AutoCloner

Multiple sequence alignment - TraesCS6D01G020200

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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	TraesCS6D01G020200	chr6D	100.000	3161	0	0	1	3161	8000063	7996903	0.000000e+00	5838.0
1	TraesCS6D01G020200	chr6D	80.428	1216	209	22	970	2172	8552828	8551629	0.000000e+00	900.0
2	TraesCS6D01G020200	chr6D	79.983	1204	210	23	977	2166	9548234	9547048	0.000000e+00	859.0
3	TraesCS6D01G020200	chr6D	82.500	120	14	5	2336	2449	8803553	8803671	7.220000e-17	99.0
4	TraesCS6D01G020200	chr6D	81.667	120	15	7	2336	2449	8817109	8817227	3.360000e-15	93.5
5	TraesCS6D01G020200	chr6A	94.197	1551	40	12	767	2311	8212735	8211229	0.000000e+00	2320.0
6	TraesCS6D01G020200	chr6A	94.610	872	20	4	2317	3161	8211131	8210260	0.000000e+00	1325.0
7	TraesCS6D01G020200	chr6A	93.952	711	35	3	13	715	8213430	8212720	0.000000e+00	1068.0
8	TraesCS6D01G020200	chr6A	88.430	847	89	4	1353	2190	8393264	8392418	0.000000e+00	1013.0
9	TraesCS6D01G020200	chr6A	89.245	781	69	7	909	1687	8398748	8397981	0.000000e+00	963.0
10	TraesCS6D01G020200	chr6A	84.137	996	144	6	1181	2174	8401936	8400953	0.000000e+00	952.0
11	TraesCS6D01G020200	chr6A	79.286	1120	195	29	1064	2166	7991359	7992458	0.000000e+00	749.0
12	TraesCS6D01G020200	chr6A	77.778	1206	242	20	994	2189	35581602	35580413	0.000000e+00	719.0
13	TraesCS6D01G020200	chr6A	84.350	754	68	14	2316	3028	8394588	8393844	0.000000e+00	693.0
14	TraesCS6D01G020200	chr6A	90.430	512	49	0	1679	2190	8395393	8394882	0.000000e+00	675.0
15	TraesCS6D01G020200	chr6A	90.690	290	20	3	2878	3160	8438947	8438658	2.300000e-101	379.0
16	TraesCS6D01G020200	chr6A	77.728	669	75	27	2501	3157	35579848	35579242	3.020000e-90	342.0
17	TraesCS6D01G020200	chr6A	90.152	264	18	2	2682	2937	8391500	8391237	1.400000e-88	337.0
18	TraesCS6D01G020200	chr6A	84.561	285	16	8	2325	2581	8392119	8391835	1.120000e-64	257.0
19	TraesCS6D01G020200	chr6A	89.510	143	12	1	2366	2508	8447611	8447472	9.010000e-41	178.0
20	TraesCS6D01G020200	chr6A	92.308	117	9	0	2191	2307	8394845	8394729	1.950000e-37	167.0
21	TraesCS6D01G020200	chr6A	88.406	138	16	0	2180	2317	8448780	8448643	1.950000e-37	167.0
22	TraesCS6D01G020200	chr6A	91.453	117	10	0	2191	2307	8392381	8392265	9.070000e-36	161.0
23	TraesCS6D01G020200	chr6A	83.929	168	23	4	2504	2669	12422307	12422472	1.170000e-34	158.0
24	TraesCS6D01G020200	chr6A	86.047	129	11	5	2338	2461	35567823	35567697	7.110000e-27	132.0
25	TraesCS6D01G020200	chr6A	85.542	83	11	1	140	222	368607711	368607630	5.620000e-13	86.1
26	TraesCS6D01G020200	chr6B	95.282	869	16	3	2317	3161	14628292	14627425	0.000000e+00	1354.0
27	TraesCS6D01G020200	chr6B	98.312	770	13	0	1548	2317	14629183	14628414	0.000000e+00	1351.0
28	TraesCS6D01G020200	chr6B	79.606	1118	195	24	1067	2169	14545316	14544217	0.000000e+00	771.0
29	TraesCS6D01G020200	chr6B	79.695	1113	187	28	1064	2158	14333500	14334591	0.000000e+00	767.0
30	TraesCS6D01G020200	chr6B	77.861	1206	233	30	979	2165	39326118	39327308	0.000000e+00	717.0
31	TraesCS6D01G020200	chr6B	88.718	585	55	9	868	1446	14629756	14629177	0.000000e+00	704.0
32	TraesCS6D01G020200	chr6B	77.655	1177	241	20	994	2162	16429000	16430162	0.000000e+00	697.0
33	TraesCS6D01G020200	chr6B	77.711	664	77	30	2501	3157	65173382	65172783	1.090000e-89	340.0
34	TraesCS6D01G020200	chr6B	78.650	548	80	15	2509	3052	15223986	15223472	2.350000e-86	329.0
35	TraesCS6D01G020200	chr6B	77.960	549	81	17	2509	3052	52572258	52571745	1.100000e-79	307.0
36	TraesCS6D01G020200	chr6B	81.102	127	17	6	2336	2457	15218226	15218102	9.330000e-16	95.3
37	TraesCS6D01G020200	chr2B	79.126	1236	210	43	964	2175	54044055	54042844	0.000000e+00	809.0
38	TraesCS6D01G020200	chr3A	78.583	1228	238	23	966	2182	45938007	45936794	0.000000e+00	787.0
39	TraesCS6D01G020200	chr3A	90.411	73	6	1	134	205	750499197	750499269	9.330000e-16	95.3
40	TraesCS6D01G020200	chr3D	77.723	1221	242	26	966	2171	33330529	33329324	0.000000e+00	721.0
41	TraesCS6D01G020200	chr7A	77.611	1130	219	28	1047	2163	162577892	162579000	0.000000e+00	654.0
42	TraesCS6D01G020200	chr1B	78.032	569	77	30	2501	3052	630646484	630647021	6.580000e-82	315.0
43	TraesCS6D01G020200	chr1B	83.691	233	29	6	2706	2934	630651434	630651661	8.880000e-51	211.0
44	TraesCS6D01G020200	chr4A	82.530	166	25	4	2504	2667	667381968	667382131	3.290000e-30	143.0
45	TraesCS6D01G020200	chr1A	89.412	85	9	0	138	222	288687142	288687226	1.200000e-19	108.0
46	TraesCS6D01G020200	chrUn	87.640	89	11	0	137	225	42479325	42479237	1.550000e-18	104.0
47	TraesCS6D01G020200	chr2D	86.170	94	6	3	136	229	81298035	81297949	9.330000e-16	95.3
48	TraesCS6D01G020200	chr2A	86.170	94	6	3	136	229	81752403	81752317	9.330000e-16	95.3
49	TraesCS6D01G020200	chr5A	89.189	74	7	1	138	211	546781433	546781361	1.210000e-14	91.6
50	TraesCS6D01G020200	chr7B	84.091	88	14	0	137	224	72609119	72609206	5.620000e-13	86.1

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	TraesCS6D01G020200	chr6D	7996903	8000063	3160	True	5838.000000	5838	100.000000	1	3161	1	chr6D.!!$R1	3160
1	TraesCS6D01G020200	chr6D	8551629	8552828	1199	True	900.000000	900	80.428000	970	2172	1	chr6D.!!$R2	1202
2	TraesCS6D01G020200	chr6D	9547048	9548234	1186	True	859.000000	859	79.983000	977	2166	1	chr6D.!!$R3	1189
3	TraesCS6D01G020200	chr6A	8210260	8213430	3170	True	1571.000000	2320	94.253000	13	3161	3	chr6A.!!$R4	3148
4	TraesCS6D01G020200	chr6A	7991359	7992458	1099	False	749.000000	749	79.286000	1064	2166	1	chr6A.!!$F1	1102
5	TraesCS6D01G020200	chr6A	8391237	8401936	10699	True	579.777778	1013	88.340667	909	3028	9	chr6A.!!$R5	2119
6	TraesCS6D01G020200	chr6A	35579242	35581602	2360	True	530.500000	719	77.753000	994	3157	2	chr6A.!!$R7	2163
7	TraesCS6D01G020200	chr6B	14627425	14629756	2331	True	1136.333333	1354	94.104000	868	3161	3	chr6B.!!$R6	2293
8	TraesCS6D01G020200	chr6B	14544217	14545316	1099	True	771.000000	771	79.606000	1067	2169	1	chr6B.!!$R1	1102
9	TraesCS6D01G020200	chr6B	14333500	14334591	1091	False	767.000000	767	79.695000	1064	2158	1	chr6B.!!$F1	1094
10	TraesCS6D01G020200	chr6B	39326118	39327308	1190	False	717.000000	717	77.861000	979	2165	1	chr6B.!!$F3	1186
11	TraesCS6D01G020200	chr6B	16429000	16430162	1162	False	697.000000	697	77.655000	994	2162	1	chr6B.!!$F2	1168
12	TraesCS6D01G020200	chr6B	65172783	65173382	599	True	340.000000	340	77.711000	2501	3157	1	chr6B.!!$R5	656
13	TraesCS6D01G020200	chr6B	15223472	15223986	514	True	329.000000	329	78.650000	2509	3052	1	chr6B.!!$R3	543
14	TraesCS6D01G020200	chr6B	52571745	52572258	513	True	307.000000	307	77.960000	2509	3052	1	chr6B.!!$R4	543
15	TraesCS6D01G020200	chr2B	54042844	54044055	1211	True	809.000000	809	79.126000	964	2175	1	chr2B.!!$R1	1211
16	TraesCS6D01G020200	chr3A	45936794	45938007	1213	True	787.000000	787	78.583000	966	2182	1	chr3A.!!$R1	1216
17	TraesCS6D01G020200	chr3D	33329324	33330529	1205	True	721.000000	721	77.723000	966	2171	1	chr3D.!!$R1	1205
18	TraesCS6D01G020200	chr7A	162577892	162579000	1108	False	654.000000	654	77.611000	1047	2163	1	chr7A.!!$F1	1116
19	TraesCS6D01G020200	chr1B	630646484	630647021	537	False	315.000000	315	78.032000	2501	3052	1	chr1B.!!$F1	551

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
860	875	0.18135	CAAGAGTGGTAGCCCATCCC	59.819	60.0	0.0	0.0	44.35	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2330	9878	5.123186	ACATAGAGATAGAGCGTGCAGATAC	59.877	44.0	0.0	0.0	0.0	2.24	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
42	43	3.570125	CAGCATCTTGATGGCAGATCATT	59.430	43.478	11.91	0.00	28.61	2.57
45	46	4.796290	GCATCTTGATGGCAGATCATTTGG	60.796	45.833	11.91	0.00	0.00	3.28
97	98	1.730902	CGAGCATCCATAGCGACCG	60.731	63.158	0.00	0.00	37.01	4.79
120	121	3.392285	TGGCCACTATGTCAGCAGATAAT	59.608	43.478	0.00	0.00	0.00	1.28
164	165	6.630131	TCCCTCTGTCCCATAATATAAGACA	58.370	40.000	4.97	4.97	36.16	3.41
211	212	7.675062	TGCAAAAACATCTTATATTGTTGGGT	58.325	30.769	0.00	0.00	36.26	4.51
321	322	5.287226	AGTCTCCTTACTACAAACACGTTG	58.713	41.667	0.00	0.00	43.43	4.10
360	361	6.166279	TCACATGTCAGAAATGAGTTCCTAC	58.834	40.000	7.66	0.00	36.86	3.18
440	441	8.857694	CCTGTTTTAGGGTTACTTAATCTTCA	57.142	34.615	0.00	0.00	43.33	3.02
462	463	7.687941	TCATTTTCTAGAATTTGAGGGTCAC	57.312	36.000	5.89	0.00	0.00	3.67
463	464	6.659242	TCATTTTCTAGAATTTGAGGGTCACC	59.341	38.462	5.89	0.00	0.00	4.02
509	511	6.033513	GGCAAACAGACGCAACTTTATTATTC	59.966	38.462	0.00	0.00	0.00	1.75
535	537	9.146984	CAGACGAAAGAATGTTTATAGGTACAA	57.853	33.333	0.00	0.00	0.00	2.41
550	552	5.373981	AGGTACAAGAAGTGAGTCGTAAG	57.626	43.478	0.00	0.00	0.00	2.34
585	587	1.412710	ACATGACGACCGATGCCTAAT	59.587	47.619	0.00	0.00	0.00	1.73
604	606	0.603569	TGAGGAGAGGAAGCGTGTTC	59.396	55.000	0.00	0.00	0.00	3.18
660	662	9.431887	TGACTTATATTACAACTCTGGAACAAC	57.568	33.333	0.00	0.00	38.70	3.32
684	686	8.879427	ACTTTTGCCTATACTTAATGTCCTTT	57.121	30.769	0.00	0.00	0.00	3.11
685	687	9.309224	ACTTTTGCCTATACTTAATGTCCTTTT	57.691	29.630	0.00	0.00	0.00	2.27
808	817	5.013495	TCTCCTTCATGATCCACTCTGTTTT	59.987	40.000	0.00	0.00	0.00	2.43
848	863	6.964370	TGAAAACAAATTCGTGTACAAGAGTG	59.036	34.615	11.35	12.73	31.80	3.51
859	874	0.912486	ACAAGAGTGGTAGCCCATCC	59.088	55.000	0.00	0.00	44.35	3.51
860	875	0.181350	CAAGAGTGGTAGCCCATCCC	59.819	60.000	0.00	0.00	44.35	3.85
861	876	0.253160	AAGAGTGGTAGCCCATCCCA	60.253	55.000	0.00	0.00	44.35	4.37
948	3225	3.535561	CTCACCACTCTCAAACAACAGT	58.464	45.455	0.00	0.00	0.00	3.55
953	3232	3.186909	CACTCTCAAACAACAGTCGACA	58.813	45.455	19.50	0.00	0.00	4.35
1059	3347	1.305718	GTCTCCAGCCACCTCTCCT	60.306	63.158	0.00	0.00	0.00	3.69
1060	3348	1.000993	TCTCCAGCCACCTCTCCTC	59.999	63.158	0.00	0.00	0.00	3.71
1062	3350	3.465403	CCAGCCACCTCTCCTCCG	61.465	72.222	0.00	0.00	0.00	4.63
1545	8901	1.330655	ATCTCGAGCGGGTGGTCAAT	61.331	55.000	7.81	0.00	42.80	2.57
2215	9616	7.094805	TGCTGGTAATTTCTGATTCAGTGTTAC	60.095	37.037	13.23	16.92	32.61	2.50
2291	9707	5.105756	CCTGGGTGAAACTGGTAATTTGATC	60.106	44.000	0.00	0.00	36.74	2.92
2330	9878	6.364976	TGATGGTTACATATCGATAAAGCGTG	59.635	38.462	9.61	5.35	37.47	5.34
2503	10109	5.767816	TTTTTGGTTGCTTCCTCTAGTTC	57.232	39.130	0.00	0.00	0.00	3.01
2504	10110	4.706842	TTTGGTTGCTTCCTCTAGTTCT	57.293	40.909	0.00	0.00	0.00	3.01
2506	10112	4.273148	TGGTTGCTTCCTCTAGTTCTTC	57.727	45.455	0.00	0.00	0.00	2.87
2507	10113	3.904339	TGGTTGCTTCCTCTAGTTCTTCT	59.096	43.478	0.00	0.00	0.00	2.85
3103	10996	0.670162	CTTGTTGGTGGAAGTGCTGG	59.330	55.000	0.00	0.00	0.00	4.85
3120	11013	5.359009	AGTGCTGGATCAAAGGATGTAAATG	59.641	40.000	0.00	0.00	32.67	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	7.108194	AGATGCTGATTAGAACATCACTTTCA	58.892	34.615	0.00	0.00	41.08	2.69
3	4	7.551035	AGATGCTGATTAGAACATCACTTTC	57.449	36.000	0.00	0.00	41.08	2.62
5	6	7.108194	TCAAGATGCTGATTAGAACATCACTT	58.892	34.615	0.00	0.00	41.08	3.16
6	7	6.647229	TCAAGATGCTGATTAGAACATCACT	58.353	36.000	0.00	0.00	41.08	3.41
7	8	6.915544	TCAAGATGCTGATTAGAACATCAC	57.084	37.500	0.00	0.00	41.08	3.06
8	9	6.485648	CCATCAAGATGCTGATTAGAACATCA	59.514	38.462	4.53	0.00	41.08	3.07
9	10	6.568081	GCCATCAAGATGCTGATTAGAACATC	60.568	42.308	4.53	0.00	39.35	3.06
10	11	5.241064	GCCATCAAGATGCTGATTAGAACAT	59.759	40.000	4.53	0.00	37.49	2.71
11	12	4.577693	GCCATCAAGATGCTGATTAGAACA	59.422	41.667	4.53	0.00	37.49	3.18
42	43	5.243507	ACATGATTGCAAATGTGACTACCAA	59.756	36.000	14.49	0.00	35.71	3.67
45	46	6.470235	GCTAACATGATTGCAAATGTGACTAC	59.530	38.462	15.66	3.46	37.11	2.73
88	89	1.113517	ATAGTGGCCACGGTCGCTAT	61.114	55.000	29.68	17.52	44.95	2.97
97	98	0.250234	TCTGCTGACATAGTGGCCAC	59.750	55.000	29.22	29.22	0.00	5.01
120	121	3.506455	GGAGTAGATGTAGGCGCATAAGA	59.494	47.826	10.83	0.00	0.00	2.10
164	165	6.989169	TGCAAACTATGTTGGCTTACAAAAAT	59.011	30.769	10.60	0.00	41.58	1.82
321	322	2.987413	TGTGATTTCGTGGCATGAAC	57.013	45.000	21.19	11.49	0.00	3.18
440	441	6.794534	AGGTGACCCTCAAATTCTAGAAAAT	58.205	36.000	9.71	0.00	35.62	1.82
452	453	1.717077	AGGAGACTAGGTGACCCTCAA	59.283	52.381	0.00	0.00	41.45	3.02
453	454	1.383963	AGGAGACTAGGTGACCCTCA	58.616	55.000	0.00	0.00	41.45	3.86
491	493	6.097356	TCGTCTGAATAATAAAGTTGCGTCT	58.903	36.000	0.00	0.00	0.00	4.18
509	511	8.697846	TGTACCTATAAACATTCTTTCGTCTG	57.302	34.615	0.00	0.00	0.00	3.51
523	525	7.458409	ACGACTCACTTCTTGTACCTATAAA	57.542	36.000	0.00	0.00	0.00	1.40
535	537	2.561858	GGGTTCCTTACGACTCACTTCT	59.438	50.000	0.00	0.00	0.00	2.85
539	541	0.971386	TGGGGTTCCTTACGACTCAC	59.029	55.000	0.00	0.00	0.00	3.51
550	552	0.321346	CATGTTTGGCTTGGGGTTCC	59.679	55.000	0.00	0.00	0.00	3.62
585	587	0.603569	GAACACGCTTCCTCTCCTCA	59.396	55.000	0.00	0.00	0.00	3.86
604	606	8.352942	ACATAGAAACTTTAACTTTGAAGGCTG	58.647	33.333	0.00	0.00	0.00	4.85
828	843	4.448210	ACCACTCTTGTACACGAATTTGT	58.552	39.130	3.43	0.00	0.00	2.83
848	863	0.329596	GATGGATGGGATGGGCTACC	59.670	60.000	0.00	0.00	37.24	3.18
859	874	2.519441	CTGGGCTGGGATGGATGG	59.481	66.667	0.00	0.00	0.00	3.51
860	875	2.203451	GCTGGGCTGGGATGGATG	60.203	66.667	0.00	0.00	0.00	3.51
861	876	3.505773	GGCTGGGCTGGGATGGAT	61.506	66.667	0.00	0.00	0.00	3.41
892	907	1.134371	GGTGTCACCTTGAGGATAGCC	60.134	57.143	15.22	0.00	38.94	3.93
893	908	1.555075	TGGTGTCACCTTGAGGATAGC	59.445	52.381	22.56	0.00	39.58	2.97
897	912	0.105964	CGTTGGTGTCACCTTGAGGA	59.894	55.000	22.56	0.00	39.58	3.71
900	915	0.393132	TTGCGTTGGTGTCACCTTGA	60.393	50.000	22.56	6.40	39.58	3.02
901	916	0.029300	CTTGCGTTGGTGTCACCTTG	59.971	55.000	22.56	12.88	39.58	3.61
962	3241	2.189521	CGAGGGAATGGGGAACGG	59.810	66.667	0.00	0.00	0.00	4.44
1059	3347	1.152525	GTGGAGAGGGGATAGCGGA	60.153	63.158	0.00	0.00	0.00	5.54
1060	3348	2.210711	GGTGGAGAGGGGATAGCGG	61.211	68.421	0.00	0.00	0.00	5.52
1062	3350	2.873525	GCGGTGGAGAGGGGATAGC	61.874	68.421	0.00	0.00	0.00	2.97
1545	8901	1.900351	CAGGAGAGCGACATTGGGA	59.100	57.895	0.00	0.00	0.00	4.37
2291	9707	5.876460	TGTAACCATCATTCAGTGAGACATG	59.124	40.000	0.00	0.00	40.92	3.21
2330	9878	5.123186	ACATAGAGATAGAGCGTGCAGATAC	59.877	44.000	0.00	0.00	0.00	2.24
2416	9967	9.096823	ACTTCATATCATCATGGCCAAAATAAT	57.903	29.630	10.96	3.86	0.00	1.28
2499	10105	6.396829	AACAAAGCTATTGCAAGAAGAACT	57.603	33.333	14.15	1.97	42.74	3.01
2500	10106	8.642020	CATAAACAAAGCTATTGCAAGAAGAAC	58.358	33.333	14.15	0.00	42.74	3.01
2501	10107	8.575589	TCATAAACAAAGCTATTGCAAGAAGAA	58.424	29.630	14.15	0.00	42.74	2.52
2503	10109	8.239314	TCTCATAAACAAAGCTATTGCAAGAAG	58.761	33.333	4.94	6.25	42.74	2.85
2504	10110	8.109705	TCTCATAAACAAAGCTATTGCAAGAA	57.890	30.769	4.94	0.00	42.74	2.52
3103	10996	7.047460	AGCCATTCATTTACATCCTTTGATC	57.953	36.000	0.00	0.00	0.00	2.92
3120	11013	7.335422	ACCATTAATCATCTAATCGAGCCATTC	59.665	37.037	0.00	0.00	0.00	2.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.