AutoCloner

Multiple sequence alignment - TraesCS2A01G290500

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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	TraesCS2A01G290500	chr2A	100.000	4135	0	0	1	4135	500534910	500530776	0.000000e+00	7637
1	TraesCS2A01G290500	chr2D	95.553	3913	110	21	1	3875	369484484	369480598	0.000000e+00	6204
2	TraesCS2A01G290500	chr2D	96.269	268	10	0	3868	4135	369480572	369480305	1.360000e-119	440
3	TraesCS2A01G290500	chr2B	95.141	2737	83	14	1	2724	439228352	439225653	0.000000e+00	4272
4	TraesCS2A01G290500	chr2B	89.132	1141	72	17	2758	3875	439225656	439224545	0.000000e+00	1373
5	TraesCS2A01G290500	chr2B	94.139	273	6	3	3868	4135	439224519	439224252	1.380000e-109	407
6	TraesCS2A01G290500	chr4A	93.465	658	38	4	1335	1988	564748298	564747642	0.000000e+00	972
7	TraesCS2A01G290500	chr7B	92.388	670	47	2	1319	1988	443642860	443643525	0.000000e+00	952
8	TraesCS2A01G290500	chr6A	92.982	627	42	1	1335	1961	449825189	449824565	0.000000e+00	913
9	TraesCS2A01G290500	chr6A	90.555	667	46	8	1335	1988	22029326	22029988	0.000000e+00	867
10	TraesCS2A01G290500	chr4B	90.601	383	29	3	1319	1694	605164390	605164008	6.170000e-138	501
11	TraesCS2A01G290500	chr4B	91.912	136	10	1	1853	1988	605164008	605163874	5.460000e-44	189

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	TraesCS2A01G290500	chr2A	500530776	500534910	4134	True	7637.000000	7637	100.0000	1	4135	1	chr2A.!!$R1	4134
1	TraesCS2A01G290500	chr2D	369480305	369484484	4179	True	3322.000000	6204	95.9110	1	4135	2	chr2D.!!$R1	4134
2	TraesCS2A01G290500	chr2B	439224252	439228352	4100	True	2017.333333	4272	92.8040	1	4135	3	chr2B.!!$R1	4134
3	TraesCS2A01G290500	chr4A	564747642	564748298	656	True	972.000000	972	93.4650	1335	1988	1	chr4A.!!$R1	653
4	TraesCS2A01G290500	chr7B	443642860	443643525	665	False	952.000000	952	92.3880	1319	1988	1	chr7B.!!$F1	669
5	TraesCS2A01G290500	chr6A	449824565	449825189	624	True	913.000000	913	92.9820	1335	1961	1	chr6A.!!$R1	626
6	TraesCS2A01G290500	chr6A	22029326	22029988	662	False	867.000000	867	90.5550	1335	1988	1	chr6A.!!$F1	653
7	TraesCS2A01G290500	chr4B	605163874	605164390	516	True	345.000000	501	91.2565	1319	1988	2	chr4B.!!$R1	669

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
539	540	0.172578	CACAGCATGCATGTTGAGGG	59.827	55.000	39.48	26.54	42.53	4.30	F
1412	1425	1.339824	CCCTGCATCAACTGAGAGCTT	60.340	52.381	0.00	0.00	32.43	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2268	2297	1.685148	GGAGAATTCCCATGAGTGCC	58.315	55.0	0.65	0.0	37.53	5.01	R
3140	3178	0.176680	GCCTCTTCTTGAGATCGGCA	59.823	55.0	9.47	0.0	45.39	5.69	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
176	177	0.687354	TTGTTCCTCTGCAGAGTCCC	59.313	55.000	35.47	24.00	40.48	4.46
179	180	0.324738	TTCCTCTGCAGAGTCCCGAT	60.325	55.000	35.47	0.00	40.48	4.18
268	269	6.893958	AAATCTTGTGACGTATGAGATGTC	57.106	37.500	0.00	0.00	43.45	3.06
301	302	6.692681	CAGTTGACAAGAATTTTTCGACATGT	59.307	34.615	0.00	0.00	32.22	3.21
347	348	6.475727	GCTTAAAAAGGAAACACTCTCCAAAC	59.524	38.462	0.00	0.00	35.20	2.93
423	424	4.689612	ACAACTCAACTCACATAGTGGT	57.310	40.909	0.00	0.00	38.88	4.16
424	425	5.036117	ACAACTCAACTCACATAGTGGTT	57.964	39.130	0.00	0.00	38.88	3.67
425	426	4.816385	ACAACTCAACTCACATAGTGGTTG	59.184	41.667	17.60	17.60	42.80	3.77
426	427	4.689612	ACTCAACTCACATAGTGGTTGT	57.310	40.909	20.39	7.82	41.17	3.32
427	428	5.036117	ACTCAACTCACATAGTGGTTGTT	57.964	39.130	20.39	11.67	41.17	2.83
486	487	6.223852	CACAAGGCTAGTAGGTAATACATGG	58.776	44.000	0.00	0.00	36.79	3.66
529	530	1.733912	TCTCGTTGATTCACAGCATGC	59.266	47.619	10.51	10.51	42.53	4.06
539	540	0.172578	CACAGCATGCATGTTGAGGG	59.827	55.000	39.48	26.54	42.53	4.30
675	678	5.373555	TCATCAATTACATCCCTTCCCTCAT	59.626	40.000	0.00	0.00	0.00	2.90
676	679	5.310409	TCAATTACATCCCTTCCCTCATC	57.690	43.478	0.00	0.00	0.00	2.92
681	684	7.594849	ATTACATCCCTTCCCTCATCATAAT	57.405	36.000	0.00	0.00	0.00	1.28
887	890	3.321968	AGGTCTGGTTTGCATTTCCTTTC	59.678	43.478	0.00	0.00	0.00	2.62
964	967	3.923017	AGCCAAGTTTGTCAGCAATAC	57.077	42.857	0.00	0.00	34.18	1.89
971	974	6.823689	CCAAGTTTGTCAGCAATACTATACCT	59.176	38.462	0.00	0.00	34.18	3.08
991	994	3.564511	CTTTATTGGTGCAACACTTCCG	58.435	45.455	2.40	0.00	39.98	4.30
1296	1299	3.891049	CAAGGGTCTTATTGGGGAAGAG	58.109	50.000	0.00	0.00	33.64	2.85
1302	1305	5.360999	GGGTCTTATTGGGGAAGAGATTTTG	59.639	44.000	0.00	0.00	33.64	2.44
1365	1369	7.068839	GTCTCTTCTCCATCTATGTCAAGGTTA	59.931	40.741	0.00	0.00	0.00	2.85
1412	1425	1.339824	CCCTGCATCAACTGAGAGCTT	60.340	52.381	0.00	0.00	32.43	3.74
1703	1721	1.973515	TGGCCTATGTAGCTCATCAGG	59.026	52.381	3.32	3.90	37.91	3.86
1990	2016	2.101917	GTGCTTGCTTCCATGCCATATT	59.898	45.455	0.00	0.00	40.37	1.28
2268	2297	7.853929	CCAATTTTGCAGAAAAAGTTCAATGAG	59.146	33.333	0.00	0.00	41.00	2.90
2674	2712	1.581223	AGTACCCCCTTAACTCCTGC	58.419	55.000	0.00	0.00	0.00	4.85
2791	2829	9.907229	CTTGTAGAAAAATTATAAGTCCCTCCT	57.093	33.333	0.00	0.00	0.00	3.69
2889	2927	6.926826	TGTGTGAGAGTACATTTACGTTGATT	59.073	34.615	0.00	0.00	32.93	2.57
3003	3041	6.721318	TCACTAATTTCTTCCTATGCCTTGT	58.279	36.000	0.00	0.00	0.00	3.16
3140	3178	5.233050	CGCATCAACTTCGATATGAAAGACT	59.767	40.000	0.00	0.00	35.79	3.24
3235	3274	9.046296	GGTTCTGGTGTGATAGTCAATAATAAG	57.954	37.037	0.00	0.00	0.00	1.73
3295	3334	7.302524	GGTGCGAACAGATATCTTTTGTTAAA	58.697	34.615	8.84	0.00	35.35	1.52
3374	3413	1.299541	CCGCTCTTATTCGGCATTGT	58.700	50.000	0.00	0.00	39.14	2.71
3485	3524	0.331616	AAATGGAAACCGGGAGAGGG	59.668	55.000	6.32	0.00	35.02	4.30
3537	3583	3.458872	CTGCTGAGTTTGCGGGATA	57.541	52.632	0.00	0.00	33.50	2.59
3544	3590	2.752354	TGAGTTTGCGGGATACATTTGG	59.248	45.455	0.00	0.00	39.74	3.28
3575	3629	3.008594	CACAAGGTGTTATGTGGTAGGGA	59.991	47.826	0.00	0.00	42.46	4.20
3583	3641	0.919289	ATGTGGTAGGGAAGGGGTGG	60.919	60.000	0.00	0.00	0.00	4.61
3714	3774	3.357079	GCACCGTTGTCCCTGCTG	61.357	66.667	0.00	0.00	0.00	4.41
3735	3795	3.271706	CTGCCAATGCACACCACGG	62.272	63.158	0.00	0.00	44.23	4.94
3741	3801	2.355197	CAATGCACACCACGGATTCTA	58.645	47.619	0.00	0.00	0.00	2.10
3784	3859	2.995939	TGACACATCAATTCTGACGAGC	59.004	45.455	0.00	0.00	33.30	5.03
3786	3861	1.667724	CACATCAATTCTGACGAGCCC	59.332	52.381	0.00	0.00	33.30	5.19
3793	3868	1.410004	TTCTGACGAGCCCCGATTAT	58.590	50.000	2.99	0.00	41.76	1.28
3794	3869	1.410004	TCTGACGAGCCCCGATTATT	58.590	50.000	2.99	0.00	41.76	1.40
3795	3870	1.068588	TCTGACGAGCCCCGATTATTG	59.931	52.381	2.99	0.00	41.76	1.90
3819	3898	6.319658	TGCTTTCACAAGAAGAGACAAGAATT	59.680	34.615	0.00	0.00	34.71	2.17
4091	4211	0.884704	TTCCTCTGCGTTTGTGCTCC	60.885	55.000	0.00	0.00	35.36	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
216	217	6.711579	AGACATGCCGTTACGTTATTATTTG	58.288	36.000	3.52	0.00	0.00	2.32
249	250	3.759418	ACGACATCTCATACGTCACAAG	58.241	45.455	0.00	0.00	33.80	3.16
301	302	1.919240	ACCACAGACGATAGGACACA	58.081	50.000	0.00	0.00	43.77	3.72
347	348	9.260002	GGTGTGATTTAATATTGGCCTTTAATG	57.740	33.333	3.32	0.00	0.00	1.90
486	487	1.335324	GCACCAGTTTGACATCTGCAC	60.335	52.381	0.00	0.00	0.00	4.57
529	530	6.183360	GGGAAAGAACATTATCCCTCAACATG	60.183	42.308	2.43	0.00	46.65	3.21
599	601	8.709272	ATAAGTACTTTGGTCTCCTATACCTC	57.291	38.462	14.49	0.00	37.91	3.85
697	700	2.717639	ACCATCCTGCTATCCAACAC	57.282	50.000	0.00	0.00	0.00	3.32
749	752	5.245350	CGAAATTAAAACTTGTTTCGGCC	57.755	39.130	10.18	0.00	45.29	6.13
819	822	9.834628	TTAGCTAAATACAACGGAAAAGAATTG	57.165	29.630	2.97	0.00	0.00	2.32
829	832	6.262601	CCAAACCATTAGCTAAATACAACGG	58.737	40.000	10.85	5.37	0.00	4.44
904	907	6.516194	GCTTACTCAAATGCCATGCTGAATAT	60.516	38.462	0.00	0.00	0.00	1.28
964	967	7.391148	AAGTGTTGCACCAATAAAGGTATAG	57.609	36.000	0.00	0.00	40.77	1.31
971	974	2.952978	ACGGAAGTGTTGCACCAATAAA	59.047	40.909	0.00	0.00	46.97	1.40
991	994	4.329462	GGTCATCCACCATCTTCTCTAC	57.671	50.000	0.00	0.00	45.98	2.59
1255	1258	6.239543	CCCTTGCATATATTTGTATTGGCCAA	60.240	38.462	23.00	23.00	0.00	4.52
1302	1305	7.121907	AAAGAATTTGGAGAATCTAGTTCTGGC	59.878	37.037	10.94	0.93	41.63	4.85
1365	1369	2.540383	TGTGAGGTGGATAGCAAGTCT	58.460	47.619	0.00	0.00	0.00	3.24
1990	2016	5.809001	AGCTTTCACTGTATCCATTTCTGA	58.191	37.500	0.00	0.00	0.00	3.27
2233	2262	8.744568	TTTTTCTGCAAAATTGGGATTAAAGT	57.255	26.923	0.00	0.00	31.39	2.66
2268	2297	1.685148	GGAGAATTCCCATGAGTGCC	58.315	55.000	0.65	0.00	37.53	5.01
2674	2712	4.380531	TCACAGAGCTTTTACTCACTTGG	58.619	43.478	0.00	0.00	39.26	3.61
2830	2868	9.676861	TCTTCATTCTCATCTGATGTTATTGTT	57.323	29.630	16.66	0.00	0.00	2.83
3140	3178	0.176680	GCCTCTTCTTGAGATCGGCA	59.823	55.000	9.47	0.00	45.39	5.69
3295	3334	1.072331	AGTCTCGGTGCACCTTTTGAT	59.928	47.619	32.28	11.99	0.00	2.57
3485	3524	3.933332	CCGGACTGGTCTTTTTCATAGAC	59.067	47.826	0.00	0.00	41.00	2.59
3502	3541	2.281276	GGACCCAACACACCGGAC	60.281	66.667	9.46	0.00	0.00	4.79
3503	3542	2.446994	AGGACCCAACACACCGGA	60.447	61.111	9.46	0.00	0.00	5.14
3504	3543	2.281484	CAGGACCCAACACACCGG	60.281	66.667	0.00	0.00	0.00	5.28
3505	3544	2.978010	GCAGGACCCAACACACCG	60.978	66.667	0.00	0.00	0.00	4.94
3506	3545	1.898574	CAGCAGGACCCAACACACC	60.899	63.158	0.00	0.00	0.00	4.16
3544	3590	1.589803	AACACCTTGTGGTCGCTAAC	58.410	50.000	0.00	0.00	46.60	2.34
3575	3629	0.776080	ACCAGGATTCACCACCCCTT	60.776	55.000	0.00	0.00	42.04	3.95
3583	3641	2.744202	GTGTGATGTGACCAGGATTCAC	59.256	50.000	3.61	3.61	43.22	3.18
3697	3757	3.357079	CAGCAGGGACAACGGTGC	61.357	66.667	0.00	0.00	36.10	5.01
3784	3859	3.694072	TCTTGTGAAAGCAATAATCGGGG	59.306	43.478	0.00	0.00	0.00	5.73
3786	3861	6.092670	TCTCTTCTTGTGAAAGCAATAATCGG	59.907	38.462	0.00	0.00	0.00	4.18
3793	3868	5.185454	TCTTGTCTCTTCTTGTGAAAGCAA	58.815	37.500	0.00	0.00	0.00	3.91
3794	3869	4.769688	TCTTGTCTCTTCTTGTGAAAGCA	58.230	39.130	0.00	0.00	0.00	3.91
3795	3870	5.741388	TTCTTGTCTCTTCTTGTGAAAGC	57.259	39.130	0.00	0.00	0.00	3.51
3819	3898	3.690628	TCTCGTGTATTGTGACGATACCA	59.309	43.478	17.87	5.94	43.26	3.25
4091	4211	1.100510	CATGGCTGGATCACCAACAG	58.899	55.000	5.56	0.00	46.32	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.