AutoCloner

Multiple sequence alignment - TraesCS5D01G409100

Loading Multiple Alignment...

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	TraesCS5D01G409100	chr5D	100.000	2597	0	0	1	2597	473070598	473073194	0.000000e+00	4796
1	TraesCS5D01G409100	chr5D	93.781	1431	69	13	593	2014	44511943	44513362	0.000000e+00	2132
2	TraesCS5D01G409100	chr3D	95.579	1425	54	7	593	2014	546485995	546487413	0.000000e+00	2274
3	TraesCS5D01G409100	chr1D	95.045	1433	56	7	588	2015	25464314	25465736	0.000000e+00	2239
4	TraesCS5D01G409100	chr1D	93.933	1434	68	14	591	2014	347252966	347251542	0.000000e+00	2148
5	TraesCS5D01G409100	chr4D	94.328	1428	65	9	593	2014	459886443	459885026	0.000000e+00	2174
6	TraesCS5D01G409100	chr4D	93.776	1430	72	9	593	2014	78732769	78731349	0.000000e+00	2132
7	TraesCS5D01G409100	chr7D	95.072	1380	57	4	593	1971	63995390	63996759	0.000000e+00	2161
8	TraesCS5D01G409100	chr4A	93.961	1424	76	4	593	2014	724524709	724523294	0.000000e+00	2145
9	TraesCS5D01G409100	chr4A	83.140	344	37	9	2013	2345	658827333	658827666	7.030000e-76	294
10	TraesCS5D01G409100	chr3A	93.357	1430	83	7	591	2014	235187477	235188900	0.000000e+00	2104
11	TraesCS5D01G409100	chr2B	94.397	589	25	4	2013	2595	151403523	151404109	0.000000e+00	898
12	TraesCS5D01G409100	chr2B	93.063	591	32	5	2013	2597	151428425	151429012	0.000000e+00	856
13	TraesCS5D01G409100	chr2B	96.250	320	10	2	2278	2597	151414456	151414773	8.230000e-145	523
14	TraesCS5D01G409100	chr2B	96.250	320	10	2	2278	2597	151418413	151418730	8.230000e-145	523
15	TraesCS5D01G409100	chr3B	93.232	591	32	4	2013	2597	570278350	570277762	0.000000e+00	863
16	TraesCS5D01G409100	chr3B	94.245	556	24	4	2048	2597	570249077	570248524	0.000000e+00	843
17	TraesCS5D01G409100	chr6B	92.761	594	35	3	2010	2597	411247719	411248310	0.000000e+00	852
18	TraesCS5D01G409100	chr5B	88.889	504	55	1	10	513	580486685	580487187	1.020000e-173	619
19	TraesCS5D01G409100	chr5B	87.797	295	28	3	2013	2301	667302563	667302855	3.200000e-89	339
20	TraesCS5D01G409100	chr5B	90.110	91	8	1	505	594	580487212	580487302	1.630000e-22	117
21	TraesCS5D01G409100	chr5A	89.315	365	30	7	3	364	593075854	593076212	1.420000e-122	449

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	TraesCS5D01G409100	chr5D	473070598	473073194	2596	False	4796	4796	100.0000	1	2597	1	chr5D.!!$F2	2596
1	TraesCS5D01G409100	chr5D	44511943	44513362	1419	False	2132	2132	93.7810	593	2014	1	chr5D.!!$F1	1421
2	TraesCS5D01G409100	chr3D	546485995	546487413	1418	False	2274	2274	95.5790	593	2014	1	chr3D.!!$F1	1421
3	TraesCS5D01G409100	chr1D	25464314	25465736	1422	False	2239	2239	95.0450	588	2015	1	chr1D.!!$F1	1427
4	TraesCS5D01G409100	chr1D	347251542	347252966	1424	True	2148	2148	93.9330	591	2014	1	chr1D.!!$R1	1423
5	TraesCS5D01G409100	chr4D	459885026	459886443	1417	True	2174	2174	94.3280	593	2014	1	chr4D.!!$R2	1421
6	TraesCS5D01G409100	chr4D	78731349	78732769	1420	True	2132	2132	93.7760	593	2014	1	chr4D.!!$R1	1421
7	TraesCS5D01G409100	chr7D	63995390	63996759	1369	False	2161	2161	95.0720	593	1971	1	chr7D.!!$F1	1378
8	TraesCS5D01G409100	chr4A	724523294	724524709	1415	True	2145	2145	93.9610	593	2014	1	chr4A.!!$R1	1421
9	TraesCS5D01G409100	chr3A	235187477	235188900	1423	False	2104	2104	93.3570	591	2014	1	chr3A.!!$F1	1423
10	TraesCS5D01G409100	chr2B	151403523	151404109	586	False	898	898	94.3970	2013	2595	1	chr2B.!!$F1	582
11	TraesCS5D01G409100	chr2B	151428425	151429012	587	False	856	856	93.0630	2013	2597	1	chr2B.!!$F2	584
12	TraesCS5D01G409100	chr2B	151414456	151418730	4274	False	523	523	96.2500	2278	2597	2	chr2B.!!$F3	319
13	TraesCS5D01G409100	chr3B	570277762	570278350	588	True	863	863	93.2320	2013	2597	1	chr3B.!!$R2	584
14	TraesCS5D01G409100	chr3B	570248524	570249077	553	True	843	843	94.2450	2048	2597	1	chr3B.!!$R1	549
15	TraesCS5D01G409100	chr6B	411247719	411248310	591	False	852	852	92.7610	2010	2597	1	chr6B.!!$F1	587
16	TraesCS5D01G409100	chr5B	580486685	580487302	617	False	368	619	89.4995	10	594	2	chr5B.!!$F2	584

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
286	287	0.390603	TACGCGTTATGCAACCAGCT	60.391	50.0	20.78	0.0	46.97	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	1888	0.106918	AAACACGCAAGAGAACCCCA	60.107	50.0	0.0	0.0	43.62	4.96	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
24	25	4.750098	AGAACGTCGATTTCATGTCACTTT	59.250	37.500	0.00	0.00	0.00	2.66
25	26	5.236478	AGAACGTCGATTTCATGTCACTTTT	59.764	36.000	0.00	0.00	0.00	2.27
39	40	6.588348	TGTCACTTTTCATATATGCGTGAG	57.412	37.500	18.60	12.11	31.45	3.51
42	43	5.985530	TCACTTTTCATATATGCGTGAGGAG	59.014	40.000	7.92	2.22	32.19	3.69
80	81	9.102453	GTAATTAGTTTATCTAGGAGGGGTGAT	57.898	37.037	0.00	0.00	0.00	3.06
89	90	0.827368	GGAGGGGTGATCAGAGTGAC	59.173	60.000	0.00	0.00	0.00	3.67
91	92	2.114616	GAGGGGTGATCAGAGTGACAT	58.885	52.381	0.00	0.00	0.00	3.06
100	101	9.593134	GGGTGATCAGAGTGACATATATTATTC	57.407	37.037	0.00	0.00	0.00	1.75
124	125	5.500546	ACCCTAAGTTTTAGAGGAGTTGG	57.499	43.478	9.09	0.00	31.45	3.77
126	127	3.933332	CCTAAGTTTTAGAGGAGTTGGCG	59.067	47.826	0.00	0.00	31.45	5.69
138	139	5.777732	AGAGGAGTTGGCGATTCTATTAGAT	59.222	40.000	0.00	0.00	0.00	1.98
145	146	5.858381	TGGCGATTCTATTAGATTTGCTCT	58.142	37.500	19.79	0.00	36.03	4.09
161	162	7.880195	AGATTTGCTCTTAGAAGCTAAAACAGA	59.120	33.333	0.00	0.00	42.94	3.41
207	208	4.698201	TCTTCATGTGGTTGTCTTACCA	57.302	40.909	0.00	0.00	45.73	3.25
245	246	3.181367	GCGACTTGCATGTCAGGG	58.819	61.111	26.67	14.93	45.45	4.45
285	286	0.444651	TTACGCGTTATGCAACCAGC	59.555	50.000	20.78	0.00	46.97	4.85
286	287	0.390603	TACGCGTTATGCAACCAGCT	60.391	50.000	20.78	0.00	46.97	4.24
300	301	2.108168	ACCAGCTAGAACAAGGCGATA	58.892	47.619	0.00	0.00	0.00	2.92
314	315	0.539986	GCGATAACCCACCTCCTCAA	59.460	55.000	0.00	0.00	0.00	3.02
316	317	1.470979	CGATAACCCACCTCCTCAACG	60.471	57.143	0.00	0.00	0.00	4.10
327	328	1.082104	CCTCAACGCGTGCCTTTTC	60.082	57.895	14.98	0.00	0.00	2.29
339	340	2.327592	CTTTTCGCGCACAGTGCA	59.672	55.556	25.19	2.88	45.36	4.57
340	341	1.081906	CTTTTCGCGCACAGTGCAT	60.082	52.632	25.19	0.00	45.36	3.96
343	344	1.576451	TTTCGCGCACAGTGCATCAT	61.576	50.000	25.19	0.00	45.36	2.45
361	362	0.842635	ATGAAGTGCCCTCCTGGATC	59.157	55.000	0.00	0.00	35.39	3.36
366	367	1.383109	TGCCCTCCTGGATCGACAT	60.383	57.895	0.00	0.00	35.39	3.06
397	398	2.677848	GGGGAGGGCTTCTTGGAC	59.322	66.667	0.00	0.00	0.00	4.02
423	424	1.198637	GCAGTTGAGCTGTGATTCCAC	59.801	52.381	0.00	0.00	46.64	4.02
436	437	2.284515	ATTCCACCCAATCCTCGGCC	62.285	60.000	0.00	0.00	0.00	6.13
441	442	4.547367	CCAATCCTCGGCCCGGAC	62.547	72.222	0.73	0.00	32.41	4.79
458	459	0.750850	GACGGGCACATCCTTAGCTA	59.249	55.000	0.00	0.00	34.39	3.32
528	562	5.869579	ACTCAACACCATTAAGACAGATGT	58.130	37.500	0.00	0.00	0.00	3.06
586	620	1.725931	GCTTTGCTTCCGATGACAACG	60.726	52.381	0.00	0.00	0.00	4.10
726	760	1.890894	CCGTCTCCGTCAGGTCAAT	59.109	57.895	0.00	0.00	39.05	2.57
755	789	3.821886	GCCCTTACAGGTGGGACT	58.178	61.111	1.75	0.00	46.15	3.85
786	820	5.768662	CAGAGATGGCCAATTCTATTCACAT	59.231	40.000	10.96	0.00	0.00	3.21
869	908	1.347320	GCTATATAAGCGGGCGACAC	58.653	55.000	0.00	0.00	42.53	3.67
870	909	1.336517	GCTATATAAGCGGGCGACACA	60.337	52.381	0.00	0.00	42.53	3.72
872	911	0.462375	ATATAAGCGGGCGACACACA	59.538	50.000	0.00	0.00	0.00	3.72
953	999	3.771160	CGGCGGTGGGAAGCTAGT	61.771	66.667	0.00	0.00	0.00	2.57
1083	1129	3.553437	CTTCGTCTGTCCGCGGTGT	62.553	63.158	27.15	0.00	0.00	4.16
1136	1183	1.835494	TCGAGGAACCAGAATCGTCT	58.165	50.000	0.00	0.00	36.58	4.18
1294	1342	4.205587	GGCCAAGACTCTGATGAATGAAT	58.794	43.478	0.00	0.00	0.00	2.57
1407	1455	0.179113	GCACTGACAGAGAGCTAGCC	60.179	60.000	12.13	2.81	35.53	3.93
1523	1574	3.068560	TGGTAATCGCACTGGTTGTAAC	58.931	45.455	0.00	0.00	0.00	2.50
1546	1597	6.608610	ACGTTGAAAATGTATAGAAAGGCAC	58.391	36.000	0.00	0.00	45.92	5.01
1830	1888	5.142806	ACTACATCCAATTAGGCCCATTT	57.857	39.130	0.00	0.00	37.29	2.32
1909	1970	9.545105	AAATCATAATGCTGAAACTTTTTGTGA	57.455	25.926	0.00	0.00	0.00	3.58
1912	1973	9.376075	TCATAATGCTGAAACTTTTTGTGAAAA	57.624	25.926	0.00	0.00	33.86	2.29
2020	2082	4.914312	TTCAAATACACCGTGTTCGATC	57.086	40.909	9.98	0.00	39.71	3.69
2034	2096	3.042887	GTTCGATCAGTTTTTGTGCACC	58.957	45.455	15.69	0.00	0.00	5.01
2112	2174	6.530019	AAGACAAGTTATAATGCAAAGGGG	57.470	37.500	0.00	0.00	0.00	4.79
2182	2250	6.619018	GCAAGAAATATGGTGCAACAAATGTG	60.619	38.462	9.38	2.04	39.98	3.21
2189	2257	2.730928	GGTGCAACAAATGTGTGTATGC	59.269	45.455	0.00	4.49	39.98	3.14
2277	2345	2.885644	CGGCGAGCTTGCATACGT	60.886	61.111	27.02	0.00	36.28	3.57
2278	2346	1.587876	CGGCGAGCTTGCATACGTA	60.588	57.895	27.02	0.00	36.28	3.57
2279	2347	1.808234	CGGCGAGCTTGCATACGTAC	61.808	60.000	27.02	7.13	36.28	3.67
2280	2348	0.527817	GGCGAGCTTGCATACGTACT	60.528	55.000	27.02	0.00	36.28	2.73
2281	2349	1.278238	GCGAGCTTGCATACGTACTT	58.722	50.000	21.53	0.00	34.15	2.24
2377	4059	4.407945	ACCCGTATTAAGCAGGTAGTCAAT	59.592	41.667	0.00	0.00	0.00	2.57
2418	4100	3.181476	GCTTGCTTTGGTCTTGAAGGAAA	60.181	43.478	0.00	0.00	33.71	3.13
2479	4161	6.348458	GCAGCTTTCACGCATATATGGAATTA	60.348	38.462	14.51	0.00	0.00	1.40
2483	4165	9.410556	GCTTTCACGCATATATGGAATTATTTT	57.589	29.630	14.51	0.00	0.00	1.82
2586	4268	4.264253	TGGCAATCAAGAAATCAGATCGT	58.736	39.130	0.00	0.00	0.00	3.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.921021	AGTGACATGAAATCGACGTTCTC	59.079	43.478	0.00	3.06	0.00	2.87
2	3	4.647291	AAGTGACATGAAATCGACGTTC	57.353	40.909	0.00	4.13	0.00	3.95
3	4	5.007234	TGAAAAGTGACATGAAATCGACGTT	59.993	36.000	0.00	0.00	0.00	3.99
4	5	4.509970	TGAAAAGTGACATGAAATCGACGT	59.490	37.500	0.00	0.00	0.00	4.34
5	6	5.017484	TGAAAAGTGACATGAAATCGACG	57.983	39.130	0.00	0.00	0.00	5.12
8	9	9.110617	GCATATATGAAAAGTGACATGAAATCG	57.889	33.333	17.10	0.00	0.00	3.34
24	25	4.407365	TCTCCTCCTCACGCATATATGAA	58.593	43.478	17.10	0.00	0.00	2.57
25	26	4.013050	CTCTCCTCCTCACGCATATATGA	58.987	47.826	17.10	0.00	0.00	2.15
39	40	8.910351	AAACTAATTACATAATGCTCTCCTCC	57.090	34.615	0.00	0.00	0.00	4.30
100	101	6.641474	CCAACTCCTCTAAAACTTAGGGTAG	58.359	44.000	0.00	0.00	0.00	3.18
105	106	4.817517	TCGCCAACTCCTCTAAAACTTAG	58.182	43.478	0.00	0.00	0.00	2.18
120	121	6.203723	AGAGCAAATCTAATAGAATCGCCAAC	59.796	38.462	0.00	0.00	36.10	3.77
124	125	8.749841	TCTAAGAGCAAATCTAATAGAATCGC	57.250	34.615	0.00	0.00	37.23	4.58
138	139	7.715249	TCTTCTGTTTTAGCTTCTAAGAGCAAA	59.285	33.333	0.00	0.00	45.12	3.68
145	146	7.015877	TGGTAGGTCTTCTGTTTTAGCTTCTAA	59.984	37.037	0.00	0.00	0.00	2.10
158	159	1.614241	CCGGGGTGGTAGGTCTTCTG	61.614	65.000	0.00	0.00	0.00	3.02
161	162	2.285144	CCCGGGGTGGTAGGTCTT	60.285	66.667	14.71	0.00	35.15	3.01
207	208	0.179073	CGGCTTCCATCAACGATCCT	60.179	55.000	0.00	0.00	0.00	3.24
208	209	1.160329	CCGGCTTCCATCAACGATCC	61.160	60.000	0.00	0.00	0.00	3.36
240	241	1.113788	GCATATGCAAAAGGCCCTGA	58.886	50.000	22.84	0.00	43.89	3.86
271	272	3.000041	TGTTCTAGCTGGTTGCATAACG	59.000	45.455	0.00	0.00	45.94	3.18
285	286	3.195661	GTGGGTTATCGCCTTGTTCTAG	58.804	50.000	0.00	0.00	0.00	2.43
286	287	2.093341	GGTGGGTTATCGCCTTGTTCTA	60.093	50.000	0.00	0.00	34.64	2.10
300	301	2.430367	GCGTTGAGGAGGTGGGTT	59.570	61.111	0.00	0.00	0.00	4.11
334	335	2.877975	GGGCACTTCATGATGCACT	58.122	52.632	20.02	0.00	42.22	4.40
339	340	0.549950	CCAGGAGGGCACTTCATGAT	59.450	55.000	0.00	0.00	0.00	2.45
340	341	0.547471	TCCAGGAGGGCACTTCATGA	60.547	55.000	0.00	0.00	36.21	3.07
343	344	1.617018	CGATCCAGGAGGGCACTTCA	61.617	60.000	0.00	0.00	36.21	3.02
385	386	1.034292	GCCATCAGTCCAAGAAGCCC	61.034	60.000	0.00	0.00	0.00	5.19
441	442	3.678056	TTATAGCTAAGGATGTGCCCG	57.322	47.619	0.00	0.00	37.37	6.13
458	459	2.034124	GCTCCATGCCACCAACATTAT	58.966	47.619	0.00	0.00	35.15	1.28
531	565	0.332632	ACCCACCATCACCCATTGAG	59.667	55.000	0.00	0.00	37.77	3.02
578	612	5.975693	AATTAACCCAACATCGTTGTCAT	57.024	34.783	0.00	0.00	34.06	3.06
586	620	6.761242	GGCAAAAGGATAATTAACCCAACATC	59.239	38.462	8.09	0.00	0.00	3.06
726	760	1.141254	TGTAAGGGCCGAGTCAAAACA	59.859	47.619	0.00	0.00	0.00	2.83
755	789	3.550431	GGCCATCTCTGCCGCCTA	61.550	66.667	0.00	0.00	39.48	3.93
890	930	0.650512	CGTCGTGCTCTCTCTCTCTC	59.349	60.000	0.00	0.00	0.00	3.20
891	931	0.742990	CCGTCGTGCTCTCTCTCTCT	60.743	60.000	0.00	0.00	0.00	3.10
893	933	1.003112	ACCGTCGTGCTCTCTCTCT	60.003	57.895	0.00	0.00	0.00	3.10
1083	1129	4.973055	CGAACAACGCCCACCCGA	62.973	66.667	0.00	0.00	34.51	5.14
1136	1183	0.663269	CTCGCTGCACACGTAGAACA	60.663	55.000	0.00	0.00	0.00	3.18
1294	1342	4.082408	CCATTCTTCATGCTCTTCTTGCAA	60.082	41.667	0.00	0.00	44.01	4.08
1407	1455	4.245660	TCTTCAACATCCTAAGCTCAACG	58.754	43.478	0.00	0.00	0.00	4.10
1523	1574	5.732647	CGTGCCTTTCTATACATTTTCAACG	59.267	40.000	0.00	0.00	0.00	4.10
1537	1588	3.199946	TCCTCCATAATTCGTGCCTTTCT	59.800	43.478	0.00	0.00	0.00	2.52
1546	1597	9.669353	CAAGATTACAAATTCCTCCATAATTCG	57.331	33.333	0.00	0.00	0.00	3.34
1830	1888	0.106918	AAACACGCAAGAGAACCCCA	60.107	50.000	0.00	0.00	43.62	4.96
1912	1973	9.860898	GTTTGGCTCTGAAATAATTCAATTAGT	57.139	29.630	0.00	0.00	44.64	2.24
2092	2154	6.926630	TTTCCCCTTTGCATTATAACTTGT	57.073	33.333	0.00	0.00	0.00	3.16
2112	2174	6.018016	GGTACATGCCATGCCAATAAATTTTC	60.018	38.462	4.17	0.00	0.00	2.29
2160	2228	5.927689	CACACATTTGTTGCACCATATTTCT	59.072	36.000	0.00	0.00	31.66	2.52
2182	2250	2.736682	GCCGGACACGTGCATACAC	61.737	63.158	17.22	0.00	43.76	2.90
2306	3987	6.425417	TCGTGTATACCCGAATACGTGTATAA	59.575	38.462	8.04	0.00	42.96	0.98
2349	4031	4.347360	ACCTGCTTAATACGGGTATTCC	57.653	45.455	7.31	0.18	45.17	3.01
2377	4059	5.179368	GCAAGCCTTATAAGTCAATCGCATA	59.821	40.000	11.50	0.00	0.00	3.14
2390	4072	4.917385	TCAAGACCAAAGCAAGCCTTATA	58.083	39.130	0.00	0.00	32.20	0.98
2418	4100	3.248125	CCTTTGCAAACATGCATCGTTTT	59.752	39.130	18.53	7.72	44.94	2.43
2444	4126	1.373748	GAAAGCTGCCGACGTACCA	60.374	57.895	0.00	0.00	0.00	3.25
2479	4161	5.633182	CACGCCTGCACAAGTAAAATAAAAT	59.367	36.000	0.00	0.00	0.00	1.82
2483	4165	3.058570	CACACGCCTGCACAAGTAAAATA	60.059	43.478	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.