AutoCloner

Multiple sequence alignment - TraesCS2D01G421900

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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	TraesCS2D01G421900	chr2D	100.000	2801	0	0	1	2801	535288076	535285276	0.000000e+00	5173.0
1	TraesCS2D01G421900	chr2D	87.532	770	64	16	1019	1775	535239668	535238918	0.000000e+00	861.0
2	TraesCS2D01G421900	chr2D	88.825	519	56	2	1894	2412	535272332	535271816	1.090000e-178	636.0
3	TraesCS2D01G421900	chr2D	79.362	940	161	20	1585	2512	535479693	535478775	5.090000e-177	630.0
4	TraesCS2D01G421900	chr2D	92.199	423	33	0	1623	2045	535233346	535232924	1.440000e-167	599.0
5	TraesCS2D01G421900	chr2D	88.866	476	52	1	1116	1590	535555541	535555066	4.020000e-163	584.0
6	TraesCS2D01G421900	chr2A	92.464	2800	173	15	1	2778	678548312	678545529	0.000000e+00	3967.0
7	TraesCS2D01G421900	chr2A	83.650	1370	192	21	1157	2512	678610745	678609394	0.000000e+00	1260.0
8	TraesCS2D01G421900	chr2A	92.484	612	36	2	1255	1865	677738427	677739029	0.000000e+00	867.0
9	TraesCS2D01G421900	chr2A	89.211	621	63	4	1894	2512	678450270	678449652	0.000000e+00	773.0
10	TraesCS2D01G421900	chr2A	93.377	453	25	3	2004	2456	677748989	677749436	0.000000e+00	665.0
11	TraesCS2D01G421900	chr2A	95.556	45	2	0	1008	1052	678610802	678610758	3.870000e-09	73.1
12	TraesCS2D01G421900	chr2B	94.802	1058	41	3	825	1869	636569235	636568179	0.000000e+00	1637.0
13	TraesCS2D01G421900	chr2B	87.782	1195	117	16	1271	2456	636555842	636554668	0.000000e+00	1371.0
14	TraesCS2D01G421900	chr2B	83.866	1407	197	19	1116	2510	636764879	636763491	0.000000e+00	1314.0
15	TraesCS2D01G421900	chr2B	93.664	868	55	0	1933	2800	636568180	636567313	0.000000e+00	1299.0
16	TraesCS2D01G421900	chr2B	81.849	1190	194	16	1265	2445	634191504	634192680	0.000000e+00	981.0
17	TraesCS2D01G421900	chr2B	89.165	563	57	4	1894	2456	636561547	636560989	0.000000e+00	699.0
18	TraesCS2D01G421900	chr2B	94.118	272	9	3	75	342	636569771	636569503	9.340000e-110	407.0
19	TraesCS2D01G421900	chr2B	96.203	79	3	0	1	79	636573057	636572979	2.260000e-26	130.0

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	TraesCS2D01G421900	chr2D	535285276	535288076	2800	True	5173.00	5173	100.00000	1	2801	1	chr2D.!!$R4	2800
1	TraesCS2D01G421900	chr2D	535238918	535239668	750	True	861.00	861	87.53200	1019	1775	1	chr2D.!!$R2	756
2	TraesCS2D01G421900	chr2D	535271816	535272332	516	True	636.00	636	88.82500	1894	2412	1	chr2D.!!$R3	518
3	TraesCS2D01G421900	chr2D	535478775	535479693	918	True	630.00	630	79.36200	1585	2512	1	chr2D.!!$R5	927
4	TraesCS2D01G421900	chr2A	678545529	678548312	2783	True	3967.00	3967	92.46400	1	2778	1	chr2A.!!$R2	2777
5	TraesCS2D01G421900	chr2A	677738427	677739029	602	False	867.00	867	92.48400	1255	1865	1	chr2A.!!$F1	610
6	TraesCS2D01G421900	chr2A	678449652	678450270	618	True	773.00	773	89.21100	1894	2512	1	chr2A.!!$R1	618
7	TraesCS2D01G421900	chr2A	678609394	678610802	1408	True	666.55	1260	89.60300	1008	2512	2	chr2A.!!$R3	1504
8	TraesCS2D01G421900	chr2B	636554668	636555842	1174	True	1371.00	1371	87.78200	1271	2456	1	chr2B.!!$R1	1185
9	TraesCS2D01G421900	chr2B	636763491	636764879	1388	True	1314.00	1314	83.86600	1116	2510	1	chr2B.!!$R3	1394
10	TraesCS2D01G421900	chr2B	634191504	634192680	1176	False	981.00	981	81.84900	1265	2445	1	chr2B.!!$F1	1180
11	TraesCS2D01G421900	chr2B	636567313	636573057	5744	True	868.25	1637	94.69675	1	2800	4	chr2B.!!$R4	2799
12	TraesCS2D01G421900	chr2B	636560989	636561547	558	True	699.00	699	89.16500	1894	2456	1	chr2B.!!$R2	562

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
777	4174	0.176680	ATCTGCCTGAGCACCGTTAG	59.823	55.000	0.00	0.0	46.52	2.34	F
892	4289	1.065851	TGCACAACTAGACGTGTTCGA	59.934	47.619	14.73	0.0	40.62	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1605	5038	0.111832	TGGCGACCCGGATATACTCT	59.888	55.0	0.73	0.0	0.00	3.24	R
2222	5671	0.895100	AAGGCACACATCGGCATTGT	60.895	50.0	0.00	0.0	32.21	2.71	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
48	49	1.966451	GGCGAGGTTGTCAACTGGG	60.966	63.158	15.17	5.99	0.00	4.45
110	3323	2.485903	TGGACGTAAAGAAACGCATGT	58.514	42.857	0.00	0.00	46.71	3.21
244	3457	8.923838	ATGGAATACATGGAGGTCTATCTTAT	57.076	34.615	0.00	0.00	38.70	1.73
245	3458	8.742125	TGGAATACATGGAGGTCTATCTTATT	57.258	34.615	0.00	0.00	0.00	1.40
325	3542	1.068588	CTCAATGCGGACGGATCCTTA	59.931	52.381	10.75	0.00	43.73	2.69
427	3824	5.696822	CAAGCAAGACCATATACATGATGC	58.303	41.667	0.00	0.00	33.67	3.91
429	3826	4.042560	AGCAAGACCATATACATGATGCCT	59.957	41.667	0.00	0.00	33.67	4.75
454	3851	0.612744	GGCTGAAGTTCTGGCTCTCT	59.387	55.000	23.59	0.00	37.78	3.10
461	3858	3.817709	AGTTCTGGCTCTCTCTAATGC	57.182	47.619	0.00	0.00	0.00	3.56
488	3885	0.392998	CTTGCGGCTGACTTGGGTAT	60.393	55.000	0.00	0.00	0.00	2.73
495	3892	2.103263	GGCTGACTTGGGTATACTGAGG	59.897	54.545	2.25	0.00	0.00	3.86
508	3905	2.052782	ACTGAGGGTGGTGTTTGAAC	57.947	50.000	0.00	0.00	0.00	3.18
516	3913	0.460722	TGGTGTTTGAACGGACTCGA	59.539	50.000	0.00	0.00	40.11	4.04
545	3942	0.321564	TTGAGGCCATGGACTTCACG	60.322	55.000	24.53	0.00	30.74	4.35
567	3964	1.868251	GTCGACTCTGCTTACGCGG	60.868	63.158	12.47	0.00	44.08	6.46
579	3976	0.245266	TTACGCGGCTGTCATTGAGA	59.755	50.000	12.47	0.00	0.00	3.27
580	3977	0.245266	TACGCGGCTGTCATTGAGAA	59.755	50.000	12.47	0.00	0.00	2.87
584	3981	0.798776	CGGCTGTCATTGAGAACACC	59.201	55.000	0.00	0.00	0.00	4.16
597	3994	4.016444	TGAGAACACCAAGTTTCAGCTTT	58.984	39.130	0.00	0.00	41.51	3.51
615	4012	6.018507	TCAGCTTTAGACGTGGTTTTCTAAAC	60.019	38.462	0.00	0.00	38.71	2.01
626	4023	8.932791	ACGTGGTTTTCTAAACATGTAATAGAG	58.067	33.333	16.46	9.28	46.67	2.43
636	4033	6.963049	AACATGTAATAGAGGTTTGTCGTC	57.037	37.500	0.00	0.00	0.00	4.20
677	4074	5.012458	AGCACATGAGCTAGCTAATATTGGA	59.988	40.000	19.38	0.00	44.50	3.53
679	4076	6.226052	CACATGAGCTAGCTAATATTGGACA	58.774	40.000	19.38	8.38	0.00	4.02
692	4089	7.387948	GCTAATATTGGACACTTGTACCCTATG	59.612	40.741	2.52	0.00	0.00	2.23
702	4099	6.442564	ACACTTGTACCCTATGAACCAGATTA	59.557	38.462	0.00	0.00	0.00	1.75
704	4101	7.442364	CACTTGTACCCTATGAACCAGATTATG	59.558	40.741	0.00	0.00	0.00	1.90
731	4128	1.005569	TCGAGGGTCTGATGTACCAGT	59.994	52.381	0.00	0.00	38.87	4.00
756	4153	1.963338	GGCTGCTTGTGCTTCGAGT	60.963	57.895	0.00	0.00	40.48	4.18
773	4170	2.580815	TGATCTGCCTGAGCACCG	59.419	61.111	0.00	0.00	46.52	4.94
777	4174	0.176680	ATCTGCCTGAGCACCGTTAG	59.823	55.000	0.00	0.00	46.52	2.34
887	4284	2.717580	TACCTGCACAACTAGACGTG	57.282	50.000	0.00	4.27	36.18	4.49
889	4286	1.138266	ACCTGCACAACTAGACGTGTT	59.862	47.619	14.73	0.00	35.51	3.32
892	4289	1.065851	TGCACAACTAGACGTGTTCGA	59.934	47.619	14.73	0.00	40.62	3.71
988	4385	6.718522	AAAGATGTACTAGGGCTAGTCTTC	57.281	41.667	0.00	0.00	44.58	2.87
1105	4523	1.138883	CGAAGGTCAATCGCTCCGA	59.861	57.895	0.00	0.00	41.13	4.55
1299	4717	3.807538	GCCTGCGACGAGTACGGA	61.808	66.667	0.00	0.00	44.46	4.69
1547	4980	1.718757	GGCAAGCATGTCATCGACCC	61.719	60.000	0.00	0.00	0.00	4.46
1605	5038	0.614697	TCCTCTGGGCACGAGATTCA	60.615	55.000	9.04	0.00	43.53	2.57
1800	5239	2.100252	CGATAAGGACGGCCTGTTCTAA	59.900	50.000	12.91	0.00	46.28	2.10
1843	5282	3.708403	TCAGTGCTGTGGATCTCAATT	57.292	42.857	0.00	0.00	0.00	2.32
1872	5311	0.107508	CGAGGCTGACCATGACCATT	60.108	55.000	0.00	0.00	39.06	3.16
1898	5337	3.181479	CCCACGTCGAGAATGAGGATTTA	60.181	47.826	0.00	0.00	0.00	1.40
1978	5417	5.017490	AGAATACCATAGATACCCCACTCG	58.983	45.833	0.00	0.00	0.00	4.18
2222	5671	1.810151	GTGCGCAATCTTTCTTGGGTA	59.190	47.619	14.00	0.00	40.21	3.69
2277	5726	3.389925	ACATTGGAACCAAACTGCATG	57.610	42.857	10.36	5.83	39.55	4.06
2311	5762	5.436175	ACGATTTTGACCATCCATCATGTA	58.564	37.500	0.00	0.00	0.00	2.29
2312	5763	6.064060	ACGATTTTGACCATCCATCATGTAT	58.936	36.000	0.00	0.00	0.00	2.29
2351	5802	6.760440	AGATCTTGGTATCTGGAACATCAT	57.240	37.500	0.00	0.00	38.20	2.45
2400	5851	0.249155	CGTGGCCAATCATGCATTCC	60.249	55.000	7.24	0.00	0.00	3.01
2420	5871	1.689273	CTGGCTAGATTTACCGGCTCT	59.311	52.381	0.00	1.03	0.00	4.09
2512	5963	4.778415	CACGACGTGCGAGGAGGG	62.778	72.222	16.06	0.00	44.57	4.30
2706	6157	3.403968	TGTATGTATGGCACACACGTTT	58.596	40.909	0.00	0.00	39.51	3.60
2714	6165	2.105528	ACACACGTTTCGGCGAGT	59.894	55.556	10.46	1.31	36.21	4.18
2730	6181	1.526887	CGAGTGAACATGCGAAAGTGT	59.473	47.619	0.00	0.00	0.00	3.55
2747	6198	6.402766	CGAAAGTGTGTACCTTTTGTCAAAGA	60.403	38.462	0.00	0.00	41.97	2.52
2761	6212	8.939201	TTTTGTCAAAGAACTTGCATTGATTA	57.061	26.923	1.79	0.00	34.62	1.75
2764	6215	7.660112	TGTCAAAGAACTTGCATTGATTATGT	58.340	30.769	1.79	0.00	36.57	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	2.996621	CCAACTCCAACAGAAGATCGAC	59.003	50.000	0.00	0.00	0.00	4.20
110	3323	6.543465	CAGAGCCACCAAAATGTCAGAATATA	59.457	38.462	0.00	0.00	0.00	0.86
244	3457	6.529829	CGACAACAATTTTCTTTGGTTCAGAA	59.470	34.615	0.00	0.00	0.00	3.02
245	3458	6.033341	CGACAACAATTTTCTTTGGTTCAGA	58.967	36.000	0.00	0.00	0.00	3.27
305	3518	4.033894	GGATCCGTCCGCATTGAG	57.966	61.111	0.00	0.00	34.13	3.02
319	3536	3.135530	GCTCATCACCTGGAACTAAGGAT	59.864	47.826	0.00	0.00	38.27	3.24
325	3542	1.681166	GCATGCTCATCACCTGGAACT	60.681	52.381	11.37	0.00	0.00	3.01
385	3606	3.357079	CCTCACTTGCGGCCACAC	61.357	66.667	2.24	0.00	0.00	3.82
395	3616	0.538287	GGTCTTGCTTGCCCTCACTT	60.538	55.000	0.00	0.00	0.00	3.16
406	3627	4.042560	AGGCATCATGTATATGGTCTTGCT	59.957	41.667	0.00	0.00	34.97	3.91
427	3824	0.954452	AGAACTTCAGCCGCAAAAGG	59.046	50.000	8.95	0.00	0.00	3.11
429	3826	0.667993	CCAGAACTTCAGCCGCAAAA	59.332	50.000	0.00	0.00	0.00	2.44
454	3851	1.077787	CAAGGGCCACGGCATTAGA	60.078	57.895	10.83	0.00	44.11	2.10
488	3885	2.484065	CGTTCAAACACCACCCTCAGTA	60.484	50.000	0.00	0.00	0.00	2.74
495	3892	0.942252	GAGTCCGTTCAAACACCACC	59.058	55.000	0.00	0.00	0.00	4.61
508	3905	1.986378	CAACTAGCAGTTTCGAGTCCG	59.014	52.381	0.00	0.00	36.03	4.79
516	3913	2.440409	CATGGCCTCAACTAGCAGTTT	58.560	47.619	3.32	0.00	36.03	2.66
564	3961	0.166814	GTGTTCTCAATGACAGCCGC	59.833	55.000	0.00	0.00	0.00	6.53
567	3964	2.880890	ACTTGGTGTTCTCAATGACAGC	59.119	45.455	0.00	0.00	0.00	4.40
579	3976	4.035208	CGTCTAAAGCTGAAACTTGGTGTT	59.965	41.667	0.00	0.00	41.29	3.32
580	3977	3.560068	CGTCTAAAGCTGAAACTTGGTGT	59.440	43.478	0.00	0.00	0.00	4.16
584	3981	3.560068	ACCACGTCTAAAGCTGAAACTTG	59.440	43.478	0.00	0.00	0.00	3.16
597	3994	8.836268	ATTACATGTTTAGAAAACCACGTCTA	57.164	30.769	2.30	0.00	0.00	2.59
615	4012	5.100259	ACGACGACAAACCTCTATTACATG	58.900	41.667	0.00	0.00	0.00	3.21
621	4018	3.427233	GCACTACGACGACAAACCTCTAT	60.427	47.826	0.00	0.00	0.00	1.98
626	4023	1.210870	TTGCACTACGACGACAAACC	58.789	50.000	0.00	0.00	0.00	3.27
636	4033	0.026285	GCTACCGCATTTGCACTACG	59.974	55.000	3.13	0.00	42.21	3.51
656	4053	6.042552	AGTGTCCAATATTAGCTAGCTCATGT	59.957	38.462	23.26	11.71	0.00	3.21
668	4065	8.555896	TCATAGGGTACAAGTGTCCAATATTA	57.444	34.615	0.00	0.00	0.00	0.98
677	4074	4.164981	TCTGGTTCATAGGGTACAAGTGT	58.835	43.478	0.00	0.00	0.00	3.55
679	4076	7.420214	CCATAATCTGGTTCATAGGGTACAAGT	60.420	40.741	0.00	0.00	40.49	3.16
692	4089	5.641209	CCTCGATCATTCCATAATCTGGTTC	59.359	44.000	0.00	0.00	46.08	3.62
702	4099	2.682594	TCAGACCCTCGATCATTCCAT	58.317	47.619	0.00	0.00	0.00	3.41
704	4101	2.366916	ACATCAGACCCTCGATCATTCC	59.633	50.000	0.00	0.00	0.00	3.01
712	4109	1.405821	GACTGGTACATCAGACCCTCG	59.594	57.143	6.18	0.00	38.20	4.63
716	4113	2.567615	ACTTGGACTGGTACATCAGACC	59.432	50.000	11.68	11.68	45.35	3.85
771	4168	6.307077	GCAAGCAAAACTTTATAACCTAACGG	59.693	38.462	0.00	0.00	36.04	4.44
773	4170	7.865889	ACAGCAAGCAAAACTTTATAACCTAAC	59.134	33.333	0.00	0.00	36.04	2.34
777	4174	6.212955	TGACAGCAAGCAAAACTTTATAACC	58.787	36.000	0.00	0.00	36.04	2.85
806	4203	4.770531	GGTTGGCCAGGTTAGTAATTTTCT	59.229	41.667	5.11	0.00	34.09	2.52
846	4243	3.215975	ACTTTAGCCTGCCACGTTTAAA	58.784	40.909	0.00	0.00	0.00	1.52
887	4284	4.142093	TGGCCAGGTTATAGTACTTCGAAC	60.142	45.833	0.00	3.26	0.00	3.95
889	4286	3.634504	TGGCCAGGTTATAGTACTTCGA	58.365	45.455	0.00	0.00	0.00	3.71
892	4289	3.201487	GGGTTGGCCAGGTTATAGTACTT	59.799	47.826	5.11	0.00	36.17	2.24
1547	4980	0.179134	GTTCTCGTCATCACTCCCGG	60.179	60.000	0.00	0.00	0.00	5.73
1605	5038	0.111832	TGGCGACCCGGATATACTCT	59.888	55.000	0.73	0.00	0.00	3.24
1800	5239	6.554982	TGATGGAGGCAGTATTATGTAGAACT	59.445	38.462	0.00	0.00	0.00	3.01
1872	5311	0.956902	TCATTCTCGACGTGGGACGA	60.957	55.000	2.62	0.00	46.05	4.20
1898	5337	4.575718	CGCGACGACGAGATACATATTAT	58.424	43.478	12.29	0.00	41.48	1.28
1978	5417	3.857665	TCTTTGTATGTCGTGCGATTCTC	59.142	43.478	0.00	0.00	0.00	2.87
2222	5671	0.895100	AAGGCACACATCGGCATTGT	60.895	50.000	0.00	0.00	32.21	2.71
2277	5726	3.550678	GGTCAAAATCGTCCGTGAGATAC	59.449	47.826	0.00	0.00	0.00	2.24
2351	5802	4.767578	AGCTTCTGCATAATCCTCTTCA	57.232	40.909	0.00	0.00	42.74	3.02
2400	5851	1.689273	AGAGCCGGTAAATCTAGCCAG	59.311	52.381	1.90	0.00	0.00	4.85
2420	5871	6.348950	CGCTAAACTTGGTGTGATCCAAATTA	60.349	38.462	0.00	0.00	45.26	1.40
2650	6101	4.380973	CGCTATCCTACCAATCGTCATCAT	60.381	45.833	0.00	0.00	0.00	2.45
2706	6157	2.757155	TTCGCATGTTCACTCGCCGA	62.757	55.000	0.00	0.00	0.00	5.54
2714	6165	2.546368	GGTACACACTTTCGCATGTTCA	59.454	45.455	0.00	0.00	0.00	3.18
2730	6181	5.184096	TGCAAGTTCTTTGACAAAAGGTACA	59.816	36.000	1.62	0.00	42.66	2.90
2747	6198	8.907222	AAGGAAAAACATAATCAATGCAAGTT	57.093	26.923	0.00	0.00	39.39	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.