AutoCloner

Multiple sequence alignment - TraesCS4A01G438600

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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	TraesCS4A01G438600	chr4A	100.000	2949	0	0	1	2949	708467208	708464260	0.000000e+00	5446
1	TraesCS4A01G438600	chr4A	88.106	227	23	3	878	1103	708540775	708540552	1.740000e-67	267
2	TraesCS4A01G438600	chr4A	84.766	256	18	7	1	235	708543827	708543572	1.370000e-58	237
3	TraesCS4A01G438600	chr4A	86.070	201	25	1	222	419	708542175	708541975	2.300000e-51	213
4	TraesCS4A01G438600	chr7D	95.195	2102	90	9	852	2949	25131069	25133163	0.000000e+00	3312
5	TraesCS4A01G438600	chr7D	96.272	617	16	4	1	616	25129945	25130555	0.000000e+00	1005
6	TraesCS4A01G438600	chr7D	83.724	897	95	20	1	867	25056800	25057675	0.000000e+00	800
7	TraesCS4A01G438600	chr7D	87.449	247	26	4	859	1103	25057731	25057974	2.240000e-71	279
8	TraesCS4A01G438600	chr7D	78.166	229	42	6	2718	2940	25116139	25116365	3.960000e-29	139
9	TraesCS4A01G438600	chr7A	96.171	1149	35	8	1410	2554	25958267	25959410	0.000000e+00	1869
10	TraesCS4A01G438600	chr7A	94.743	875	32	8	1	867	25956627	25957495	0.000000e+00	1349
11	TraesCS4A01G438600	chr7A	93.478	552	30	4	852	1402	25957545	25958091	0.000000e+00	815
12	TraesCS4A01G438600	chr7A	85.486	689	71	5	1	666	25941452	25942134	0.000000e+00	691
13	TraesCS4A01G438600	chr7A	88.546	227	22	3	878	1103	25942375	25942598	3.750000e-69	272

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	TraesCS4A01G438600	chr4A	708464260	708467208	2948	True	5446.000000	5446	100.000000	1	2949	1	chr4A.!!$R1	2948
1	TraesCS4A01G438600	chr4A	708540552	708543827	3275	True	239.000000	267	86.314000	1	1103	3	chr4A.!!$R2	1102
2	TraesCS4A01G438600	chr7D	25129945	25133163	3218	False	2158.500000	3312	95.733500	1	2949	2	chr7D.!!$F3	2948
3	TraesCS4A01G438600	chr7D	25056800	25057974	1174	False	539.500000	800	85.586500	1	1103	2	chr7D.!!$F2	1102
4	TraesCS4A01G438600	chr7A	25956627	25959410	2783	False	1344.333333	1869	94.797333	1	2554	3	chr7A.!!$F2	2553
5	TraesCS4A01G438600	chr7A	25941452	25942598	1146	False	481.500000	691	87.016000	1	1103	2	chr7A.!!$F1	1102

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
836	3334	0.461516	GGCGCTTAGGGGTTACAGTC	60.462	60.0	7.64	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2444	5314	1.179174	GGGGAACAGCTGGTCAAACC	61.179	60.0	31.85	25.01	39.22	3.27	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
22	25	4.223320	TCAACGGATGCTTCTGAAAAAC	57.777	40.909	14.94	0.00	32.20	2.43
125	137	3.512033	TCAACGGTTGGTTTTGGAAAG	57.488	42.857	19.91	0.00	36.49	2.62
129	141	2.563620	ACGGTTGGTTTTGGAAAGTTGT	59.436	40.909	0.00	0.00	0.00	3.32
311	1762	9.103861	GGGTTATTTCTGAAACAAACAATGAAA	57.896	29.630	21.82	0.00	0.00	2.69
482	2678	9.435688	GATTTTATGGCCAAGAACATTTTTACT	57.564	29.630	10.96	0.00	0.00	2.24
484	2680	9.699703	TTTTATGGCCAAGAACATTTTTACTAC	57.300	29.630	10.96	0.00	0.00	2.73
555	2760	8.791327	TGTACATGAAGATATTGCTCAAAAGA	57.209	30.769	0.00	0.00	0.00	2.52
627	2851	2.806434	ACAAAGATTGTGGCCATAGCA	58.194	42.857	9.72	0.00	43.48	3.49
639	2863	2.575532	GCCATAGCATGCTAAAGTGGA	58.424	47.619	34.73	16.34	39.53	4.02
688	2912	3.966026	GAAGTGACTCCCGGACGCG	62.966	68.421	0.73	3.53	0.00	6.01
707	2932	3.017323	GCATGGATTGCCGAGTCG	58.983	61.111	5.29	5.29	46.15	4.18
803	3038	6.697395	CGGTGATGGAACCATAAGTATATGA	58.303	40.000	6.31	0.00	41.25	2.15
836	3334	0.461516	GGCGCTTAGGGGTTACAGTC	60.462	60.000	7.64	0.00	0.00	3.51
842	3340	2.466547	TAGGGGTTACAGTCTAGGGC	57.533	55.000	0.00	0.00	0.00	5.19
867	3365	2.626780	GCCTCCGCAAAAGGACCAC	61.627	63.158	0.00	0.00	35.83	4.16
868	3366	1.228124	CCTCCGCAAAAGGACCACA	60.228	57.895	0.00	0.00	35.83	4.17
897	3592	4.141597	TGGCATCCATAATCGTTGGACTTA	60.142	41.667	0.00	0.00	45.71	2.24
959	3655	2.355108	CGACACCTGAATCCCTCATTGT	60.355	50.000	0.00	0.00	34.40	2.71
1096	3792	2.935238	GCTCGACCTCCATGTAAGCAAA	60.935	50.000	0.00	0.00	31.06	3.68
1178	3874	6.281848	CACATGTTTCGTTGTGTAACTACT	57.718	37.500	0.00	0.00	40.47	2.57
1179	3875	6.126741	CACATGTTTCGTTGTGTAACTACTG	58.873	40.000	0.00	0.00	40.47	2.74
1211	3907	1.839994	GGATCAGTCCATCCACCTCAA	59.160	52.381	0.00	0.00	44.42	3.02
1261	3957	3.576118	AGCTACATCATCTAGGCATCGTT	59.424	43.478	0.00	0.00	0.00	3.85
1312	4008	1.227999	TTTCGCCGAGAAAGCCACTG	61.228	55.000	2.60	0.00	43.35	3.66
1315	4011	2.383527	GCCGAGAAAGCCACTGTCG	61.384	63.158	0.00	0.00	0.00	4.35
1348	4044	3.519510	CCAGGAGGGTATCAGAACTTGAA	59.480	47.826	0.00	0.00	39.77	2.69
1537	4401	8.103924	CGCAAAACATATTTAAATTGAGCTGAC	58.896	33.333	5.91	0.00	0.00	3.51
1556	4420	0.313987	CTTTGTCGGAAAGTTGGCCC	59.686	55.000	0.00	0.00	0.00	5.80
1925	4795	5.505159	GCTTCGTTGGGTTATATTGCCTTAC	60.505	44.000	0.00	0.00	0.00	2.34
1982	4852	4.044336	TGTTCAGTTTGTTGGCAATCTG	57.956	40.909	1.92	10.22	46.19	2.90
1994	4864	9.770097	TTTGTTGGCAATCTGAAATATGTAAAA	57.230	25.926	1.92	0.00	34.18	1.52
2145	5015	8.446599	ACCTTGGGAAAATTATATACTTCACG	57.553	34.615	0.00	0.00	0.00	4.35
2181	5051	4.023792	TGTTTATGTCTTCAGCAGCAACTG	60.024	41.667	0.00	0.00	39.12	3.16
2232	5102	6.641169	ACACGATGTGATGTATCAGATACT	57.359	37.500	19.39	7.08	40.41	2.12
2240	5110	7.484140	TGTGATGTATCAGATACTGAGTCAAC	58.516	38.462	19.39	9.78	44.08	3.18
2350	5220	3.558033	TGGTTTTGGGAAGTTCTACACC	58.442	45.455	2.25	3.56	0.00	4.16
2444	5314	3.940303	GCGACTGGCATAAACATAGTTG	58.060	45.455	0.00	0.00	42.87	3.16
2707	5577	0.104487	TTGGTTGCAAGCATGTGGTG	59.896	50.000	30.05	0.00	36.16	4.17
2804	5674	1.937223	ACCAACACACACACATACACG	59.063	47.619	0.00	0.00	0.00	4.49
2824	5694	5.122396	ACACGGAGAGCATAGAAAATTGAAC	59.878	40.000	0.00	0.00	0.00	3.18
2833	5703	7.380536	AGCATAGAAAATTGAACAAGCATTCA	58.619	30.769	0.00	0.00	36.80	2.57
2861	5731	7.939039	ACTACATTATAGGCACTGCATTAACAT	59.061	33.333	2.82	0.00	41.52	2.71
2862	5732	6.973843	ACATTATAGGCACTGCATTAACATG	58.026	36.000	2.82	0.00	41.52	3.21
2923	5793	4.804139	AGTCATAATAACTACACACGCTGC	59.196	41.667	0.00	0.00	0.00	5.25
2938	5808	1.732259	CGCTGCCAGACTAACGAAAAT	59.268	47.619	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	25	2.624316	AGTCAAAGTCATGCGCATTG	57.376	45.000	22.81	17.22	0.00	2.82
125	137	8.573035	TCAAGTAAAATCCAAATCCTACACAAC	58.427	33.333	0.00	0.00	0.00	3.32
129	141	8.673711	CGAATCAAGTAAAATCCAAATCCTACA	58.326	33.333	0.00	0.00	0.00	2.74
255	1703	8.035394	GGCTTCCTCATATATTCTATCGTTGAA	58.965	37.037	0.00	0.00	0.00	2.69
311	1762	3.564352	GGTCCCTGGATCAAGAAAACCAT	60.564	47.826	0.00	0.00	0.00	3.55
482	2678	4.709250	TGCATGCCATTATTTACCTCGTA	58.291	39.130	16.68	0.00	0.00	3.43
483	2679	3.550820	TGCATGCCATTATTTACCTCGT	58.449	40.909	16.68	0.00	0.00	4.18
484	2680	3.565482	ACTGCATGCCATTATTTACCTCG	59.435	43.478	16.68	0.00	0.00	4.63
496	2692	5.476599	ACTTTAATAACTTGACTGCATGCCA	59.523	36.000	16.68	2.66	0.00	4.92
555	2760	4.324331	GGTTAGGAGCCTGGTCTTGTAATT	60.324	45.833	0.00	0.00	0.00	1.40
627	2851	4.922206	TGGATCAGTTTCCACTTTAGCAT	58.078	39.130	0.00	0.00	40.90	3.79
639	2863	2.915869	TGGACTAGGGTGGATCAGTTT	58.084	47.619	0.00	0.00	0.00	2.66
707	2932	3.058224	CCCAAACAAACTCATTCGTCTCC	60.058	47.826	0.00	0.00	0.00	3.71
718	2944	0.475044	TCCGGCTACCCAAACAAACT	59.525	50.000	0.00	0.00	0.00	2.66
803	3038	0.323725	AGCGCCATCACCCTTCAAAT	60.324	50.000	2.29	0.00	0.00	2.32
842	3340	3.248630	TTTTGCGGAGGCGCTTTCG	62.249	57.895	16.98	16.98	44.10	3.46
867	3365	1.267806	GATTATGGATGCCACGCCTTG	59.732	52.381	0.00	0.00	35.80	3.61
868	3366	1.609208	GATTATGGATGCCACGCCTT	58.391	50.000	0.00	0.00	35.80	4.35
897	3592	7.817962	AGTAGCGTCAGATTAACTTTTACACAT	59.182	33.333	0.00	0.00	0.00	3.21
976	3672	7.199541	TCTTCAAAATCAGAGCTCAAAAGAG	57.800	36.000	17.77	0.00	0.00	2.85
1047	3743	1.078759	CGATGAGTTGGACGAGCACC	61.079	60.000	0.00	0.00	0.00	5.01
1096	3792	3.710209	AAGTCATGCACTTAAGAGGCT	57.290	42.857	10.09	0.00	44.13	4.58
1136	3832	9.607988	AACATGTGTCGGTAAATCAATATCTAA	57.392	29.630	0.00	0.00	0.00	2.10
1147	3843	3.622163	ACAACGAAACATGTGTCGGTAAA	59.378	39.130	35.06	0.00	41.56	2.01
1156	3852	5.277154	GCAGTAGTTACACAACGAAACATGT	60.277	40.000	0.00	0.00	39.78	3.21
1173	3869	6.325028	ACTGATCCATGTAACTATGCAGTAGT	59.675	38.462	0.00	0.00	45.56	2.73
1177	3873	4.993584	GGACTGATCCATGTAACTATGCAG	59.006	45.833	0.00	0.00	45.47	4.41
1178	3874	4.960938	GGACTGATCCATGTAACTATGCA	58.039	43.478	0.00	0.00	45.47	3.96
1193	3889	4.560739	TCTATTGAGGTGGATGGACTGAT	58.439	43.478	0.00	0.00	0.00	2.90
1292	3988	0.321653	AGTGGCTTTCTCGGCGAAAT	60.322	50.000	12.13	0.00	40.62	2.17
1312	4008	0.175760	TCCTGGATGCTAGTTGCGAC	59.824	55.000	0.00	0.00	46.63	5.19
1315	4011	0.179034	CCCTCCTGGATGCTAGTTGC	60.179	60.000	0.00	0.00	38.23	4.17
1348	4044	4.074970	AGATCAGCTCACGGTTCAAAATT	58.925	39.130	0.00	0.00	0.00	1.82
1512	4376	9.143631	AGTCAGCTCAATTTAAATATGTTTTGC	57.856	29.630	0.01	0.62	0.00	3.68
1537	4401	0.313987	GGGCCAACTTTCCGACAAAG	59.686	55.000	4.39	5.53	0.00	2.77
1542	4406	0.536460	GTTCAGGGCCAACTTTCCGA	60.536	55.000	6.18	0.00	0.00	4.55
1747	4617	4.214310	TGTTGATCAACCAACCTTGTGAT	58.786	39.130	30.66	0.00	44.20	3.06
1784	4654	9.538508	GAAAAGAGTAGTAAGACAACTGGTAAA	57.461	33.333	0.00	0.00	0.00	2.01
1786	4656	8.139989	GTGAAAAGAGTAGTAAGACAACTGGTA	58.860	37.037	0.00	0.00	0.00	3.25
2181	5051	2.591133	AGTGTGTTGTTGTTCGTTTGC	58.409	42.857	0.00	0.00	0.00	3.68
2232	5102	2.499693	TCCAATAGCATCCGTTGACTCA	59.500	45.455	0.00	0.00	0.00	3.41
2240	5110	5.571784	ATGCAATATTCCAATAGCATCCG	57.428	39.130	0.00	0.00	38.19	4.18
2444	5314	1.179174	GGGGAACAGCTGGTCAAACC	61.179	60.000	31.85	25.01	39.22	3.27
2560	5430	3.118920	CGGGTCACATATGTAAGGACACA	60.119	47.826	20.76	0.00	38.76	3.72
2707	5577	2.796031	CAACAACATGTTCCATGTGTGC	59.204	45.455	8.48	0.00	38.77	4.57
2709	5579	4.734398	AACAACAACATGTTCCATGTGT	57.266	36.364	8.48	0.00	38.77	3.72
2712	5582	4.440880	ACCAAACAACAACATGTTCCATG	58.559	39.130	8.48	10.30	42.49	3.66
2804	5674	6.032717	GCTTGTTCAATTTTCTATGCTCTCC	58.967	40.000	0.00	0.00	0.00	3.71
2824	5694	6.260714	TGCCTATAATGTAGTGTGAATGCTTG	59.739	38.462	0.00	0.00	0.00	4.01
2833	5703	4.753516	TGCAGTGCCTATAATGTAGTGT	57.246	40.909	13.72	0.00	0.00	3.55
2921	5791	7.413657	GCTTAATGTATTTTCGTTAGTCTGGCA	60.414	37.037	0.00	0.00	0.00	4.92
2923	5793	8.197988	AGCTTAATGTATTTTCGTTAGTCTGG	57.802	34.615	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.