AutoCloner

Multiple sequence alignment - TraesCS7D01G186400

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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	TraesCS7D01G186400	chr7D	100.000	3830	0	0	1	3830	139086833	139090662	0.000000e+00	7073.0
1	TraesCS7D01G186400	chr7B	92.490	2996	166	24	838	3830	104468509	104471448	0.000000e+00	4231.0
2	TraesCS7D01G186400	chr7B	89.932	1172	66	26	778	1921	104251997	104253144	0.000000e+00	1463.0
3	TraesCS7D01G186400	chr7B	89.694	980	72	15	1974	2944	104253312	104254271	0.000000e+00	1223.0
4	TraesCS7D01G186400	chr7B	80.989	789	76	39	1163	1933	104299931	104300663	3.340000e-155	558.0
5	TraesCS7D01G186400	chr7B	85.814	430	29	5	25	453	104248672	104249070	9.830000e-116	427.0
6	TraesCS7D01G186400	chr7B	83.900	441	38	13	2552	2986	104301302	104301715	1.290000e-104	390.0
7	TraesCS7D01G186400	chr7B	92.245	245	11	3	3335	3579	104302266	104302502	1.320000e-89	340.0
8	TraesCS7D01G186400	chr7B	80.619	485	42	28	851	1307	104248105	104248565	1.030000e-85	327.0
9	TraesCS7D01G186400	chr7B	82.353	323	36	14	462	780	104251991	104251686	1.060000e-65	261.0
10	TraesCS7D01G186400	chr7B	92.135	178	12	2	2170	2347	104300942	104301117	2.280000e-62	250.0
11	TraesCS7D01G186400	chr7B	94.891	137	7	0	3692	3828	104305438	104305574	8.330000e-52	215.0
12	TraesCS7D01G186400	chr7B	93.151	146	7	1	1974	2119	104300784	104300926	1.080000e-50	211.0
13	TraesCS7D01G186400	chr7B	83.333	198	32	1	2	199	678676120	678676316	8.450000e-42	182.0
14	TraesCS7D01G186400	chr7B	90.152	132	12	1	3564	3694	104304604	104304735	1.830000e-38	171.0
15	TraesCS7D01G186400	chr7A	96.137	1579	39	8	779	2355	139108740	139110298	0.000000e+00	2558.0
16	TraesCS7D01G186400	chr7A	96.781	1491	35	4	2348	3828	139123443	139124930	0.000000e+00	2475.0
17	TraesCS7D01G186400	chr7A	93.734	782	30	5	1	780	139107853	139108617	0.000000e+00	1155.0
18	TraesCS7D01G186400	chr7A	86.280	984	78	21	1404	2347	139103724	139104690	0.000000e+00	1016.0
19	TraesCS7D01G186400	chr7A	78.845	1281	153	39	2552	3828	139104875	139106041	0.000000e+00	756.0
20	TraesCS7D01G186400	chr7A	87.755	392	24	8	1	380	138985724	138986103	1.630000e-118	436.0
21	TraesCS7D01G186400	chr7A	91.061	179	16	0	1163	1341	139103471	139103649	3.820000e-60	243.0
22	TraesCS7D01G186400	chr3D	79.274	1240	180	52	1163	2365	313893452	313894651	0.000000e+00	795.0
23	TraesCS7D01G186400	chr3B	79.538	650	96	23	1736	2365	405659588	405658956	2.730000e-116	429.0
24	TraesCS7D01G186400	chr3B	83.051	472	65	12	1166	1633	405660212	405659752	7.660000e-112	414.0
25	TraesCS7D01G186400	chr3B	84.706	170	25	1	8	176	668891195	668891364	6.580000e-38	169.0
26	TraesCS7D01G186400	chr3B	86.813	91	9	3	16	104	8079167	8079256	8.760000e-17	99.0
27	TraesCS7D01G186400	chr3B	88.889	54	6	0	123	176	8079258	8079311	2.470000e-07	67.6
28	TraesCS7D01G186400	chr3A	79.300	657	94	26	1736	2365	416449624	416450265	4.570000e-114	422.0
29	TraesCS7D01G186400	chr3A	82.231	484	65	14	1163	1633	416449005	416449480	7.710000e-107	398.0
30	TraesCS7D01G186400	chr3A	91.525	59	5	0	118	176	13528395	13528337	8.820000e-12	82.4
31	TraesCS7D01G186400	chr4A	85.714	70	7	3	729	796	669245365	669245433	1.910000e-08	71.3

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	TraesCS7D01G186400	chr7D	139086833	139090662	3829	False	7073.0	7073	100.000000	1	3830	1	chr7D.!!$F1	3829
1	TraesCS7D01G186400	chr7B	104468509	104471448	2939	False	4231.0	4231	92.490000	838	3830	1	chr7B.!!$F1	2992
2	TraesCS7D01G186400	chr7B	104248105	104254271	6166	False	860.0	1463	86.514750	25	2944	4	chr7B.!!$F3	2919
3	TraesCS7D01G186400	chr7B	104299931	104305574	5643	False	305.0	558	89.637571	1163	3828	7	chr7B.!!$F4	2665
4	TraesCS7D01G186400	chr7A	139123443	139124930	1487	False	2475.0	2475	96.781000	2348	3828	1	chr7A.!!$F2	1480
5	TraesCS7D01G186400	chr7A	139103471	139110298	6827	False	1145.6	2558	89.211400	1	3828	5	chr7A.!!$F3	3827
6	TraesCS7D01G186400	chr3D	313893452	313894651	1199	False	795.0	795	79.274000	1163	2365	1	chr3D.!!$F1	1202
7	TraesCS7D01G186400	chr3B	405658956	405660212	1256	True	421.5	429	81.294500	1166	2365	2	chr3B.!!$R1	1199
8	TraesCS7D01G186400	chr3A	416449005	416450265	1260	False	410.0	422	80.765500	1163	2365	2	chr3A.!!$F1	1202

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
912	8367	0.245813	TCACTGCTCACTGCTGCTAG	59.754	55.0	0.00	0.0	43.25	3.42	F
1038	8499	0.608856	CACTGCCACTGCCATTGGTA	60.609	55.0	4.26	0.0	36.40	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2425	10189	3.057033	ACCAGAATGCATGCAAGAAAGAC	60.057	43.478	26.68	10.64	31.97	3.01	R
3000	11077	1.730064	TCTCGGTCTTTTGTTATGCGC	59.270	47.619	0.00	0.00	0.00	6.09	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
77	4787	6.421801	GCATTTGGTATTGAAACTCATATGCC	59.578	38.462	0.00	0.00	37.06	4.40
78	4788	7.490840	CATTTGGTATTGAAACTCATATGCCA	58.509	34.615	0.00	0.00	32.58	4.92
106	4816	7.649533	ATTTGATTTGATAGTGAAGCATCCA	57.350	32.000	0.00	0.00	0.00	3.41
156	4866	6.753279	AGTGATTTGGTAATTGAAATGCATCG	59.247	34.615	0.00	0.00	0.00	3.84
176	4886	9.982291	TGCATCGAATAACTAAGTTATTGAAAC	57.018	29.630	0.00	0.00	45.16	2.78
177	4887	9.982291	GCATCGAATAACTAAGTTATTGAAACA	57.018	29.630	0.00	0.00	45.16	2.83
221	4932	4.393371	TGAAATTCAACACACGAGTTGTCA	59.607	37.500	15.64	11.04	46.78	3.58
277	5002	2.429930	TGGCTTTGGGTCAGACGG	59.570	61.111	0.00	0.00	0.00	4.79
278	5003	2.359975	GGCTTTGGGTCAGACGGG	60.360	66.667	0.00	0.00	0.00	5.28
279	5004	2.747686	GCTTTGGGTCAGACGGGA	59.252	61.111	0.00	0.00	0.00	5.14
280	5005	1.671379	GCTTTGGGTCAGACGGGAC	60.671	63.158	0.00	0.00	37.06	4.46
281	5006	1.752198	CTTTGGGTCAGACGGGACA	59.248	57.895	6.50	0.00	39.59	4.02
282	5007	0.602905	CTTTGGGTCAGACGGGACAC	60.603	60.000	6.50	3.45	41.65	3.67
283	5008	2.372040	TTTGGGTCAGACGGGACACG	62.372	60.000	0.00	0.00	44.26	4.49
601	5461	8.414629	AGATATGAAAAAGGAAAGGATATGGC	57.585	34.615	0.00	0.00	0.00	4.40
627	5487	5.772825	CAAAAGTGGATTGTTTCCTCTCA	57.227	39.130	0.00	0.00	45.53	3.27
912	8367	0.245813	TCACTGCTCACTGCTGCTAG	59.754	55.000	0.00	0.00	43.25	3.42
1014	8469	2.440247	GCCATGGAGGAAACCCCG	60.440	66.667	18.40	0.00	41.22	5.73
1022	8483	4.660938	GGAAACCCCGCTGCCACT	62.661	66.667	0.00	0.00	0.00	4.00
1023	8484	3.365265	GAAACCCCGCTGCCACTG	61.365	66.667	0.00	0.00	0.00	3.66
1032	8493	4.960866	CTGCCACTGCCACTGCCA	62.961	66.667	0.00	0.00	36.33	4.92
1033	8494	4.289101	TGCCACTGCCACTGCCAT	62.289	61.111	0.00	0.00	36.33	4.40
1038	8499	0.608856	CACTGCCACTGCCATTGGTA	60.609	55.000	4.26	0.00	36.40	3.25
1109	8572	3.258622	CCCTCTCCACCGATTAACTATCC	59.741	52.174	0.00	0.00	0.00	2.59
1164	8637	2.161486	CAACGACGAGGCTAGCAGC	61.161	63.158	18.24	6.52	41.46	5.25
1334	8807	4.379243	ACGCTCCTCGGCAAGGTG	62.379	66.667	4.46	3.62	46.32	4.00
1445	8943	4.341783	GAGCAGGTGCAGGTGGCT	62.342	66.667	4.48	2.11	45.15	4.75
2156	9895	5.294306	CAGCAGTCAGTTCTTTTCAGTTACA	59.706	40.000	0.00	0.00	0.00	2.41
2415	10179	7.388776	TCATAATTCTCATAGAAGGCGGAAATG	59.611	37.037	0.00	0.00	37.69	2.32
2425	10189	0.305922	GGCGGAAATGCTCAAGATCG	59.694	55.000	0.00	0.00	34.52	3.69
3000	11077	5.967674	GGAATCATGTAAATTTCTGTCTGCG	59.032	40.000	0.00	0.00	0.00	5.18
3001	11078	4.340894	TCATGTAAATTTCTGTCTGCGC	57.659	40.909	0.00	0.00	0.00	6.09
3536	11622	8.589335	TCTCTTCATAACTGAACTTACACAAC	57.411	34.615	0.00	0.00	36.46	3.32
3543	11629	2.476619	CTGAACTTACACAACAGCGGAG	59.523	50.000	0.00	0.00	0.00	4.63
3574	13776	1.374947	GCAGTAGCCCTGGTGACAA	59.625	57.895	3.43	0.00	41.81	3.18
3581	13783	0.181350	GCCCTGGTGACAAGGGATAG	59.819	60.000	29.43	2.14	46.03	2.08
3595	13797	5.192927	CAAGGGATAGGCTTACAATTGACA	58.807	41.667	13.59	0.00	0.00	3.58
3606	13808	3.110447	ACAATTGACAACACCAATGCC	57.890	42.857	13.59	0.00	34.75	4.40
3626	13828	6.169557	TGCCGATTATGGTAGATGTTAAGT	57.830	37.500	0.00	0.00	0.00	2.24
3743	14651	4.503714	TTTCTGGACAACCAAGACTTCT	57.496	40.909	0.00	0.00	46.32	2.85
3751	14659	4.455606	ACAACCAAGACTTCTGAGAAAGG	58.544	43.478	0.00	0.00	0.00	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	8.650143	ACCACTTTCAGTACCATATTCATTTT	57.350	30.769	0.00	0.00	0.00	1.82
13	14	9.920946	ATACCACTTTCAGTACCATATTCATTT	57.079	29.630	0.00	0.00	0.00	2.32
14	15	9.342308	CATACCACTTTCAGTACCATATTCATT	57.658	33.333	0.00	0.00	0.00	2.57
15	16	7.939039	CCATACCACTTTCAGTACCATATTCAT	59.061	37.037	0.00	0.00	0.00	2.57
16	17	7.092623	ACCATACCACTTTCAGTACCATATTCA	60.093	37.037	0.00	0.00	0.00	2.57
17	18	7.280356	ACCATACCACTTTCAGTACCATATTC	58.720	38.462	0.00	0.00	0.00	1.75
19	20	6.824958	ACCATACCACTTTCAGTACCATAT	57.175	37.500	0.00	0.00	0.00	1.78
20	21	7.736881	TTACCATACCACTTTCAGTACCATA	57.263	36.000	0.00	0.00	0.00	2.74
21	22	6.630203	TTACCATACCACTTTCAGTACCAT	57.370	37.500	0.00	0.00	0.00	3.55
22	23	6.630203	ATTACCATACCACTTTCAGTACCA	57.370	37.500	0.00	0.00	0.00	3.25
23	24	9.452287	TTTAATTACCATACCACTTTCAGTACC	57.548	33.333	0.00	0.00	0.00	3.34
77	4787	8.920509	TGCTTCACTATCAAATCAAATTGATG	57.079	30.769	9.47	0.00	46.63	3.07
189	4899	8.716646	TCGTGTGTTGAATTTCATATATCACT	57.283	30.769	0.00	0.00	0.00	3.41
190	4900	8.604035	ACTCGTGTGTTGAATTTCATATATCAC	58.396	33.333	0.00	6.21	0.00	3.06
191	4901	8.716646	ACTCGTGTGTTGAATTTCATATATCA	57.283	30.769	0.00	0.00	0.00	2.15
221	4932	3.938963	CTCATGTGTTGCTTTACGGGTAT	59.061	43.478	0.00	0.00	0.00	2.73
273	4998	3.264104	TGATTTTATTCCGTGTCCCGTC	58.736	45.455	0.00	0.00	33.66	4.79
274	4999	3.337694	TGATTTTATTCCGTGTCCCGT	57.662	42.857	0.00	0.00	33.66	5.28
275	5000	3.874543	TGATGATTTTATTCCGTGTCCCG	59.125	43.478	0.00	0.00	0.00	5.14
276	5001	4.260620	CGTGATGATTTTATTCCGTGTCCC	60.261	45.833	0.00	0.00	0.00	4.46
277	5002	4.785341	GCGTGATGATTTTATTCCGTGTCC	60.785	45.833	0.00	0.00	0.00	4.02
278	5003	4.271687	GCGTGATGATTTTATTCCGTGTC	58.728	43.478	0.00	0.00	0.00	3.67
279	5004	3.242284	CGCGTGATGATTTTATTCCGTGT	60.242	43.478	0.00	0.00	0.00	4.49
280	5005	3.279950	CGCGTGATGATTTTATTCCGTG	58.720	45.455	0.00	0.00	0.00	4.94
281	5006	2.286833	CCGCGTGATGATTTTATTCCGT	59.713	45.455	4.92	0.00	0.00	4.69
282	5007	2.903678	CCGCGTGATGATTTTATTCCG	58.096	47.619	4.92	0.00	0.00	4.30
283	5008	2.604614	GGCCGCGTGATGATTTTATTCC	60.605	50.000	4.92	0.00	0.00	3.01
284	5009	2.604614	GGGCCGCGTGATGATTTTATTC	60.605	50.000	4.92	0.00	0.00	1.75
285	5010	1.336755	GGGCCGCGTGATGATTTTATT	59.663	47.619	4.92	0.00	0.00	1.40
286	5011	0.951558	GGGCCGCGTGATGATTTTAT	59.048	50.000	4.92	0.00	0.00	1.40
601	5461	3.401033	GAAACAATCCACTTTTGGGGG	57.599	47.619	0.00	0.00	45.12	5.40
626	5486	1.878953	ACTTGGGTAGTGCGAAAGTG	58.121	50.000	0.00	0.00	35.19	3.16
627	5487	2.632987	AACTTGGGTAGTGCGAAAGT	57.367	45.000	0.00	0.00	37.12	2.66
816	8253	0.533032	CTTCCTCCGTTCACTCCTCC	59.467	60.000	0.00	0.00	0.00	4.30
912	8367	3.365265	CCGGAACTTGCAGGGCAC	61.365	66.667	0.00	0.00	38.71	5.01
1022	8483	1.304052	GGTACCAATGGCAGTGGCA	60.304	57.895	31.99	22.88	43.71	4.92
1023	8484	1.000896	AGGTACCAATGGCAGTGGC	60.001	57.895	31.99	17.48	40.02	5.01
1024	8485	0.744414	CGAGGTACCAATGGCAGTGG	60.744	60.000	30.65	30.65	42.28	4.00
1025	8486	1.369091	GCGAGGTACCAATGGCAGTG	61.369	60.000	15.94	8.18	0.00	3.66
1026	8487	1.078426	GCGAGGTACCAATGGCAGT	60.078	57.895	15.94	0.00	0.00	4.40
1027	8488	2.173669	CGCGAGGTACCAATGGCAG	61.174	63.158	15.94	4.68	0.00	4.85
1028	8489	2.125310	CGCGAGGTACCAATGGCA	60.125	61.111	15.94	0.00	0.00	4.92
1029	8490	2.125269	ACGCGAGGTACCAATGGC	60.125	61.111	15.93	10.31	0.00	4.40
1030	8491	0.806102	CTGACGCGAGGTACCAATGG	60.806	60.000	15.93	0.00	0.00	3.16
1031	8492	0.806102	CCTGACGCGAGGTACCAATG	60.806	60.000	15.93	4.07	0.00	2.82
1032	8493	1.515954	CCTGACGCGAGGTACCAAT	59.484	57.895	15.93	0.00	0.00	3.16
1033	8494	2.967397	CCTGACGCGAGGTACCAA	59.033	61.111	15.93	0.00	0.00	3.67
1109	8572	1.528129	GGTGCCCAACAAGAAGAGAG	58.472	55.000	0.00	0.00	0.00	3.20
1128	8591	3.545078	CGTTGGGTCGTTAGTTAGATTCG	59.455	47.826	0.00	0.00	0.00	3.34
1164	8637	0.108138	CCGAACCCCAGCTTAGACAG	60.108	60.000	0.00	0.00	0.00	3.51
1334	8807	3.003480	GGTAAATCAGTGGACAGAGCAC	58.997	50.000	0.00	0.00	0.00	4.40
1343	8816	3.420893	TGCAAAGGAGGTAAATCAGTGG	58.579	45.455	0.00	0.00	0.00	4.00
1445	8943	0.539986	GCTGGATCCCGAACTTGGTA	59.460	55.000	9.90	0.00	0.00	3.25
2156	9895	5.819901	GTGAGAAAGATACAGCAAAGCCTAT	59.180	40.000	0.00	0.00	0.00	2.57
2425	10189	3.057033	ACCAGAATGCATGCAAGAAAGAC	60.057	43.478	26.68	10.64	31.97	3.01
3000	11077	1.730064	TCTCGGTCTTTTGTTATGCGC	59.270	47.619	0.00	0.00	0.00	6.09
3001	11078	2.993899	AGTCTCGGTCTTTTGTTATGCG	59.006	45.455	0.00	0.00	0.00	4.73
3574	13776	5.193679	GTTGTCAATTGTAAGCCTATCCCT	58.806	41.667	5.13	0.00	0.00	4.20
3581	13783	4.314740	TTGGTGTTGTCAATTGTAAGCC	57.685	40.909	5.13	8.09	0.00	4.35
3595	13797	2.733956	ACCATAATCGGCATTGGTGTT	58.266	42.857	0.00	0.00	40.87	3.32
3606	13808	5.408604	GCCCACTTAACATCTACCATAATCG	59.591	44.000	0.00	0.00	0.00	3.34
3743	14651	0.034767	CATGCTCCTGCCCTTTCTCA	60.035	55.000	0.00	0.00	38.71	3.27
3751	14659	1.147153	GGTCTACCATGCTCCTGCC	59.853	63.158	0.00	0.00	35.50	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.