AutoCloner

Multiple sequence alignment - TraesCS4A01G114400

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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	TraesCS4A01G114400	chr4A	100.000	2540	0	0	1	2540	138834036	138831497	0.000000e+00	4691.0
1	TraesCS4A01G114400	chr4D	92.835	1926	71	31	366	2264	334631620	334633505	0.000000e+00	2730.0
2	TraesCS4A01G114400	chr4D	90.956	387	16	13	1	383	334631238	334631609	1.050000e-138	503.0
3	TraesCS4A01G114400	chr4D	94.909	275	10	3	2269	2540	334633563	334633836	6.490000e-116	427.0
4	TraesCS4A01G114400	chr4D	97.059	34	1	0	242	275	366225747	366225714	9.810000e-05	58.4
5	TraesCS4A01G114400	chr4B	94.397	1767	46	28	334	2076	412590081	412591818	0.000000e+00	2665.0
6	TraesCS4A01G114400	chr4B	91.649	467	14	6	2075	2540	412591889	412592331	7.720000e-175	623.0
7	TraesCS4A01G114400	chr4B	88.563	341	19	11	1	332	412588494	412588823	1.830000e-106	396.0
8	TraesCS4A01G114400	chr2B	84.831	534	72	7	1004	1532	65883477	65882948	1.730000e-146	529.0
9	TraesCS4A01G114400	chr2B	100.000	30	0	0	246	275	229184214	229184243	3.530000e-04	56.5
10	TraesCS4A01G114400	chr2D	84.701	536	69	10	1004	1532	37646346	37645817	8.050000e-145	523.0
11	TraesCS4A01G114400	chr2A	84.171	537	70	12	1004	1532	42495221	42494692	8.110000e-140	507.0
12	TraesCS4A01G114400	chr1D	81.065	507	79	8	1027	1529	392697011	392697504	3.060000e-104	388.0
13	TraesCS4A01G114400	chr1A	80.830	506	80	7	1027	1528	492652782	492652290	5.130000e-102	381.0
14	TraesCS4A01G114400	chr1B	80.473	507	82	7	1027	1529	529998581	529998088	3.090000e-99	372.0
15	TraesCS4A01G114400	chr3D	78.389	509	85	16	1012	1503	454904066	454904566	8.830000e-80	307.0
16	TraesCS4A01G114400	chr5B	100.000	32	0	0	246	277	22766065	22766096	2.730000e-05	60.2
17	TraesCS4A01G114400	chr5B	100.000	32	0	0	246	277	22766428	22766459	2.730000e-05	60.2
18	TraesCS4A01G114400	chr5B	94.286	35	2	0	243	277	532460194	532460228	1.000000e-03	54.7
19	TraesCS4A01G114400	chr6B	100.000	30	0	0	247	276	157666705	157666734	3.530000e-04	56.5
20	TraesCS4A01G114400	chr5D	94.286	35	2	0	243	277	437990208	437990242	1.000000e-03	54.7

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	TraesCS4A01G114400	chr4A	138831497	138834036	2539	True	4691	4691	100.000000	1	2540	1	chr4A.!!$R1	2539
1	TraesCS4A01G114400	chr4D	334631238	334633836	2598	False	1220	2730	92.900000	1	2540	3	chr4D.!!$F1	2539
2	TraesCS4A01G114400	chr4B	412588494	412592331	3837	False	1228	2665	91.536333	1	2540	3	chr4B.!!$F1	2539
3	TraesCS4A01G114400	chr2B	65882948	65883477	529	True	529	529	84.831000	1004	1532	1	chr2B.!!$R1	528
4	TraesCS4A01G114400	chr2D	37645817	37646346	529	True	523	523	84.701000	1004	1532	1	chr2D.!!$R1	528
5	TraesCS4A01G114400	chr2A	42494692	42495221	529	True	507	507	84.171000	1004	1532	1	chr2A.!!$R1	528
6	TraesCS4A01G114400	chr3D	454904066	454904566	500	False	307	307	78.389000	1012	1503	1	chr3D.!!$F1	491

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
322	331	0.588252	CACCCAGTATTGCGCTATGC	59.412	55.0	14.76	13.12	46.7	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1963	3284	2.125147	TGCTGGCTACCGATGCAC	60.125	61.111	0.0	0.0	0.0	4.57	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
171	178	4.477536	TGCCTCTCTCCCTATTCTATGT	57.522	45.455	0.00	0.00	0.00	2.29
184	192	1.019673	TCTATGTCCGGCACTCGTAC	58.980	55.000	0.00	0.00	37.11	3.67
284	293	9.738832	GAGACATAGTTATTTCTCACTTACTCC	57.261	37.037	9.38	0.00	38.66	3.85
285	294	8.407064	AGACATAGTTATTTCTCACTTACTCCG	58.593	37.037	0.00	0.00	0.00	4.63
296	305	3.878103	TCACTTACTCCGTAGATGAGAGC	59.122	47.826	0.00	0.00	33.95	4.09
297	306	3.628032	CACTTACTCCGTAGATGAGAGCA	59.372	47.826	0.00	0.00	33.95	4.26
320	329	1.209504	ACACACCCAGTATTGCGCTAT	59.790	47.619	9.73	9.73	0.00	2.97
321	330	1.599071	CACACCCAGTATTGCGCTATG	59.401	52.381	14.76	0.00	0.00	2.23
322	331	0.588252	CACCCAGTATTGCGCTATGC	59.412	55.000	14.76	13.12	46.70	3.14
358	1621	5.316987	AGTAAGCAATGATATTACCCCAGC	58.683	41.667	0.00	0.00	31.21	4.85
359	1622	3.160679	AGCAATGATATTACCCCAGCC	57.839	47.619	0.00	0.00	0.00	4.85
360	1623	2.446666	AGCAATGATATTACCCCAGCCA	59.553	45.455	0.00	0.00	0.00	4.75
361	1624	2.821969	GCAATGATATTACCCCAGCCAG	59.178	50.000	0.00	0.00	0.00	4.85
362	1625	2.821969	CAATGATATTACCCCAGCCAGC	59.178	50.000	0.00	0.00	0.00	4.85
363	1626	1.517238	TGATATTACCCCAGCCAGCA	58.483	50.000	0.00	0.00	0.00	4.41
364	1627	2.065007	TGATATTACCCCAGCCAGCAT	58.935	47.619	0.00	0.00	0.00	3.79
490	1782	4.821589	GGCCGGCTGGTCTCTTCG	62.822	72.222	28.56	0.00	36.72	3.79
599	1891	3.945981	TTTGCTCCGGAATTTAAACCC	57.054	42.857	5.23	0.00	0.00	4.11
609	1901	6.213195	TCCGGAATTTAAACCCTTAGAGTACA	59.787	38.462	0.00	0.00	0.00	2.90
680	1972	6.093633	GGAAAACACAAGTGGGAGATACATAC	59.906	42.308	5.08	0.00	34.19	2.39
786	2080	4.097361	GTCGGCCTCCTCCCCAAC	62.097	72.222	0.00	0.00	0.00	3.77
931	2231	1.379176	CACCACAACCACCACCACA	60.379	57.895	0.00	0.00	0.00	4.17
1374	2692	4.555709	GTCACCACCGTGCACCCA	62.556	66.667	12.15	0.00	40.04	4.51
1547	2865	3.680786	CGTGTCGTGAGGCCTCCA	61.681	66.667	29.95	17.37	32.11	3.86
1550	2868	4.083862	GTCGTGAGGCCTCCACCC	62.084	72.222	29.95	13.73	0.00	4.61
1573	2891	1.539560	CCCTGGATGCGATCGATCCT	61.540	60.000	29.81	11.66	40.26	3.24
1643	2963	0.840722	TTCTCCCCACTTGGTCCTCC	60.841	60.000	0.00	0.00	0.00	4.30
1674	2994	6.015940	ACATTTGACCATCTTGTTTCCTCTTC	60.016	38.462	0.00	0.00	0.00	2.87
1675	2995	4.982241	TGACCATCTTGTTTCCTCTTCT	57.018	40.909	0.00	0.00	0.00	2.85
1676	2996	5.310409	TGACCATCTTGTTTCCTCTTCTT	57.690	39.130	0.00	0.00	0.00	2.52
1861	3181	2.459934	TCGACATCGGATGTTCATTCG	58.540	47.619	23.40	20.26	45.03	3.34
1885	3205	5.988310	TTGTCAAGTTTACTCGATCCCTA	57.012	39.130	0.00	0.00	0.00	3.53
1963	3284	1.525197	TCGAGCTTGTTAAACTGCACG	59.475	47.619	0.00	8.19	39.92	5.34
1964	3285	1.260561	CGAGCTTGTTAAACTGCACGT	59.739	47.619	0.00	0.00	35.49	4.49
2038	3364	1.717032	TGTGTGTCTCCTAGCTGGTT	58.283	50.000	0.00	0.00	37.07	3.67
2112	3510	9.988815	AATCTTAATCTAGCCATTACAGTACAG	57.011	33.333	0.00	0.00	0.00	2.74
2140	3538	3.934068	ACCAATCGACCGATAACTTTGT	58.066	40.909	5.27	0.00	33.97	2.83
2143	3541	4.630069	CCAATCGACCGATAACTTTGTTCT	59.370	41.667	5.27	0.00	33.97	3.01
2147	3545	5.535333	TCGACCGATAACTTTGTTCTCTTT	58.465	37.500	0.00	0.00	0.00	2.52
2221	3621	3.963383	AATTAAACTAAGCGGCCGATG	57.037	42.857	33.48	15.38	0.00	3.84
2222	3622	1.011333	TTAAACTAAGCGGCCGATGC	58.989	50.000	33.48	12.00	0.00	3.91
2223	3623	0.108089	TAAACTAAGCGGCCGATGCA	60.108	50.000	33.48	14.22	40.13	3.96
2224	3624	0.748005	AAACTAAGCGGCCGATGCAT	60.748	50.000	33.48	11.09	40.13	3.96
2225	3625	1.439353	AACTAAGCGGCCGATGCATG	61.439	55.000	33.48	16.24	40.13	4.06
2226	3626	1.595109	CTAAGCGGCCGATGCATGA	60.595	57.895	33.48	5.62	40.13	3.07
2227	3627	1.153269	TAAGCGGCCGATGCATGAA	60.153	52.632	33.48	1.49	40.13	2.57
2233	3633	1.102809	GGCCGATGCATGAACCATGA	61.103	55.000	2.46	0.00	43.81	3.07
2267	3667	8.658499	ATCTTTCCTACGACAATGTATAAACC	57.342	34.615	0.00	0.00	0.00	3.27
2274	3674	7.655732	CCTACGACAATGTATAAACCATGATGA	59.344	37.037	0.00	0.00	0.00	2.92
2388	3842	8.530269	ACGTTTCTGAGACGAAAAATATAGTT	57.470	30.769	24.82	0.00	42.82	2.24
2403	3857	4.329545	GTTCCGGGGTGCTCAGCA	62.330	66.667	0.00	0.00	35.60	4.41
2420	3874	0.250467	GCAGGAAGGTGCAGTTCAGA	60.250	55.000	10.21	0.00	43.41	3.27
2466	3920	4.035208	GCGATTAAATCAATCACGTCCCTT	59.965	41.667	0.00	0.00	42.86	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
143	150	6.625267	AGAATAGGGAGAGAGGCAAGTAATA	58.375	40.000	0.00	0.00	0.00	0.98
171	178	1.184431	TTAATGGTACGAGTGCCGGA	58.816	50.000	5.05	0.00	43.93	5.14
275	284	3.628032	TGCTCTCATCTACGGAGTAAGTG	59.372	47.826	0.00	0.00	45.13	3.16
277	286	4.576873	TCTTGCTCTCATCTACGGAGTAAG	59.423	45.833	11.71	11.71	45.13	2.34
279	288	3.878103	GTCTTGCTCTCATCTACGGAGTA	59.122	47.826	0.00	0.00	45.11	2.59
281	290	2.685388	TGTCTTGCTCTCATCTACGGAG	59.315	50.000	0.00	0.00	0.00	4.63
282	291	2.423892	GTGTCTTGCTCTCATCTACGGA	59.576	50.000	0.00	0.00	0.00	4.69
283	292	2.164422	TGTGTCTTGCTCTCATCTACGG	59.836	50.000	0.00	0.00	0.00	4.02
284	293	3.175152	GTGTGTCTTGCTCTCATCTACG	58.825	50.000	0.00	0.00	0.00	3.51
285	294	3.516615	GGTGTGTCTTGCTCTCATCTAC	58.483	50.000	0.00	0.00	0.00	2.59
296	305	1.464608	CGCAATACTGGGTGTGTCTTG	59.535	52.381	0.00	0.00	0.00	3.02
297	306	1.808411	CGCAATACTGGGTGTGTCTT	58.192	50.000	0.00	0.00	0.00	3.01
315	324	0.242286	AGCTAGACGGATGCATAGCG	59.758	55.000	0.00	0.00	44.21	4.26
320	329	2.293677	GCTTACTAGCTAGACGGATGCA	59.706	50.000	27.45	0.00	44.27	3.96
321	330	2.936316	GCTTACTAGCTAGACGGATGC	58.064	52.381	27.45	16.51	44.27	3.91
358	1621	5.540400	ATTCCATTATTTCACCATGCTGG	57.460	39.130	1.16	1.16	45.02	4.85
359	1622	8.199449	ACTAAATTCCATTATTTCACCATGCTG	58.801	33.333	0.00	0.00	0.00	4.41
360	1623	8.310122	ACTAAATTCCATTATTTCACCATGCT	57.690	30.769	0.00	0.00	0.00	3.79
399	1691	2.530497	CCACACCCACACGAACACG	61.530	63.158	0.00	0.00	0.00	4.49
405	1697	1.674817	GGACTAATCCACACCCACACG	60.675	57.143	0.00	0.00	45.47	4.49
786	2080	4.347000	TGGAATATCTTTCGAAGGTAGGGG	59.653	45.833	7.20	0.00	0.00	4.79
931	2231	2.115911	CGACGCCTGCTAGGACTCT	61.116	63.158	6.40	0.00	37.67	3.24
1550	2868	2.746359	GATCGCATCCAGGGAGGG	59.254	66.667	1.81	0.00	42.97	4.30
1587	2905	3.073678	CGAAGAAACACACATCCATCCA	58.926	45.455	0.00	0.00	0.00	3.41
1861	3181	4.995487	AGGGATCGAGTAAACTTGACAAAC	59.005	41.667	2.11	0.00	39.07	2.93
1885	3205	5.491070	TGATTAGCTATGCTCAACAACACT	58.509	37.500	0.00	0.00	40.44	3.55
1963	3284	2.125147	TGCTGGCTACCGATGCAC	60.125	61.111	0.00	0.00	0.00	4.57
1964	3285	2.125147	GTGCTGGCTACCGATGCA	60.125	61.111	0.00	0.00	0.00	3.96
2038	3364	6.377712	TGATGCAATAAATTGGTCATCTGACA	59.622	34.615	12.10	0.00	46.47	3.58
2221	3621	5.475909	AGATCATGGTTATCATGGTTCATGC	59.524	40.000	5.56	0.00	46.48	4.06
2222	3622	7.520451	AAGATCATGGTTATCATGGTTCATG	57.480	36.000	5.56	9.15	46.48	3.07
2223	3623	7.232127	GGAAAGATCATGGTTATCATGGTTCAT	59.768	37.037	5.56	0.00	46.48	2.57
2224	3624	6.547141	GGAAAGATCATGGTTATCATGGTTCA	59.453	38.462	5.56	0.00	46.48	3.18
2225	3625	6.774656	AGGAAAGATCATGGTTATCATGGTTC	59.225	38.462	5.56	3.80	46.48	3.62
2226	3626	6.676558	AGGAAAGATCATGGTTATCATGGTT	58.323	36.000	5.56	0.00	46.48	3.67
2233	3633	6.479972	TGTCGTAGGAAAGATCATGGTTAT	57.520	37.500	0.00	0.00	0.00	1.89
2246	3646	7.557724	TCATGGTTTATACATTGTCGTAGGAA	58.442	34.615	0.00	0.00	0.00	3.36
2274	3674	9.412460	TGGATTCATAACATTTGCTCTATTCTT	57.588	29.630	0.00	0.00	0.00	2.52
2403	3857	0.398318	GGTCTGAACTGCACCTTCCT	59.602	55.000	0.00	0.00	0.00	3.36
2420	3874	0.468029	CAAGTTGAGCCCCAAGTGGT	60.468	55.000	0.00	0.00	38.38	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.