AutoCloner

Multiple sequence alignment - TraesCS4D01G304300

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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	TraesCS4D01G304300	chr4D	100.000	4822	0	0	1	4822	472523599	472518778	0.000000e+00	8905.0
1	TraesCS4D01G304300	chr4D	99.345	763	5	0	1	763	40571476	40570714	0.000000e+00	1382.0
2	TraesCS4D01G304300	chr4D	97.619	210	3	1	557	764	472528900	472529109	4.590000e-95	359.0
3	TraesCS4D01G304300	chr4D	97.115	208	5	1	557	763	40576777	40576984	2.760000e-92	350.0
4	TraesCS4D01G304300	chr7D	93.333	3855	134	40	806	4595	78505142	78501346	0.000000e+00	5581.0
5	TraesCS4D01G304300	chr7D	89.367	442	38	6	4387	4821	511194450	511194011	9.120000e-152	547.0
6	TraesCS4D01G304300	chr7D	90.708	226	16	4	4598	4821	78501112	78500890	3.650000e-76	296.0
7	TraesCS4D01G304300	chr7D	91.045	134	10	1	4185	4316	407792828	407792695	3.830000e-41	180.0
8	TraesCS4D01G304300	chr7D	97.959	49	1	0	764	812	78505209	78505161	8.600000e-13	86.1
9	TraesCS4D01G304300	chr4A	91.513	4112	193	74	809	4821	679277391	679273337	0.000000e+00	5517.0
10	TraesCS4D01G304300	chr4B	92.706	3455	151	49	805	4198	594875839	594872425	0.000000e+00	4891.0
11	TraesCS4D01G304300	chr4B	93.792	596	22	8	4236	4821	594872422	594871832	0.000000e+00	881.0
12	TraesCS4D01G304300	chr4B	97.297	37	1	0	776	812	594875921	594875885	4.030000e-06	63.9
13	TraesCS4D01G304300	chr2D	98.427	763	12	0	1	763	11238084	11237322	0.000000e+00	1343.0
14	TraesCS4D01G304300	chr2D	94.836	213	9	2	553	764	11243359	11243570	1.000000e-86	331.0
15	TraesCS4D01G304300	chr2D	93.182	132	9	0	4185	4316	538390887	538391018	1.370000e-45	195.0
16	TraesCS4D01G304300	chr2D	87.097	124	14	2	997	1119	406959626	406959504	6.510000e-29	139.0
17	TraesCS4D01G304300	chr2B	89.651	918	59	20	859	1762	70753542	70754437	0.000000e+00	1136.0
18	TraesCS4D01G304300	chr2B	86.290	124	15	2	997	1119	482740236	482740114	3.030000e-27	134.0
19	TraesCS4D01G304300	chr3D	89.842	443	35	7	4387	4821	581945332	581944892	1.170000e-155	560.0
20	TraesCS4D01G304300	chr3D	93.182	132	9	0	4185	4316	464061401	464061270	1.370000e-45	195.0
21	TraesCS4D01G304300	chr5B	85.445	584	27	14	213	761	114931711	114931151	5.450000e-154	555.0
22	TraesCS4D01G304300	chr5B	95.327	214	9	1	1	214	114944977	114944765	5.980000e-89	339.0
23	TraesCS4D01G304300	chr5B	92.424	132	10	0	4185	4316	434924098	434923967	6.370000e-44	189.0
24	TraesCS4D01G304300	chr7A	76.402	767	135	29	10	763	669700734	669700001	5.890000e-99	372.0
25	TraesCS4D01G304300	chrUn	93.182	132	9	0	4185	4316	477284097	477284228	1.370000e-45	195.0
26	TraesCS4D01G304300	chrUn	84.762	105	13	2	2391	2495	121743434	121743333	8.540000e-18	102.0
27	TraesCS4D01G304300	chr5D	93.182	132	9	0	4185	4316	367592008	367591877	1.370000e-45	195.0
28	TraesCS4D01G304300	chr5D	83.553	152	21	2	2344	2495	190271502	190271355	6.510000e-29	139.0
29	TraesCS4D01G304300	chr5D	90.000	60	6	0	2289	2348	190271580	190271521	1.440000e-10	78.7
30	TraesCS4D01G304300	chr2A	86.290	124	15	2	997	1119	574980457	574980335	3.030000e-27	134.0
31	TraesCS4D01G304300	chr5A	81.818	154	20	5	2344	2495	229524116	229524263	6.550000e-24	122.0
32	TraesCS4D01G304300	chr5A	89.394	66	7	0	2283	2348	229524032	229524097	3.090000e-12	84.2

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	TraesCS4D01G304300	chr4D	472518778	472523599	4821	True	8905.0	8905	100.000000	1	4822	1	chr4D.!!$R2	4821
1	TraesCS4D01G304300	chr4D	40570714	40571476	762	True	1382.0	1382	99.345000	1	763	1	chr4D.!!$R1	762
2	TraesCS4D01G304300	chr7D	78500890	78505209	4319	True	1987.7	5581	94.000000	764	4821	3	chr7D.!!$R3	4057
3	TraesCS4D01G304300	chr4A	679273337	679277391	4054	True	5517.0	5517	91.513000	809	4821	1	chr4A.!!$R1	4012
4	TraesCS4D01G304300	chr4B	594871832	594875921	4089	True	1945.3	4891	94.598333	776	4821	3	chr4B.!!$R1	4045
5	TraesCS4D01G304300	chr2D	11237322	11238084	762	True	1343.0	1343	98.427000	1	763	1	chr2D.!!$R1	762
6	TraesCS4D01G304300	chr2B	70753542	70754437	895	False	1136.0	1136	89.651000	859	1762	1	chr2B.!!$F1	903
7	TraesCS4D01G304300	chr5B	114931151	114931711	560	True	555.0	555	85.445000	213	761	1	chr5B.!!$R1	548
8	TraesCS4D01G304300	chr7A	669700001	669700734	733	True	372.0	372	76.402000	10	763	1	chr7A.!!$R1	753

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
910	1014	0.175073	CCCAAGTCGGTACTACTGGC	59.825	60.0	2.76	0.0	33.52	4.85	F
2064	2245	0.250901	GTGGAGCAAGCCCAGAAAGA	60.251	55.0	3.03	0.0	33.75	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2332	2515	1.268899	GCAATGTGATCCAGCATAGCC	59.731	52.381	0.0	0.0	0.0	3.93	R
4035	4259	2.099098	ACGGAAAACAACAGCAAGAAGG	59.901	45.455	0.0	0.0	0.0	3.46	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
406	408	1.476891	AGTTGATATGTCGTCGCCACT	59.523	47.619	0.00	0.00	0.00	4.00
745	785	1.131928	AACCCACCAGTACCAGGACC	61.132	60.000	8.83	0.00	0.00	4.46
774	814	2.410322	ATTCACTCCCACCAGCGCAA	62.410	55.000	11.47	0.00	0.00	4.85
905	1009	1.683943	CGATCCCCAAGTCGGTACTA	58.316	55.000	0.00	0.00	33.75	1.82
906	1010	1.336125	CGATCCCCAAGTCGGTACTAC	59.664	57.143	0.00	0.00	33.75	2.73
907	1011	2.664015	GATCCCCAAGTCGGTACTACT	58.336	52.381	0.00	0.00	35.21	2.57
908	1012	1.843368	TCCCCAAGTCGGTACTACTG	58.157	55.000	2.76	0.00	33.52	2.74
909	1013	0.822164	CCCCAAGTCGGTACTACTGG	59.178	60.000	2.76	6.39	33.52	4.00
910	1014	0.175073	CCCAAGTCGGTACTACTGGC	59.825	60.000	2.76	0.00	33.52	4.85
1433	1564	3.265791	AGATGCTGTTCCTGTTTCGATC	58.734	45.455	0.00	0.00	0.00	3.69
1444	1592	3.120199	CCTGTTTCGATCATGTGTGTTCC	60.120	47.826	0.00	0.00	0.00	3.62
1478	1626	6.380111	CGAGAGGTTGCATTTTTAATGTTG	57.620	37.500	0.00	0.00	0.00	3.33
1533	1681	1.845809	GATTCCGCATGGACCGATGC	61.846	60.000	15.13	15.13	46.45	3.91
1611	1759	7.323052	AGGGAGAGGATAATATGTTTTCTCC	57.677	40.000	8.71	8.71	45.33	3.71
1662	1810	9.643693	ATTGGCTAAATTGTTTTGTGATTCTAG	57.356	29.630	0.00	0.00	0.00	2.43
1837	1996	4.142293	GCCTCAGTTTCCTTCATTTCCATC	60.142	45.833	0.00	0.00	0.00	3.51
1843	2002	3.726557	TCCTTCATTTCCATCTGCTGT	57.273	42.857	0.00	0.00	0.00	4.40
1863	2022	5.911280	GCTGTGTCATATACAAATCACATGC	59.089	40.000	0.00	0.00	40.63	4.06
1892	2055	6.874134	ACATATTATATCTGAACCGCCACTTC	59.126	38.462	0.00	0.00	0.00	3.01
1898	2062	0.948623	TGAACCGCCACTTCATCACG	60.949	55.000	0.00	0.00	0.00	4.35
1907	2071	2.963101	CCACTTCATCACGTATCCCCTA	59.037	50.000	0.00	0.00	0.00	3.53
1976	2154	3.366476	GGCCTATAGTGTGATGCGTAGAG	60.366	52.174	0.00	0.00	0.00	2.43
1986	2164	0.461961	ATGCGTAGAGGAAGTCAGCC	59.538	55.000	0.00	0.00	0.00	4.85
2060	2241	2.116983	GACTGTGGAGCAAGCCCAGA	62.117	60.000	12.31	1.91	33.75	3.86
2062	2243	0.538057	CTGTGGAGCAAGCCCAGAAA	60.538	55.000	3.03	0.00	33.75	2.52
2063	2244	0.538057	TGTGGAGCAAGCCCAGAAAG	60.538	55.000	3.03	0.00	33.75	2.62
2064	2245	0.250901	GTGGAGCAAGCCCAGAAAGA	60.251	55.000	3.03	0.00	33.75	2.52
2065	2246	0.478072	TGGAGCAAGCCCAGAAAGAA	59.522	50.000	0.00	0.00	0.00	2.52
2066	2247	1.172175	GGAGCAAGCCCAGAAAGAAG	58.828	55.000	0.00	0.00	0.00	2.85
2068	2249	1.809547	GAGCAAGCCCAGAAAGAAGTC	59.190	52.381	0.00	0.00	0.00	3.01
2069	2250	1.423161	AGCAAGCCCAGAAAGAAGTCT	59.577	47.619	0.00	0.00	0.00	3.24
2072	2253	3.551659	GCAAGCCCAGAAAGAAGTCTTTG	60.552	47.826	10.95	0.00	45.37	2.77
2294	2477	3.046374	GGTAGGGCCTTTTATCTGGAGA	58.954	50.000	13.45	0.00	0.00	3.71
2299	2482	3.458487	GGGCCTTTTATCTGGAGACCTTA	59.542	47.826	0.84	0.00	0.00	2.69
2419	2634	5.408604	TCAGAAGAAGAAAACAGGCGTTATC	59.591	40.000	0.00	0.00	33.99	1.75
3300	3517	5.927689	GTCACAGGCATTCATTTTCATTTCA	59.072	36.000	0.00	0.00	0.00	2.69
3301	3518	6.090358	GTCACAGGCATTCATTTTCATTTCAG	59.910	38.462	0.00	0.00	0.00	3.02
3575	3792	4.713553	TGGAGCTTAAACTCATGAACACA	58.286	39.130	8.10	0.00	38.50	3.72
3830	4047	2.299326	AAACAAGCTGATGCCTTCCT	57.701	45.000	0.00	0.00	40.80	3.36
4315	4552	2.290896	TGATTTGGGAGCTTGTTCCGAT	60.291	45.455	0.00	0.00	38.17	4.18
4329	4566	0.752009	TCCGATCGTGCTAAGCTCCT	60.752	55.000	15.09	0.00	0.00	3.69
4334	4572	2.831685	TCGTGCTAAGCTCCTGAAAA	57.168	45.000	0.00	0.00	0.00	2.29
4336	4574	3.674997	TCGTGCTAAGCTCCTGAAAATT	58.325	40.909	0.00	0.00	0.00	1.82
4337	4575	3.436704	TCGTGCTAAGCTCCTGAAAATTG	59.563	43.478	0.00	0.00	0.00	2.32
4514	4755	1.202222	GCTGATTCTGCATTTCGTGGG	60.202	52.381	10.32	0.00	0.00	4.61
4525	4766	2.754946	TTTCGTGGGTGTGTCTATCC	57.245	50.000	0.00	0.00	0.00	2.59
4615	5087	7.336931	AGTTACCACTACAGGCAAGATATTTTG	59.663	37.037	1.63	1.63	0.00	2.44
4701	5180	5.626543	CGACAACAGTTACGTACAATACACT	59.373	40.000	0.00	0.00	0.00	3.55
4782	5261	2.159653	CGACTGGCATAGCAAAGTGAAC	60.160	50.000	0.00	0.00	29.41	3.18
4792	5271	4.675029	AAGTGAACCGTCCGGCCG	62.675	66.667	21.04	21.04	39.32	6.13
4814	5293	3.793559	CATAGGTTAACGGGAACAGAGG	58.206	50.000	0.00	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
406	408	1.379977	AAGGAGGCGATCGGAGACA	60.380	57.895	18.30	0.00	42.51	3.41
1125	1236	1.645402	ATCTCGGATTTGGGGTGGGG	61.645	60.000	0.00	0.00	0.00	4.96
1129	1240	0.464452	GACGATCTCGGATTTGGGGT	59.536	55.000	4.44	0.00	44.95	4.95
1203	1321	4.346129	GCATTGAACAGGACGAATCAATC	58.654	43.478	0.00	0.00	39.74	2.67
1433	1564	4.111916	GGTTCAAAGTTGGAACACACATG	58.888	43.478	21.91	0.00	44.96	3.21
1478	1626	3.650281	ATCCCCCATTGCCAAAATTTC	57.350	42.857	0.00	0.00	0.00	2.17
1524	1672	0.165944	CAAAACTCACGCATCGGTCC	59.834	55.000	0.00	0.00	0.00	4.46
1528	1676	1.154225	GGGCAAAACTCACGCATCG	60.154	57.895	0.00	0.00	0.00	3.84
1533	1681	5.123186	TCAATTATACAGGGCAAAACTCACG	59.877	40.000	0.00	0.00	0.00	4.35
1611	1759	8.138928	TCCCATGAGGAGTACAGATATAAATG	57.861	38.462	0.00	0.00	40.93	2.32
1662	1810	2.031682	CACAGAAGTAAAGTGCCTGCAC	60.032	50.000	14.25	14.25	46.50	4.57
1837	1996	6.667007	TGTGATTTGTATATGACACAGCAG	57.333	37.500	0.00	0.00	34.93	4.24
1843	2002	8.302438	TGTTTTGCATGTGATTTGTATATGACA	58.698	29.630	0.00	0.00	35.78	3.58
1863	2022	7.803189	GTGGCGGTTCAGATATAATATGTTTTG	59.197	37.037	0.00	0.00	0.00	2.44
1892	2055	6.371548	CCATGTTATTTAGGGGATACGTGATG	59.628	42.308	0.00	0.00	37.60	3.07
1907	2071	5.842339	ACCAGAGGAAATCCCATGTTATTT	58.158	37.500	0.00	2.97	37.41	1.40
1948	2112	3.553922	GCATCACACTATAGGCCTCTGAC	60.554	52.174	9.68	0.00	0.00	3.51
1976	2154	4.781280	AGACTGCCAAAGGCTGACTTCC	62.781	54.545	19.71	5.36	45.40	3.46
1986	2164	2.355818	GGGGGTTACTAGACTGCCAAAG	60.356	54.545	0.00	0.00	0.00	2.77
2332	2515	1.268899	GCAATGTGATCCAGCATAGCC	59.731	52.381	0.00	0.00	0.00	3.93
2511	2726	7.864307	AAGACGACATAACACACTAGTAAAC	57.136	36.000	0.00	0.00	0.00	2.01
3272	3489	6.587206	TGAAAATGAATGCCTGTGACATAA	57.413	33.333	0.00	0.00	0.00	1.90
3575	3792	2.307768	TCCAAGTCTGAGTTGTCGACT	58.692	47.619	20.53	0.00	42.70	4.18
3830	4047	3.113322	GTTGCTAATCACGAGATACGCA	58.887	45.455	12.55	12.55	46.94	5.24
4035	4259	2.099098	ACGGAAAACAACAGCAAGAAGG	59.901	45.455	0.00	0.00	0.00	3.46
4219	4454	6.550121	TTGTTCGCGAATTAGCAAACAGCA	62.550	41.667	26.23	10.46	43.67	4.41
4315	4552	2.831685	TTTTCAGGAGCTTAGCACGA	57.168	45.000	7.07	0.00	0.00	4.35
4336	4574	5.759059	ACATATCTGAATTTGGCTTCTCCA	58.241	37.500	0.00	0.00	44.85	3.86
4337	4575	6.767902	TGTACATATCTGAATTTGGCTTCTCC	59.232	38.462	0.00	0.00	0.00	3.71
4478	4719	1.949525	TCAGCTTTGTTGCTTCCTCAC	59.050	47.619	0.00	0.00	41.98	3.51
4514	4755	0.108615	AGCTGCACGGATAGACACAC	60.109	55.000	1.02	0.00	0.00	3.82
4615	5087	0.381801	CGTGCATATGGTTTCTGGGC	59.618	55.000	4.56	0.00	0.00	5.36
4701	5180	4.968719	TCAGCTAGAATGTTCTATTCCCCA	59.031	41.667	3.15	0.00	38.95	4.96
4792	5271	3.195661	CTCTGTTCCCGTTAACCTATGC	58.804	50.000	0.00	0.00	0.00	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.