AutoCloner

Multiple sequence alignment - TraesCS2B01G581400

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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	TraesCS2B01G581400	chr2B	100.000	4286	0	0	1	4286	769049180	769044895	0.000000e+00	7915.0
1	TraesCS2B01G581400	chr2B	95.912	1688	55	8	2240	3914	768663391	768661705	0.000000e+00	2723.0
2	TraesCS2B01G581400	chr2B	81.649	2692	437	39	913	3560	768615440	768612762	0.000000e+00	2182.0
3	TraesCS2B01G581400	chr2B	83.299	2395	371	24	917	3291	769039894	769037509	0.000000e+00	2180.0
4	TraesCS2B01G581400	chr2B	92.891	1266	89	1	978	2242	768775454	768774189	0.000000e+00	1838.0
5	TraesCS2B01G581400	chr2B	80.988	1215	207	18	2129	3337	752591382	752590186	0.000000e+00	942.0
6	TraesCS2B01G581400	chr2B	94.778	383	20	0	3903	4285	768661690	768661308	7.930000e-167	597.0
7	TraesCS2B01G581400	chr2B	88.539	349	32	6	10	356	768778333	768777991	2.380000e-112	416.0
8	TraesCS2B01G581400	chr2B	93.284	134	8	1	4002	4135	768612456	768612324	3.380000e-46	196.0
9	TraesCS2B01G581400	chr2B	89.209	139	15	0	526	664	768775591	768775453	1.580000e-39	174.0
10	TraesCS2B01G581400	chr2B	82.524	103	14	3	119	220	768617842	768617743	2.120000e-13	87.9
11	TraesCS2B01G581400	chr2D	94.634	4305	185	27	1	4285	627235842	627231564	0.000000e+00	6628.0
12	TraesCS2B01G581400	chr2D	81.166	3207	505	56	1105	4283	627198886	627195751	0.000000e+00	2484.0
13	TraesCS2B01G581400	chr2D	80.741	3022	491	51	913	3902	627168854	627165892	0.000000e+00	2272.0
14	TraesCS2B01G581400	chr2D	83.892	2328	349	20	979	3294	627174117	627171804	0.000000e+00	2198.0
15	TraesCS2B01G581400	chr2D	85.714	182	24	2	3984	4165	627165875	627165696	1.570000e-44	191.0
16	TraesCS2B01G581400	chr2D	74.477	239	41	15	1	220	627171194	627170957	7.640000e-13	86.1
17	TraesCS2B01G581400	chr2A	81.335	3386	524	56	910	4252	757929565	757926245	0.000000e+00	2652.0
18	TraesCS2B01G581400	chr2A	80.092	3034	500	56	913	3902	757920472	757917499	0.000000e+00	2161.0
19	TraesCS2B01G581400	chr2A	89.809	157	14	1	3981	4135	757917485	757917329	2.610000e-47	200.0

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	TraesCS2B01G581400	chr2B	769044895	769049180	4285	True	7915.000000	7915	100.0000	1	4286	1	chr2B.!!$R3	4285
1	TraesCS2B01G581400	chr2B	769037509	769039894	2385	True	2180.000000	2180	83.2990	917	3291	1	chr2B.!!$R2	2374
2	TraesCS2B01G581400	chr2B	768661308	768663391	2083	True	1660.000000	2723	95.3450	2240	4285	2	chr2B.!!$R5	2045
3	TraesCS2B01G581400	chr2B	752590186	752591382	1196	True	942.000000	942	80.9880	2129	3337	1	chr2B.!!$R1	1208
4	TraesCS2B01G581400	chr2B	768612324	768617842	5518	True	821.966667	2182	85.8190	119	4135	3	chr2B.!!$R4	4016
5	TraesCS2B01G581400	chr2B	768774189	768778333	4144	True	809.333333	1838	90.2130	10	2242	3	chr2B.!!$R6	2232
6	TraesCS2B01G581400	chr2D	627231564	627235842	4278	True	6628.000000	6628	94.6340	1	4285	1	chr2D.!!$R2	4284
7	TraesCS2B01G581400	chr2D	627195751	627198886	3135	True	2484.000000	2484	81.1660	1105	4283	1	chr2D.!!$R1	3178
8	TraesCS2B01G581400	chr2D	627165696	627174117	8421	True	1186.775000	2272	81.2060	1	4165	4	chr2D.!!$R3	4164
9	TraesCS2B01G581400	chr2A	757926245	757929565	3320	True	2652.000000	2652	81.3350	910	4252	1	chr2A.!!$R1	3342
10	TraesCS2B01G581400	chr2A	757917329	757920472	3143	True	1180.500000	2161	84.9505	913	4135	2	chr2A.!!$R2	3222

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
389	2382	1.669265	GTTACCGGGCATTTAGACTGC	59.331	52.381	6.32	0.00	38.93	4.40	F
1137	5016	0.609957	CTCTGAACCAGGCATGCCAA	60.610	55.000	37.18	14.62	38.92	4.52	F
1224	5104	1.376609	GATGGCATCCCAACGACACC	61.377	60.000	16.75	0.00	46.14	4.16	F
2127	11341	0.391661	GTCTCATGTGGTGCACCGAT	60.392	55.000	30.07	21.22	39.43	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1621	5501	0.112995	AATTGCAGGGCCTTGACTGA	59.887	50.000	20.85	0.46	36.86	3.41	R
2010	5893	1.266718	GCAATTTCACCTGACAGCGAA	59.733	47.619	0.00	0.00	0.00	4.70	R
2187	11401	1.271325	TGTGACAGGGATCGCAAATGT	60.271	47.619	12.83	7.66	36.19	2.71	R
3763	13058	0.811915	TCTTCTCTTTCGCCTCCTCG	59.188	55.000	0.00	0.00	0.00	4.63	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
25	26	3.257469	TCTGTGATCACCAGCAGAATC	57.743	47.619	22.85	0.00	33.31	2.52
171	172	6.094719	CACATTAATCATTTGTCAGGTGTGG	58.905	40.000	0.00	0.00	32.03	4.17
277	278	9.651718	GTTCTAACAGAAGACAAAAATGTACAG	57.348	33.333	0.33	0.00	34.42	2.74
337	338	1.693640	CCAGTCAAGCCCTTCCCAT	59.306	57.895	0.00	0.00	0.00	4.00
389	2382	1.669265	GTTACCGGGCATTTAGACTGC	59.331	52.381	6.32	0.00	38.93	4.40
464	2469	8.598916	TCACACCCTTATCAAGACAACTAAATA	58.401	33.333	0.00	0.00	0.00	1.40
922	4788	5.800438	GTCTTTCCTTGTTTGTGTGTTCTTC	59.200	40.000	0.00	0.00	0.00	2.87
966	4836	4.980573	TGTAATAAGGTGTGAGTTTGGCT	58.019	39.130	0.00	0.00	0.00	4.75
1137	5016	0.609957	CTCTGAACCAGGCATGCCAA	60.610	55.000	37.18	14.62	38.92	4.52
1224	5104	1.376609	GATGGCATCCCAACGACACC	61.377	60.000	16.75	0.00	46.14	4.16
1342	5222	3.531207	CCTCGCTCGATGGCCTCA	61.531	66.667	3.32	0.00	0.00	3.86
1368	5248	2.972713	ACTAAACCTCTCCTGCAACTCA	59.027	45.455	0.00	0.00	0.00	3.41
1494	5374	4.528596	GGCTTCCTAGCTATTGAGATGGTA	59.471	45.833	0.00	0.00	46.90	3.25
1544	5424	1.684734	ATCCTACGTTCCCTGGCGT	60.685	57.895	0.00	3.46	44.02	5.68
1621	5501	4.643387	GGGCCCTCTGTGTTGCGT	62.643	66.667	17.04	0.00	0.00	5.24
1779	5659	3.449018	TGTTATCAGAGTTGAGGAGGCTC	59.551	47.826	5.78	5.78	36.61	4.70
2127	11341	0.391661	GTCTCATGTGGTGCACCGAT	60.392	55.000	30.07	21.22	39.43	4.18
2187	11401	4.409247	GGGGAGATACCAGAGAGCTTTAAA	59.591	45.833	0.00	0.00	41.20	1.52
2209	11423	0.107643	TTTGCGATCCCTGTCACACA	59.892	50.000	0.00	0.00	0.00	3.72
2711	11928	3.304391	GCGCTGATCCTCTCTAGTAACTG	60.304	52.174	0.00	0.00	0.00	3.16
2874	12091	2.306512	TGGTTTAAACGGGAGCATACCT	59.693	45.455	12.07	0.00	0.00	3.08
3430	12699	5.854010	TTACCTGGATAGAGTTAGCAGTG	57.146	43.478	0.00	0.00	0.00	3.66
3457	12726	6.406512	GGGTTGTGTGGTTAGATTTTGAGTTT	60.407	38.462	0.00	0.00	0.00	2.66
3462	12731	5.768164	TGTGGTTAGATTTTGAGTTTCCCTC	59.232	40.000	0.00	0.00	40.89	4.30
3472	12741	2.978978	TGAGTTTCCCTCCATGTTGAGA	59.021	45.455	0.93	0.00	39.65	3.27
3474	12743	4.006319	GAGTTTCCCTCCATGTTGAGAAG	58.994	47.826	0.93	0.00	34.11	2.85
3475	12744	3.395941	AGTTTCCCTCCATGTTGAGAAGT	59.604	43.478	0.93	0.00	34.11	3.01
3476	12745	3.423539	TTCCCTCCATGTTGAGAAGTG	57.576	47.619	0.93	0.00	34.11	3.16
3477	12746	2.619931	TCCCTCCATGTTGAGAAGTGA	58.380	47.619	0.93	0.00	34.11	3.41
3763	13058	0.315251	GCAAGGCTTTTGGTCCTCAC	59.685	55.000	0.00	0.00	0.00	3.51
3875	13172	1.750778	CAGGAAAATAGGCCGTTGCAT	59.249	47.619	0.00	0.00	40.13	3.96
4082	13406	7.267128	AGTTCTGAAAATGAATTGCTGTCAAA	58.733	30.769	0.00	0.00	35.56	2.69
4086	13410	6.289834	TGAAAATGAATTGCTGTCAAATGGT	58.710	32.000	0.00	0.00	35.56	3.55
4161	13487	7.406620	TTGGGGATTGATACTTGATAAGGAT	57.593	36.000	0.00	0.00	33.76	3.24
4166	13493	4.537135	TGATACTTGATAAGGATCCCGC	57.463	45.455	8.55	0.00	46.42	6.13
4167	13494	3.901222	TGATACTTGATAAGGATCCCGCA	59.099	43.478	8.55	0.00	46.42	5.69
4231	13558	1.228769	GGTGGTTGGAAAGGACCCC	60.229	63.158	0.00	0.00	0.00	4.95
4285	13612	2.426522	CTGCTAAGTGGCTAAGTTGCA	58.573	47.619	0.00	0.00	34.04	4.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
171	172	2.289694	TGTCTTTCCTAGAAGCAGCCAC	60.290	50.000	0.00	0.00	33.81	5.01
277	278	1.387295	GGCCATGCCCTCAGTTAAGC	61.387	60.000	0.00	0.00	44.06	3.09
337	338	6.530120	TGTAAACTCAGGAAGCTTACATGAA	58.470	36.000	12.25	0.00	40.12	2.57
362	363	6.485648	AGTCTAAATGCCCGGTAACATTAATC	59.514	38.462	13.18	6.67	35.49	1.75
438	2436	4.974645	AGTTGTCTTGATAAGGGTGTGA	57.025	40.909	0.00	0.00	0.00	3.58
464	2469	9.236006	AGTCACTTAATTTAGAACATCAGCATT	57.764	29.630	0.00	0.00	0.00	3.56
922	4788	3.028850	AGGGTGCATGGATTCAAGAATG	58.971	45.455	0.00	0.00	0.00	2.67
966	4836	5.281037	GGAAGGACTTGGGAAGGAATTCTTA	60.281	44.000	5.23	0.00	35.50	2.10
1137	5016	2.930562	GCCTCCAGGTCAGTGGGT	60.931	66.667	0.00	0.00	38.26	4.51
1224	5104	1.503542	GGTCCAGAAACAGCATGCG	59.496	57.895	13.01	9.99	42.53	4.73
1342	5222	2.906389	TGCAGGAGAGGTTTAGTGTCAT	59.094	45.455	0.00	0.00	0.00	3.06
1494	5374	6.515832	GGTGAATTTGTTGAAGGAGATGTTT	58.484	36.000	0.00	0.00	0.00	2.83
1621	5501	0.112995	AATTGCAGGGCCTTGACTGA	59.887	50.000	20.85	0.46	36.86	3.41
1779	5659	4.003648	AGAGCTGATTTTCCCGTAAACTG	58.996	43.478	0.00	0.00	0.00	3.16
2010	5893	1.266718	GCAATTTCACCTGACAGCGAA	59.733	47.619	0.00	0.00	0.00	4.70
2097	5981	2.103771	CCACATGAGACTGGGAGGTATG	59.896	54.545	0.00	0.00	0.00	2.39
2127	11341	1.864711	CCGAAGTTCAGCGTCTTCAAA	59.135	47.619	3.32	0.00	39.70	2.69
2187	11401	1.271325	TGTGACAGGGATCGCAAATGT	60.271	47.619	12.83	7.66	36.19	2.71
2209	11423	3.428532	AGCCATTTTGAGCAAGTGAGAT	58.571	40.909	0.00	0.00	0.00	2.75
2961	12178	5.954296	AACTCTCATTTGTGAATGTGGAG	57.046	39.130	15.60	15.60	42.61	3.86
3320	12550	4.789012	ACATTTGCACATAAACTCCCTG	57.211	40.909	0.00	0.00	0.00	4.45
3430	12699	4.339814	TCAAAATCTAACCACACAACCCAC	59.660	41.667	0.00	0.00	0.00	4.61
3457	12726	2.619931	TCACTTCTCAACATGGAGGGA	58.380	47.619	0.00	0.00	35.58	4.20
3462	12731	6.764308	ACCAATATTCACTTCTCAACATGG	57.236	37.500	0.00	0.00	0.00	3.66
3763	13058	0.811915	TCTTCTCTTTCGCCTCCTCG	59.188	55.000	0.00	0.00	0.00	4.63
3815	13111	2.941891	CGCAATGTTTGTGTCTACGT	57.058	45.000	0.00	0.00	36.45	3.57
3875	13172	6.346477	TCTAGCTGCTTTCTTAGTTTCAGA	57.654	37.500	7.79	0.00	0.00	3.27
4086	13410	8.579850	ACTGAAATCTATTCATGGCAACTTAA	57.420	30.769	0.00	0.00	37.61	1.85
4144	13470	4.346709	TGCGGGATCCTTATCAAGTATCAA	59.653	41.667	12.58	0.00	33.41	2.57
4231	13558	6.130298	TCACAACTACACTTTCAACCATTG	57.870	37.500	0.00	0.00	0.00	2.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.