AutoCloner

Multiple sequence alignment - TraesCS5D01G262200

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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	TraesCS5D01G262200	chr5D	100.000	4722	0	0	1	4722	368284533	368289254	0.000000e+00	8720.0
1	TraesCS5D01G262200	chr5D	84.734	2522	307	46	1238	3726	368029249	368031725	0.000000e+00	2453.0
2	TraesCS5D01G262200	chr5D	84.388	2498	310	50	1266	3726	368078401	368080855	0.000000e+00	2379.0
3	TraesCS5D01G262200	chr5D	86.550	2000	234	19	1542	3510	368244605	368246600	0.000000e+00	2170.0
4	TraesCS5D01G262200	chr5D	77.660	752	113	29	3742	4474	368031715	368032430	1.580000e-109	407.0
5	TraesCS5D01G262200	chr5A	94.997	4757	167	35	1	4722	470168910	470173630	0.000000e+00	7400.0
6	TraesCS5D01G262200	chr5A	85.178	2530	316	40	1233	3726	470076280	470078786	0.000000e+00	2540.0
7	TraesCS5D01G262200	chr5A	79.077	1018	152	35	3743	4722	469900723	469901717	1.110000e-180	643.0
8	TraesCS5D01G262200	chr5A	78.129	759	111	29	3742	4481	470078776	470079498	9.390000e-117	431.0
9	TraesCS5D01G262200	chr5B	94.646	4763	173	38	1	4722	436207661	436212382	0.000000e+00	7308.0
10	TraesCS5D01G262200	chr5B	84.822	2530	302	45	1234	3726	436152476	436154960	0.000000e+00	2470.0
11	TraesCS5D01G262200	chr5B	86.471	1981	234	21	1542	3493	436162915	436164890	0.000000e+00	2143.0
12	TraesCS5D01G262200	chr5B	86.047	1978	205	38	1234	3180	436095745	436097682	0.000000e+00	2058.0
13	TraesCS5D01G262200	chr5B	78.129	759	111	29	3742	4481	436098071	436098793	9.390000e-117	431.0
14	TraesCS5D01G262200	chr5B	81.967	488	65	9	3742	4225	436154950	436155418	4.430000e-105	392.0
15	TraesCS5D01G262200	chr5B	82.051	78	11	3	5	81	530102668	530102743	3.940000e-06	63.9
16	TraesCS5D01G262200	chr7D	82.524	103	14	4	58	158	620459053	620459153	2.340000e-13	87.9
17	TraesCS5D01G262200	chr4D	78.571	112	15	8	52	158	442153271	442153378	1.100000e-06	65.8
18	TraesCS5D01G262200	chr7B	87.037	54	1	6	70	122	708437572	708437524	6.600000e-04	56.5
19	TraesCS5D01G262200	chr7B	88.636	44	4	1	54	97	640785563	640785605	9.000000e-03	52.8

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	TraesCS5D01G262200	chr5D	368284533	368289254	4721	False	8720.0	8720	100.0000	1	4722	1	chr5D.!!$F3	4721
1	TraesCS5D01G262200	chr5D	368078401	368080855	2454	False	2379.0	2379	84.3880	1266	3726	1	chr5D.!!$F1	2460
2	TraesCS5D01G262200	chr5D	368244605	368246600	1995	False	2170.0	2170	86.5500	1542	3510	1	chr5D.!!$F2	1968
3	TraesCS5D01G262200	chr5D	368029249	368032430	3181	False	1430.0	2453	81.1970	1238	4474	2	chr5D.!!$F4	3236
4	TraesCS5D01G262200	chr5A	470168910	470173630	4720	False	7400.0	7400	94.9970	1	4722	1	chr5A.!!$F2	4721
5	TraesCS5D01G262200	chr5A	470076280	470079498	3218	False	1485.5	2540	81.6535	1233	4481	2	chr5A.!!$F3	3248
6	TraesCS5D01G262200	chr5A	469900723	469901717	994	False	643.0	643	79.0770	3743	4722	1	chr5A.!!$F1	979
7	TraesCS5D01G262200	chr5B	436207661	436212382	4721	False	7308.0	7308	94.6460	1	4722	1	chr5B.!!$F2	4721
8	TraesCS5D01G262200	chr5B	436162915	436164890	1975	False	2143.0	2143	86.4710	1542	3493	1	chr5B.!!$F1	1951
9	TraesCS5D01G262200	chr5B	436152476	436155418	2942	False	1431.0	2470	83.3945	1234	4225	2	chr5B.!!$F5	2991
10	TraesCS5D01G262200	chr5B	436095745	436098793	3048	False	1244.5	2058	82.0880	1234	4481	2	chr5B.!!$F4	3247

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	Hairpin	End Stability	Orientation
662	695	2.550101	GCCGCCATTGAGATCCAGC	61.550	63.158	0.00	0.00	4.85	F
1720	1776	0.034960	TATTTGTAAGGCCTGCCGCA	60.035	50.000	5.69	41.95	5.69	F
3343	3433	0.179097	TGTGCTGCCGCGTATATTGA	60.179	50.000	4.92	39.65	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2606	2690	0.384309	CATAACTGCATGCTGCCAGG	59.616	55.000	22.92	9.88	44.23	4.45	R
3576	3672	0.881118	CCGTGCCACACAATTAAGCT	59.119	50.000	0.00	0.00	33.40	3.74	R
4671	4827	1.140852	TCACAAGTCAGGGGAAGTGTG	59.859	52.381	0.00	0.00	39.60	3.82	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
72	74	5.964958	ATGAACATTTTTCAGATGGACGT	57.035	34.783	0.00	0.00	0.00	4.34
92	94	6.866248	GGACGTTGAACATTTTCCAAATACAT	59.134	34.615	0.00	0.00	0.00	2.29
436	446	5.395642	ACGAAAAACAAAGAGCGAAAGAAA	58.604	33.333	0.00	0.00	0.00	2.52
662	695	2.550101	GCCGCCATTGAGATCCAGC	61.550	63.158	0.00	0.00	0.00	4.85
901	935	7.011669	GGGAATTGATAAGCACATTTGGATTTG	59.988	37.037	0.00	0.00	0.00	2.32
1008	1046	2.309528	TGGTGGTTCGCATCTCATAC	57.690	50.000	0.00	0.00	0.00	2.39
1009	1047	1.831106	TGGTGGTTCGCATCTCATACT	59.169	47.619	0.00	0.00	0.00	2.12
1055	1093	3.317993	GCAACCTACCAAACAACATCTGT	59.682	43.478	0.00	0.00	41.27	3.41
1089	1127	7.583625	TCATCTCTCATACACCCTTAGTAGAA	58.416	38.462	0.00	0.00	0.00	2.10
1168	1206	6.734104	AACACACATCTGAGCTTATCTTTC	57.266	37.500	0.00	0.00	0.00	2.62
1197	1235	0.105453	AGCCAGGATCCCAGATACGT	60.105	55.000	8.55	0.00	0.00	3.57
1251	1290	2.817844	ACCCTTATTTTCTGTTCCACGC	59.182	45.455	0.00	0.00	0.00	5.34
1369	1408	2.686558	TTTGTCGCTGATGCAGTTTC	57.313	45.000	0.00	0.00	39.64	2.78
1390	1429	1.945819	GCTGCTTGATTCCGGAGTTCA	60.946	52.381	13.51	13.51	0.00	3.18
1412	1451	7.072177	TCATACGTCTTTTCTAATGCCAAAG	57.928	36.000	0.00	0.00	0.00	2.77
1720	1776	0.034960	TATTTGTAAGGCCTGCCGCA	60.035	50.000	5.69	0.00	41.95	5.69
1800	1864	8.576442	CACCTAAACTTCATGTTATTTTCCTGT	58.424	33.333	0.00	0.00	38.03	4.00
1846	1911	7.826690	TCTATTCAGTTTGCCCTATTGTTTTC	58.173	34.615	0.00	0.00	0.00	2.29
2194	2272	1.179174	TGAGACCTGGTCACAGTCGG	61.179	60.000	27.48	0.00	43.36	4.79
2292	2370	5.411831	AGTCATCAACACTCAAGATAGCA	57.588	39.130	0.00	0.00	0.00	3.49
2435	2516	1.596934	GTGATTCTGTCGAGGGCCA	59.403	57.895	6.18	0.00	0.00	5.36
2606	2690	5.044558	GCTAACTGAAGACATGGTAGCTAC	58.955	45.833	15.88	15.88	32.15	3.58
2648	2732	6.356556	TGACCTTTGATCTCAGTGAAGAAAA	58.643	36.000	0.00	0.00	0.00	2.29
2679	2763	1.308047	TACAACTGCCAGCAACTGTG	58.692	50.000	13.70	4.06	0.00	3.66
2945	3030	4.889409	TCGTGACCGTAACCTATATTCCTT	59.111	41.667	0.00	0.00	35.01	3.36
3046	3131	5.744171	ACAACATGCAATCCTACATCTGTA	58.256	37.500	0.00	0.00	0.00	2.74
3343	3433	0.179097	TGTGCTGCCGCGTATATTGA	60.179	50.000	4.92	0.00	39.65	2.57
3557	3653	3.777106	TTTCTTGCATGAGACTCCAGT	57.223	42.857	0.00	0.00	0.00	4.00
3758	3877	7.124347	TGCGGACTAATAAAGTTAACTTGTG	57.876	36.000	21.22	11.76	39.07	3.33
4012	4133	8.429641	GTGAATGACTTCCCCTCTAATACAATA	58.570	37.037	0.00	0.00	0.00	1.90
4190	4321	5.532032	GGTTAACATAGGCGCCCTAAATTTA	59.468	40.000	26.15	7.39	39.77	1.40
4315	4450	4.913924	GCATCTTTGAATCGCATGGTATTC	59.086	41.667	0.00	0.00	33.57	1.75
4321	4456	3.181462	TGAATCGCATGGTATTCTCTGCT	60.181	43.478	0.00	0.00	34.00	4.24
4386	4530	2.734755	ATTGGGCATAGCTGTGCTTA	57.265	45.000	30.86	18.97	44.45	3.09
4391	4535	2.551459	GGGCATAGCTGTGCTTAGAATG	59.449	50.000	30.86	9.00	44.45	2.67
4402	4549	7.018235	GCTGTGCTTAGAATGAAAAGTTACTC	58.982	38.462	0.00	0.00	0.00	2.59
4419	4567	2.480845	ACTCGGTTGCTGTCAAGTAAC	58.519	47.619	0.00	0.00	45.35	2.50
4440	4588	6.847421	AACGTAGTGGAGAGGTACTTAAAT	57.153	37.500	0.00	0.00	45.00	1.40
4441	4589	6.847421	ACGTAGTGGAGAGGTACTTAAATT	57.153	37.500	0.00	0.00	42.51	1.82
4442	4590	6.628185	ACGTAGTGGAGAGGTACTTAAATTG	58.372	40.000	0.00	0.00	42.51	2.32
4445	4593	7.275123	CGTAGTGGAGAGGTACTTAAATTGTTC	59.725	40.741	0.00	0.00	41.55	3.18
4447	4595	8.431910	AGTGGAGAGGTACTTAAATTGTTCTA	57.568	34.615	0.00	0.00	41.55	2.10
4448	4596	8.532819	AGTGGAGAGGTACTTAAATTGTTCTAG	58.467	37.037	0.00	0.00	41.55	2.43
4506	4654	5.241728	GCACAGGAAGAGTTAAGGAACATTT	59.758	40.000	0.00	0.00	38.10	2.32
4527	4675	8.582437	ACATTTAGAATATGAAGCATGGATTGG	58.418	33.333	0.00	0.00	0.00	3.16
4577	4729	5.993441	CCCATTTTCTGTTTTGAGCTTTGAT	59.007	36.000	0.00	0.00	0.00	2.57
4619	4774	6.312399	TGTAAAACAGTCTATGCACCTTTG	57.688	37.500	0.00	0.00	0.00	2.77
4620	4775	6.058833	TGTAAAACAGTCTATGCACCTTTGA	58.941	36.000	0.00	0.00	0.00	2.69
4671	4827	4.012374	TGCTCTCCTCAAATGTGAATTCC	58.988	43.478	2.27	0.00	31.88	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	74	8.591940	TCCATCATGTATTTGGAAAATGTTCAA	58.408	29.630	0.00	0.00	36.62	2.69
404	414	7.485277	TCGCTCTTTGTTTTTCGTTCATTTTTA	59.515	29.630	0.00	0.00	0.00	1.52
436	446	4.994217	CACAGGTTGGTTTGTTTTCTTTGT	59.006	37.500	0.00	0.00	0.00	2.83
624	649	2.811542	AAAGGAGCAGAAGGAGCCGC	62.812	60.000	0.00	0.00	0.00	6.53
746	779	4.163268	TCTGAGTGAGAGAAGCTAGCTAGA	59.837	45.833	25.15	10.01	0.00	2.43
747	780	4.450976	TCTGAGTGAGAGAAGCTAGCTAG	58.549	47.826	19.70	16.84	0.00	3.42
817	851	7.843490	TTCTGTGCCACTAGAAATACATTAC	57.157	36.000	0.00	0.00	30.49	1.89
874	908	4.097741	TCCAAATGTGCTTATCAATTCCCG	59.902	41.667	0.00	0.00	0.00	5.14
901	935	3.053831	TGAGCAAACTAGTACAAGGCC	57.946	47.619	0.00	0.00	0.00	5.19
1008	1046	7.579726	CACCTAGTTGAAAAACTTCTGATCAG	58.420	38.462	17.07	17.07	34.37	2.90
1009	1047	6.017109	GCACCTAGTTGAAAAACTTCTGATCA	60.017	38.462	0.00	0.00	34.37	2.92
1055	1093	9.159254	AGGGTGTATGAGAGATGATGTATTTAA	57.841	33.333	0.00	0.00	0.00	1.52
1089	1127	6.332630	CAGAGATGTTGTTTGGTTGTTTCTT	58.667	36.000	0.00	0.00	0.00	2.52
1168	1206	1.476471	GGATCCTGGCTGAGTTGATGG	60.476	57.143	3.84	0.00	0.00	3.51
1197	1235	1.350684	TCACATTACTCCAGCCTGCAA	59.649	47.619	0.00	0.00	0.00	4.08
1369	1408	1.021390	AACTCCGGAATCAAGCAGCG	61.021	55.000	5.23	0.00	0.00	5.18
1390	1429	7.681939	TTCTTTGGCATTAGAAAAGACGTAT	57.318	32.000	9.37	0.00	39.10	3.06
1412	1451	4.917415	ACAAAACAAGCAGATAACGCATTC	59.083	37.500	0.00	0.00	0.00	2.67
1846	1911	5.404366	CCAAATTCTTCTGCAGACACATTTG	59.596	40.000	27.93	27.93	37.17	2.32
2194	2272	2.257371	CACTGGCACTGCACATGC	59.743	61.111	9.32	9.32	42.62	4.06
2292	2370	1.068434	CATTCACCCGTTGCAAGGTTT	59.932	47.619	17.23	1.48	32.72	3.27
2435	2516	7.459125	TGAATCTGCTATTATTATGGAGAGGGT	59.541	37.037	0.00	0.00	0.00	4.34
2606	2690	0.384309	CATAACTGCATGCTGCCAGG	59.616	55.000	22.92	9.88	44.23	4.45
2648	2732	2.094752	GGCAGTTGTATCCGTGCAAAAT	60.095	45.455	0.00	0.00	37.68	1.82
2679	2763	1.155042	CACCTGCAGAGTCTTCAAGC	58.845	55.000	17.39	0.00	0.00	4.01
2788	2872	3.386078	TCCAAATTTGCAGCTTACCAACA	59.614	39.130	12.92	0.00	0.00	3.33
2945	3030	1.398692	GTTGTCCCCAAGCAACTCAA	58.601	50.000	0.00	0.00	41.05	3.02
3046	3131	7.717568	ACATCTAAGCGTATAAGTGACTTCAT	58.282	34.615	0.00	0.00	0.00	2.57
3155	3240	6.709846	GGTCCATATTCTTTCATTCTCAGAGG	59.290	42.308	0.00	0.00	0.00	3.69
3343	3433	5.964958	ATTTCCAGTTGAATCGTGTCATT	57.035	34.783	0.00	0.00	31.67	2.57
3576	3672	0.881118	CCGTGCCACACAATTAAGCT	59.119	50.000	0.00	0.00	33.40	3.74
3646	3742	4.387862	ACTTGAAACACTATTACCTTCGCG	59.612	41.667	0.00	0.00	0.00	5.87
3730	3848	9.453325	CAAGTTAACTTTATTAGTCCGCAAAAA	57.547	29.630	18.25	0.00	35.54	1.94
3731	3849	8.623030	ACAAGTTAACTTTATTAGTCCGCAAAA	58.377	29.630	18.25	0.00	35.54	2.44
3732	3850	8.071368	CACAAGTTAACTTTATTAGTCCGCAAA	58.929	33.333	18.25	0.00	35.54	3.68
3733	3851	7.227116	ACACAAGTTAACTTTATTAGTCCGCAA	59.773	33.333	18.25	0.00	35.54	4.85
3734	3852	6.707161	ACACAAGTTAACTTTATTAGTCCGCA	59.293	34.615	18.25	0.00	35.54	5.69
3735	3853	7.125536	ACACAAGTTAACTTTATTAGTCCGC	57.874	36.000	18.25	0.00	35.54	5.54
3736	3854	9.195411	TGTACACAAGTTAACTTTATTAGTCCG	57.805	33.333	18.25	6.56	35.54	4.79
3739	3857	8.996271	GCCTGTACACAAGTTAACTTTATTAGT	58.004	33.333	18.25	9.95	39.32	2.24
3740	3858	9.216117	AGCCTGTACACAAGTTAACTTTATTAG	57.784	33.333	18.25	9.32	33.11	1.73
3758	3877	1.736365	GCCTCCCTCGTAGCCTGTAC	61.736	65.000	0.00	0.00	0.00	2.90
4066	4188	5.531122	ACTAGACAACTTGCACAGTAAGA	57.469	39.130	0.00	0.00	32.94	2.10
4161	4292	1.669265	GGCGCCTATGTTAACCTTGAC	59.331	52.381	22.15	0.00	0.00	3.18
4190	4321	4.686191	TTTGCAATCAAACCCAGTTCAT	57.314	36.364	0.00	0.00	37.28	2.57
4292	4427	2.857592	ACCATGCGATTCAAAGATGC	57.142	45.000	0.00	0.00	0.00	3.91
4386	4530	5.049405	CAGCAACCGAGTAACTTTTCATTCT	60.049	40.000	0.00	0.00	0.00	2.40
4391	4535	3.558418	TGACAGCAACCGAGTAACTTTTC	59.442	43.478	0.00	0.00	0.00	2.29
4402	4549	1.214367	ACGTTACTTGACAGCAACCG	58.786	50.000	0.00	0.00	0.00	4.44
4419	4567	6.628185	ACAATTTAAGTACCTCTCCACTACG	58.372	40.000	0.00	0.00	0.00	3.51
4440	4588	5.586877	AGGGTGTAGGATGTACTAGAACAA	58.413	41.667	0.00	0.00	32.02	2.83
4441	4589	5.202746	AGGGTGTAGGATGTACTAGAACA	57.797	43.478	0.00	0.00	0.00	3.18
4442	4590	7.836479	ATAAGGGTGTAGGATGTACTAGAAC	57.164	40.000	0.00	0.00	0.00	3.01
4445	4593	9.122779	GCTATATAAGGGTGTAGGATGTACTAG	57.877	40.741	0.00	0.00	0.00	2.57
4447	4595	7.476153	TGCTATATAAGGGTGTAGGATGTACT	58.524	38.462	0.00	0.00	0.00	2.73
4448	4596	7.614583	TCTGCTATATAAGGGTGTAGGATGTAC	59.385	40.741	0.00	0.00	0.00	2.90
4506	4654	6.491062	CCAACCAATCCATGCTTCATATTCTA	59.509	38.462	0.00	0.00	0.00	2.10
4527	4675	9.877137	GAAATGGAAATTTTGACATTTACCAAC	57.123	29.630	20.03	10.38	41.90	3.77
4577	4729	9.704098	GTTTTACAATGCCGTTAAATTTCAAAA	57.296	25.926	0.00	0.00	0.00	2.44
4619	4774	8.642020	CATCATTGTTTTCTTTTCCTCGAAATC	58.358	33.333	0.00	0.00	31.34	2.17
4620	4775	7.116805	GCATCATTGTTTTCTTTTCCTCGAAAT	59.883	33.333	0.00	0.00	31.34	2.17
4671	4827	1.140852	TCACAAGTCAGGGGAAGTGTG	59.859	52.381	0.00	0.00	39.60	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.