AutoCloner

Multiple sequence alignment - TraesCS1B01G323800

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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	TraesCS1B01G323800	chr1B	100.000	2432	0	0	1	2432	548976921	548974490	0.000000e+00	4492
1	TraesCS1B01G323800	chr2A	93.813	1972	85	13	325	2288	40830688	40828746	0.000000e+00	2931
2	TraesCS1B01G323800	chr2A	85.032	775	72	17	1674	2426	179296849	179297601	0.000000e+00	749
3	TraesCS1B01G323800	chr2A	92.163	319	10	8	1	304	40831446	40831764	1.030000e-118	436
4	TraesCS1B01G323800	chr2A	87.500	336	41	1	1133	1468	179270271	179269937	1.050000e-103	387
5	TraesCS1B01G323800	chr2A	93.878	147	9	0	2286	2432	40828665	40828519	3.150000e-54	222
6	TraesCS1B01G323800	chr1D	94.583	1680	67	11	773	2432	408250319	408248644	0.000000e+00	2577
7	TraesCS1B01G323800	chr1D	92.822	404	23	1	313	710	408250721	408250318	4.510000e-162	580
8	TraesCS1B01G323800	chr1D	85.185	324	26	9	3	304	408251893	408251570	1.820000e-81	313
9	TraesCS1B01G323800	chr1A	95.719	1425	55	2	313	1731	504251745	504250321	0.000000e+00	2289
10	TraesCS1B01G323800	chr1A	89.370	762	45	6	1705	2432	504250315	504249556	0.000000e+00	926
11	TraesCS1B01G323800	chr1A	88.994	318	17	9	3	304	504252927	504252612	6.350000e-101	377
12	TraesCS1B01G323800	chr2D	84.695	771	75	20	1677	2426	170613335	170612587	0.000000e+00	730
13	TraesCS1B01G323800	chr2B	83.694	785	71	23	1674	2426	226700511	226701270	0.000000e+00	688
14	TraesCS1B01G323800	chr2B	83.082	662	91	14	821	1468	226686576	226685922	1.250000e-162	582
15	TraesCS1B01G323800	chr2B	88.506	87	6	4	156	238	71736031	71735945	4.280000e-18	102

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	TraesCS1B01G323800	chr1B	548974490	548976921	2431	True	4492.000000	4492	100.000000	1	2432	1	chr1B.!!$R1	2431
1	TraesCS1B01G323800	chr2A	40828519	40830688	2169	True	1576.500000	2931	93.845500	325	2432	2	chr2A.!!$R2	2107
2	TraesCS1B01G323800	chr2A	179296849	179297601	752	False	749.000000	749	85.032000	1674	2426	1	chr2A.!!$F2	752
3	TraesCS1B01G323800	chr1D	408248644	408251893	3249	True	1156.666667	2577	90.863333	3	2432	3	chr1D.!!$R1	2429
4	TraesCS1B01G323800	chr1A	504249556	504252927	3371	True	1197.333333	2289	91.361000	3	2432	3	chr1A.!!$R1	2429
5	TraesCS1B01G323800	chr2D	170612587	170613335	748	True	730.000000	730	84.695000	1677	2426	1	chr2D.!!$R1	749
6	TraesCS1B01G323800	chr2B	226700511	226701270	759	False	688.000000	688	83.694000	1674	2426	1	chr2B.!!$F1	752
7	TraesCS1B01G323800	chr2B	226685922	226686576	654	True	582.000000	582	83.082000	821	1468	1	chr2B.!!$R2	647

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
602	1495	0.379669	GATCCTGCCGCAATCAACAG	59.62	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1559	2471	2.038387	AAACGATGGCCCAGTGATAC	57.962	50.0	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
91	100	0.963856	TTGGCCAGAGATGCTGCTTG	60.964	55.000	5.11	0.00	43.50	4.01
133	148	4.163078	ACCACTATCTCCTCACTGGATTTG	59.837	45.833	0.00	0.00	45.16	2.32
135	150	5.071519	CCACTATCTCCTCACTGGATTTGAT	59.928	44.000	0.00	0.00	45.16	2.57
136	151	5.990386	CACTATCTCCTCACTGGATTTGATG	59.010	44.000	0.00	0.00	45.16	3.07
139	154	1.019673	CCTCACTGGATTTGATGCCG	58.980	55.000	0.00	0.00	38.35	5.69
140	155	1.679944	CCTCACTGGATTTGATGCCGT	60.680	52.381	0.00	0.00	38.35	5.68
141	156	2.086869	CTCACTGGATTTGATGCCGTT	58.913	47.619	0.00	0.00	0.00	4.44
142	157	1.811965	TCACTGGATTTGATGCCGTTG	59.188	47.619	0.00	0.00	0.00	4.10
143	158	0.527565	ACTGGATTTGATGCCGTTGC	59.472	50.000	0.00	0.00	38.26	4.17
269	292	5.065988	GCTTTTGATTAGAAACCGAGGCATA	59.934	40.000	0.00	0.00	0.00	3.14
275	298	3.914426	AGAAACCGAGGCATAGATTGT	57.086	42.857	0.00	0.00	0.00	2.71
304	327	1.174712	GCAGGGTTGAAGCTGCTTGA	61.175	55.000	21.25	8.91	39.48	3.02
305	328	1.542492	CAGGGTTGAAGCTGCTTGAT	58.458	50.000	21.25	0.00	0.00	2.57
306	329	1.891150	CAGGGTTGAAGCTGCTTGATT	59.109	47.619	21.25	0.00	0.00	2.57
308	331	1.135575	GGGTTGAAGCTGCTTGATTCG	60.136	52.381	21.25	0.00	43.42	3.34
309	332	1.135575	GGTTGAAGCTGCTTGATTCGG	60.136	52.381	21.25	0.00	43.42	4.30
310	333	0.523072	TTGAAGCTGCTTGATTCGGC	59.477	50.000	21.25	3.78	43.42	5.54
329	1216	6.012658	TCGGCATAGATCATTAAAATTGGC	57.987	37.500	0.00	0.00	0.00	4.52
365	1252	2.094545	AGCATGATTTTCAAGTTCCCGC	60.095	45.455	0.00	0.00	0.00	6.13
480	1367	3.417101	AGTGGTGGATGAAATTGCGTAA	58.583	40.909	0.00	0.00	0.00	3.18
499	1386	3.174265	GATGGAGCAGGGGGAGGG	61.174	72.222	0.00	0.00	0.00	4.30
580	1473	1.068333	CAAGGCCGGACAAAATGAGTG	60.068	52.381	11.69	0.00	0.00	3.51
602	1495	0.379669	GATCCTGCCGCAATCAACAG	59.620	55.000	0.00	0.00	0.00	3.16
674	1567	1.902508	AGAAATGGTGAAGAGCGAGGA	59.097	47.619	0.00	0.00	0.00	3.71
685	1578	2.035632	AGAGCGAGGATTAACTCAGGG	58.964	52.381	0.00	0.00	37.34	4.45
747	1640	2.167861	GGACAAGATCGCCGCACTC	61.168	63.158	0.00	0.00	0.00	3.51
783	1676	4.690748	TCTTTCTCATGCGTTTGGTTCTAG	59.309	41.667	0.00	0.00	0.00	2.43
881	1774	2.998670	CTGCTTCGTCATGAACACTGAT	59.001	45.455	0.00	0.00	31.87	2.90
922	1815	3.250040	AGGTCGTACTTTTGTGATGCAAC	59.750	43.478	0.00	0.00	36.72	4.17
1125	2021	1.997311	CAGGGAGGAGACATGCCCA	60.997	63.158	6.60	0.00	39.94	5.36
1140	2036	0.471617	GCCCATCACTAGTGGCTGAT	59.528	55.000	22.48	6.01	40.77	2.90
1536	2448	4.393834	TGCAATACTAACCACTTGCTGAA	58.606	39.130	7.52	0.00	43.33	3.02
1559	2471	9.912634	TGAATTTTGTATGCTTTCTCCTTAAAG	57.087	29.630	0.00	0.00	39.10	1.85
1578	2490	1.559682	AGTATCACTGGGCCATCGTTT	59.440	47.619	6.72	0.00	0.00	3.60
1593	2505	6.260050	GGCCATCGTTTTAATGTCTTGAGATA	59.740	38.462	0.00	0.00	0.00	1.98
1638	2556	9.881649	CTCATAGAAGATTTAGCAAGCCATATA	57.118	33.333	0.00	0.00	0.00	0.86
1734	2685	8.052748	AGGCAAGAGTTTGATTATATGTTACCA	58.947	33.333	0.00	0.00	36.36	3.25
1773	2725	6.200665	TGTTTATGAAATTGCTCAACTGTTGC	59.799	34.615	15.52	5.81	0.00	4.17
1792	2744	8.671921	ACTGTTGCTCTCATAATTTGATTACAG	58.328	33.333	0.00	0.00	32.72	2.74
1807	2759	6.951062	TGATTACAGAATGGTTGAAACACA	57.049	33.333	0.00	0.00	43.62	3.72
1882	2834	2.959030	ACTTCAGGTTCTTGAAAAGGCC	59.041	45.455	0.00	0.00	46.24	5.19
1897	2849	2.355010	AGGCCTATTCTTGTCCATGC	57.645	50.000	1.29	0.00	0.00	4.06
1915	2867	1.069358	TGCACGATACTCACACAACCA	59.931	47.619	0.00	0.00	0.00	3.67
1934	2886	2.083774	CATACTGCCTTCCTTTCGCAA	58.916	47.619	0.00	0.00	30.85	4.85
2098	3110	5.055144	TGCTCTTGTCAGCATTCTCATATC	58.945	41.667	0.00	0.00	44.73	1.63
2115	3127	6.928492	TCTCATATCGTATGCATGCAGTTTTA	59.072	34.615	26.69	10.64	0.00	1.52
2116	3128	7.440856	TCTCATATCGTATGCATGCAGTTTTAA	59.559	33.333	26.69	10.52	0.00	1.52
2117	3129	8.098220	TCATATCGTATGCATGCAGTTTTAAT	57.902	30.769	26.69	15.54	0.00	1.40
2179	3192	7.930217	TCAGTTAGTTTGATGGCTTATAATGC	58.070	34.615	0.00	0.00	0.00	3.56
2278	3292	6.015434	CCAGAAATTTTACTTTACTGCCAGGT	60.015	38.462	0.00	0.00	0.00	4.00
2324	3421	3.890756	TCATTTGTTGTTGACAGCATCCT	59.109	39.130	1.51	0.00	39.94	3.24
2355	3452	9.595823	TTCTATATGTTCTGTTAGTAACTTGGC	57.404	33.333	14.00	3.61	0.00	4.52
2375	3472	7.816031	ACTTGGCATATGCAATAAATTATCTGC	59.184	33.333	28.07	6.92	44.36	4.26
2378	3475	7.599621	TGGCATATGCAATAAATTATCTGCAAC	59.400	33.333	28.07	5.60	46.97	4.17
2407	3514	2.842208	TCAAGTTTGTGTTGCCTTCG	57.158	45.000	0.00	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.083862	GAGGGAGGTGCCGGTGTC	62.084	72.222	1.90	0.00	37.63	3.67
109	118	3.019799	TCCAGTGAGGAGATAGTGGTC	57.980	52.381	0.00	0.00	43.07	4.02
147	162	5.724328	TCAGAACCAGATACTAACTGCAAG	58.276	41.667	0.00	0.00	42.29	4.01
182	203	5.075067	TCCCACATCTGTCTCCTATCATCTA	59.925	44.000	0.00	0.00	0.00	1.98
183	204	4.140829	TCCCACATCTGTCTCCTATCATCT	60.141	45.833	0.00	0.00	0.00	2.90
187	208	4.709397	CCTATCCCACATCTGTCTCCTATC	59.291	50.000	0.00	0.00	0.00	2.08
194	217	4.810191	GATACCCTATCCCACATCTGTC	57.190	50.000	0.00	0.00	0.00	3.51
269	292	4.040755	ACCCTGCACCTTCTATACAATCT	58.959	43.478	0.00	0.00	0.00	2.40
275	298	3.370527	GCTTCAACCCTGCACCTTCTATA	60.371	47.826	0.00	0.00	0.00	1.31
304	327	7.039504	AGCCAATTTTAATGATCTATGCCGAAT	60.040	33.333	0.00	0.00	0.00	3.34
305	328	6.265196	AGCCAATTTTAATGATCTATGCCGAA	59.735	34.615	0.00	0.00	0.00	4.30
306	329	5.769662	AGCCAATTTTAATGATCTATGCCGA	59.230	36.000	0.00	0.00	0.00	5.54
308	331	9.196552	GTAAAGCCAATTTTAATGATCTATGCC	57.803	33.333	0.00	0.00	32.01	4.40
309	332	9.748708	TGTAAAGCCAATTTTAATGATCTATGC	57.251	29.630	0.00	0.00	32.01	3.14
329	1216	9.815936	GAAAATCATGCTTCCAAAATTGTAAAG	57.184	29.630	0.00	0.00	0.00	1.85
480	1367	2.040043	CTCCCCCTGCTCCATCCT	60.040	66.667	0.00	0.00	0.00	3.24
499	1386	1.716826	CTCTAGCCCGAGACACGACC	61.717	65.000	0.00	0.00	45.77	4.79
580	1473	3.654020	GATTGCGGCAGGATCGGC	61.654	66.667	1.67	0.00	0.00	5.54
602	1495	1.728490	GGCTTGGTGCGATCCAATCC	61.728	60.000	13.32	13.32	44.94	3.01
653	1546	2.303022	TCCTCGCTCTTCACCATTTCTT	59.697	45.455	0.00	0.00	0.00	2.52
662	1555	3.131223	CCTGAGTTAATCCTCGCTCTTCA	59.869	47.826	0.00	0.00	34.04	3.02
674	1567	1.815757	ATACCGCCCCCTGAGTTAAT	58.184	50.000	0.00	0.00	0.00	1.40
685	1578	1.452953	GGCTTGCCTTTATACCGCCC	61.453	60.000	4.11	0.00	0.00	6.13
722	1615	1.534729	GGCGATCTTGTCCCTTTTGT	58.465	50.000	0.00	0.00	0.00	2.83
747	1640	4.775058	TGAGAAAGAGGAGAAGACGAAG	57.225	45.455	0.00	0.00	0.00	3.79
783	1676	2.564553	CTAGACCAGCGTCCAGGCAC	62.565	65.000	0.00	0.00	40.12	5.01
832	1725	1.529226	CTGTACCGGGCAATTGAACA	58.471	50.000	10.34	2.32	0.00	3.18
881	1774	1.339291	CTCGCTGCATCTAGTCCATGA	59.661	52.381	0.00	0.00	0.00	3.07
922	1815	1.590238	GTGCGCATGAACTAGCTACAG	59.410	52.381	15.91	0.00	0.00	2.74
1125	2021	2.360483	CGTCTCATCAGCCACTAGTGAT	59.640	50.000	24.68	9.53	33.52	3.06
1182	2078	2.586245	CCAGGCTCGAAGGCATCA	59.414	61.111	10.20	0.00	44.19	3.07
1353	2249	2.669133	CCTTGGGTCGCCTGGATCA	61.669	63.158	0.00	0.00	0.00	2.92
1559	2471	2.038387	AAACGATGGCCCAGTGATAC	57.962	50.000	0.00	0.00	0.00	2.24
1593	2505	4.832248	TGAGCTCCGTTTACATGAGAAAT	58.168	39.130	12.15	0.00	0.00	2.17
1638	2556	2.346766	TCACATCAACACAGCTTGGT	57.653	45.000	0.00	0.00	0.00	3.67
1708	2626	8.052748	TGGTAACATATAATCAAACTCTTGCCT	58.947	33.333	0.00	0.00	46.17	4.75
1792	2744	5.049167	TGCATTTCTGTGTTTCAACCATTC	58.951	37.500	0.00	0.00	0.00	2.67
1807	2759	5.479375	ACCATCAGAATTTCAGTGCATTTCT	59.521	36.000	0.00	0.00	0.00	2.52
1882	2834	5.292765	AGTATCGTGCATGGACAAGAATAG	58.707	41.667	18.05	0.00	31.82	1.73
1897	2849	4.562789	CAGTATGGTTGTGTGAGTATCGTG	59.437	45.833	0.00	0.00	38.61	4.35
1915	2867	2.489938	TTGCGAAAGGAAGGCAGTAT	57.510	45.000	0.00	0.00	36.14	2.12
2098	3110	7.508965	ACAAAAATTAAAACTGCATGCATACG	58.491	30.769	22.97	12.59	0.00	3.06
2115	3127	5.848406	TCGGCAATACCTGAAACAAAAATT	58.152	33.333	0.00	0.00	35.61	1.82
2116	3128	5.461032	TCGGCAATACCTGAAACAAAAAT	57.539	34.783	0.00	0.00	35.61	1.82
2117	3129	4.920640	TCGGCAATACCTGAAACAAAAA	57.079	36.364	0.00	0.00	35.61	1.94
2179	3192	3.679389	ACAGGAATGCTTGTGTAGAAGG	58.321	45.455	0.00	0.00	32.54	3.46
2278	3292	9.447279	TGAAAGGAGATATAATCTACCTTCCAA	57.553	33.333	15.12	6.93	41.37	3.53
2375	3472	7.363205	ACACAAACTTGATTCCAAAAAGTTG	57.637	32.000	1.15	0.00	41.93	3.16
2378	3475	6.250089	GCAACACAAACTTGATTCCAAAAAG	58.750	36.000	0.00	0.00	0.00	2.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.