGAATCACAATCTACAGACC	60.142	45.833	0.00	0.00	0.00	3.85
730	752	4.025563	GCGGTTTTGTTTTACCAATTCCAC	60.026	41.667	0.00	0.00	33.94	4.02
870	892	1.138671	GGCGCGTGTTTTGGCATAT	59.861	52.632	8.43	0.00	0.00	1.78
923	946	4.152223	TGTCGTGCACATTCATCTAGTTTG	59.848	41.667	18.64	0.00	0.00	2.93
938	961	6.312399	AGATTTGAAATTTACTGTCGTGCA	57.688	33.333	0.00	0.00	0.00	4.57
939	962	5.795441	GGAGATTTGAAATTTACTGTCGTGC	59.205	40.000	0.00	0.00	0.00	5.34
1461	1523	4.892934	TGCACCCACTCAAAAATAACTTCT	59.107	37.500	0.00	0.00	0.00	2.85
1527	1589	7.606135	TTCAGAATCCCGTATTACTATTCCA	57.394	36.000	0.00	0.00	0.00	3.53
1802	1997	4.144297	AGAGCTGGAGTTGCAAAATAACA	58.856	39.130	0.00	0.00	0.00	2.41
1925	2122	3.513515	GCATTTGAAACCATGGTTCCCTA	59.486	43.478	29.91	17.89	37.35	3.53
1930	2127	3.834489	TGTGCATTTGAAACCATGGTT	57.166	38.095	24.86	24.86	40.45	3.67
1986	2183	4.849813	GGTATATAACCCGGGGCTAAAT	57.150	45.455	27.92	13.73	43.16	1.40
2543	2954	6.767524	AAATAATGACGGCATGGAAGTTTA	57.232	33.333	3.39	0.00	34.26	2.01
2974	3389	4.494091	CCAGGTGTGGTCAAGAATAGAT	57.506	45.455	0.00	0.00	39.30	1.98
2991	3406	5.088680	ACATAAATGGCATCAAAACCAGG	57.911	39.130	0.00	0.00	39.88	4.45
2992	3407	6.042143	GGTACATAAATGGCATCAAAACCAG	58.958	40.000	0.00	0.00	39.88	4.00
3006	3421	3.454375	CAGGTTCGCTCGGTACATAAAT	58.546	45.455	0.00	0.00	0.00	1.40
3008	3423	1.135527	CCAGGTTCGCTCGGTACATAA	59.864	52.381	0.00	0.00	0.00	1.90
3010	3425	1.255667	ACCAGGTTCGCTCGGTACAT	61.256	55.000	0.00	0.00	0.00	2.29
3019	3434	1.949257	CACTTTGGACCAGGTTCGC	59.051	57.895	0.00	0.00	0.00	4.70
3147	3562	6.238211	GCAGCAAATAGAGTGATCGTGTAATT	60.238	38.462	0.00	0.00	0.00	1.40
3154	3569	2.799412	GAGGCAGCAAATAGAGTGATCG	59.201	50.000	0.00	0.00	0.00	3.69
3216	3631	7.710907	AGAGTTATATTTGTTCTAGAATGCGCA	59.289	33.333	14.96	14.96	0.00	6.09

Showing 1 to 25 of 182 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.