AutoCloner

Multiple sequence alignment - TraesCS2D01G377400

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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	TraesCS2D01G377400	chr2D	100.000	4265	0	0	1	4265	481687641	481691905	0.000000e+00	7877
1	TraesCS2D01G377400	chr2D	95.608	3074	125	6	889	3958	481655978	481659045	0.000000e+00	4920
2	TraesCS2D01G377400	chr2D	91.336	3001	203	23	523	3505	481961019	481963980	0.000000e+00	4048
3	TraesCS2D01G377400	chr2D	88.915	3004	247	41	523	3505	481987951	481990889	0.000000e+00	3624
4	TraesCS2D01G377400	chr2D	83.218	435	31	20	420	841	481655570	481655975	1.130000e-95	361
5	TraesCS2D01G377400	chr2D	82.828	396	35	10	3	374	481960606	481960992	1.480000e-84	324
6	TraesCS2D01G377400	chr2D	87.611	226	27	1	3953	4178	481659605	481659829	1.180000e-65	261
7	TraesCS2D01G377400	chr2D	86.905	168	13	5	1	167	481703152	481703311	3.390000e-41	180
8	TraesCS2D01G377400	chr2D	89.855	138	12	2	214	350	481987620	481987756	4.380000e-40	176
9	TraesCS2D01G377400	chr2B	92.871	4068	212	38	214	4265	565188245	565192250	0.000000e+00	5834
10	TraesCS2D01G377400	chr2B	93.227	3071	167	19	975	4005	565076406	565079475	0.000000e+00	4481
11	TraesCS2D01G377400	chr2B	90.644	2533	202	24	979	3505	565210005	565212508	0.000000e+00	3332
12	TraesCS2D01G377400	chr2B	86.667	210	25	2	3	212	565209289	565209495	3.320000e-56	230
13	TraesCS2D01G377400	chr2B	86.592	179	11	5	456	626	565209581	565209754	7.280000e-43	185
14	TraesCS2D01G377400	chr2B	85.475	179	6	5	674	841	565209751	565209920	7.330000e-38	169
15	TraesCS2D01G377400	chr2A	93.439	3734	166	32	544	4265	624393905	624397571	0.000000e+00	5465
16	TraesCS2D01G377400	chr2A	94.079	3513	171	19	761	4265	624446916	624450399	0.000000e+00	5301
17	TraesCS2D01G377400	chr2A	89.229	3008	250	32	523	3502	624457821	624460782	0.000000e+00	3692
18	TraesCS2D01G377400	chr2A	87.590	2627	264	38	928	3524	624359498	624362092	0.000000e+00	2988
19	TraesCS2D01G377400	chr2A	86.854	213	19	6	3	215	624457277	624457480	3.320000e-56	230
20	TraesCS2D01G377400	chr2A	79.403	335	23	17	319	628	624446440	624446753	1.210000e-45	195

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	TraesCS2D01G377400	chr2D	481687641	481691905	4264	False	7877.000000	7877	100.000000	1	4265	1	chr2D.!!$F1	4264
1	TraesCS2D01G377400	chr2D	481960606	481963980	3374	False	2186.000000	4048	87.082000	3	3505	2	chr2D.!!$F4	3502
2	TraesCS2D01G377400	chr2D	481987620	481990889	3269	False	1900.000000	3624	89.385000	214	3505	2	chr2D.!!$F5	3291
3	TraesCS2D01G377400	chr2D	481655570	481659829	4259	False	1847.333333	4920	88.812333	420	4178	3	chr2D.!!$F3	3758
4	TraesCS2D01G377400	chr2B	565188245	565192250	4005	False	5834.000000	5834	92.871000	214	4265	1	chr2B.!!$F2	4051
5	TraesCS2D01G377400	chr2B	565076406	565079475	3069	False	4481.000000	4481	93.227000	975	4005	1	chr2B.!!$F1	3030
6	TraesCS2D01G377400	chr2B	565209289	565212508	3219	False	979.000000	3332	87.344500	3	3505	4	chr2B.!!$F3	3502
7	TraesCS2D01G377400	chr2A	624393905	624397571	3666	False	5465.000000	5465	93.439000	544	4265	1	chr2A.!!$F2	3721
8	TraesCS2D01G377400	chr2A	624359498	624362092	2594	False	2988.000000	2988	87.590000	928	3524	1	chr2A.!!$F1	2596
9	TraesCS2D01G377400	chr2A	624446440	624450399	3959	False	2748.000000	5301	86.741000	319	4265	2	chr2A.!!$F3	3946
10	TraesCS2D01G377400	chr2A	624457277	624460782	3505	False	1961.000000	3692	88.041500	3	3502	2	chr2A.!!$F4	3499

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
430	806	0.389817	CGACGAGCACCTGGAAATGA	60.390	55.000	0.00	0.00	2.57	F
847	1384	0.523966	ACAGCTCCTCTTCGTCTTCG	59.476	55.000	0.00	38.55	3.79	F
848	1385	0.805614	CAGCTCCTCTTCGTCTTCGA	59.194	55.000	0.00	44.66	3.71	F
849	1386	0.806241	AGCTCCTCTTCGTCTTCGAC	59.194	55.000	0.00	46.03	4.20	F
1788	2385	1.002134	CCCAAACTCCATGGCGACT	60.002	57.895	9.17	36.58	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1374	1936	0.390124	GGATGAGCTCTCTCTGCAGG	59.610	60.000	15.13	4.77	40.03	4.85	R
1788	2385	1.078918	CTTCGTGCCATCTGGAGCA	60.079	57.895	0.00	0.00	37.39	4.26	R
2221	2818	1.511305	GCTCGATCGACTTGGTGGA	59.489	57.895	15.15	0.00	0.00	4.02	R
2760	3357	2.301870	GAGATGGCCATTGGTATCGGTA	59.698	50.000	21.84	0.00	0.00	4.02	R
3590	4214	3.202829	AGGCACGAGTTTTACTTTCCA	57.797	42.857	0.00	0.00	0.00	3.53	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
20	21	3.771577	GGAAGACCCTCAAGTTTCTCA	57.228	47.619	0.00	0.00	0.00	3.27
21	22	4.293662	GGAAGACCCTCAAGTTTCTCAT	57.706	45.455	0.00	0.00	0.00	2.90
22	23	4.657013	GGAAGACCCTCAAGTTTCTCATT	58.343	43.478	0.00	0.00	0.00	2.57
74	75	1.718757	GGACGCCAATGCCTTGCTAG	61.719	60.000	0.00	0.00	0.00	3.42
75	76	1.002134	ACGCCAATGCCTTGCTAGT	60.002	52.632	0.00	0.00	0.00	2.57
76	77	0.609131	ACGCCAATGCCTTGCTAGTT	60.609	50.000	0.00	0.00	0.00	2.24
93	117	1.143684	AGTTGTGGCAGTTGAGTCCAT	59.856	47.619	0.00	0.00	31.83	3.41
126	150	6.374417	ACGGAGTGATATATAAGCCCATTT	57.626	37.500	0.00	0.00	42.51	2.32
127	151	6.779860	ACGGAGTGATATATAAGCCCATTTT	58.220	36.000	0.00	0.00	42.51	1.82
130	154	7.495934	CGGAGTGATATATAAGCCCATTTTAGG	59.504	40.741	0.00	0.00	0.00	2.69
131	155	8.329502	GGAGTGATATATAAGCCCATTTTAGGT	58.670	37.037	0.00	0.00	0.00	3.08
132	156	9.740710	GAGTGATATATAAGCCCATTTTAGGTT	57.259	33.333	0.00	0.00	0.00	3.50
183	207	1.470098	CCAAGCTTTGATCAACCTCCG	59.530	52.381	7.89	3.28	0.00	4.63
207	231	3.879295	ACACACATTTCAGACAACTGGAG	59.121	43.478	0.00	0.00	43.60	3.86
291	509	2.784347	TCAATCCATACCAACGTTGCA	58.216	42.857	22.93	12.66	0.00	4.08
333	553	4.447724	TCGGAAACAAGATCGAAGAAACAG	59.552	41.667	0.00	0.00	43.58	3.16
430	806	0.389817	CGACGAGCACCTGGAAATGA	60.390	55.000	0.00	0.00	0.00	2.57
470	848	1.295423	CACCCCCTCACGAAACGAT	59.705	57.895	0.00	0.00	0.00	3.73
481	859	1.355796	CGAAACGATAACGCCCAGCA	61.356	55.000	0.00	0.00	43.96	4.41
533	917	1.621992	GATATCAGAGCCCTCCGTGA	58.378	55.000	0.00	0.00	0.00	4.35
540	932	2.185310	GAGCCCTCCGTGACACCAAT	62.185	60.000	0.00	0.00	0.00	3.16
546	938	3.124921	CGTGACACCAATCCCCGC	61.125	66.667	0.00	0.00	0.00	6.13
712	1165	2.432628	CAACCTCGCCGTCCAGTC	60.433	66.667	0.00	0.00	0.00	3.51
713	1166	4.052229	AACCTCGCCGTCCAGTCG	62.052	66.667	0.00	0.00	0.00	4.18
715	1168	4.477975	CCTCGCCGTCCAGTCGTC	62.478	72.222	0.00	0.00	0.00	4.20
716	1169	4.477975	CTCGCCGTCCAGTCGTCC	62.478	72.222	0.00	0.00	0.00	4.79
718	1171	4.778415	CGCCGTCCAGTCGTCCAG	62.778	72.222	0.00	0.00	0.00	3.86
719	1172	4.436998	GCCGTCCAGTCGTCCAGG	62.437	72.222	0.00	0.00	0.00	4.45
733	1256	1.189524	TCCAGGTCTACACCAACCCG	61.190	60.000	0.00	0.00	46.68	5.28
756	1293	2.310945	TGCCTCACACCTACCTACTACT	59.689	50.000	0.00	0.00	0.00	2.57
777	1314	1.142870	TGCGCTGCCTATTTAATCCCT	59.857	47.619	9.73	0.00	0.00	4.20
843	1380	3.633573	GCTACAGCTCCTCTTCGTC	57.366	57.895	0.00	0.00	38.21	4.20
844	1381	1.099689	GCTACAGCTCCTCTTCGTCT	58.900	55.000	0.00	0.00	38.21	4.18
845	1382	1.474879	GCTACAGCTCCTCTTCGTCTT	59.525	52.381	0.00	0.00	38.21	3.01
846	1383	2.478879	GCTACAGCTCCTCTTCGTCTTC	60.479	54.545	0.00	0.00	38.21	2.87
847	1384	0.523966	ACAGCTCCTCTTCGTCTTCG	59.476	55.000	0.00	0.00	38.55	3.79
848	1385	0.805614	CAGCTCCTCTTCGTCTTCGA	59.194	55.000	0.00	0.00	44.66	3.71
849	1386	0.806241	AGCTCCTCTTCGTCTTCGAC	59.194	55.000	0.00	0.00	46.03	4.20
910	1471	2.288948	ACATACACCTGCCGACGTTTAA	60.289	45.455	0.00	0.00	0.00	1.52
1092	1654	1.464198	ACTGAACTGGGGGAAGGCT	60.464	57.895	0.00	0.00	0.00	4.58
1788	2385	1.002134	CCCAAACTCCATGGCGACT	60.002	57.895	9.17	0.00	36.58	4.18
2043	2640	3.642848	ACTTGACCCACAAATTGAAGCAT	59.357	39.130	0.00	0.00	38.08	3.79
2112	2709	5.875182	AAGGCAGCTCCTACATGATGCTG	62.875	52.174	18.12	18.12	46.94	4.41
2221	2818	3.197766	TCAGATTGAGGTTATCCGTGCTT	59.802	43.478	0.00	0.00	39.05	3.91
2247	2844	1.315690	AGTCGATCGAGCGGGAAATA	58.684	50.000	24.18	0.00	0.00	1.40
2691	3288	1.828660	CCAGGCTATCGACCTCCGT	60.829	63.158	0.00	0.00	39.75	4.69
2760	3357	2.310779	TGGCTAGGAAGACACTGAGT	57.689	50.000	0.00	0.00	35.10	3.41
3321	3940	3.878103	CAGATTTCTGAAGGCTCTGATGG	59.122	47.826	15.76	0.00	46.59	3.51
3330	3949	4.101585	TGAAGGCTCTGATGGTAATACTGG	59.898	45.833	0.00	0.00	0.00	4.00
3590	4214	0.249953	TGGTGTGTGTACGGCGATTT	60.250	50.000	16.62	0.00	0.00	2.17
3620	4244	0.614979	ACTCGTGCCTAGGTGGTCAT	60.615	55.000	11.31	0.00	38.35	3.06
3756	4382	4.646492	GGATTTCTATGGAGGCACACAATT	59.354	41.667	0.00	0.00	0.00	2.32
3772	4398	6.346518	GCACACAATTATGTTTAACTTGGTGC	60.347	38.462	16.64	16.64	37.82	5.01
3792	4418	3.765511	TGCTATTCAACTACCGTACCACT	59.234	43.478	0.00	0.00	0.00	4.00
3809	4461	3.245229	ACCACTGCATACCTTGAATCCAA	60.245	43.478	0.00	0.00	0.00	3.53
4023	5240	7.710907	TCTTTAATCTACACGCATCAATAGCTT	59.289	33.333	0.00	0.00	0.00	3.74
4024	5241	7.786178	TTAATCTACACGCATCAATAGCTTT	57.214	32.000	0.00	0.00	0.00	3.51
4027	5244	3.492421	ACACGCATCAATAGCTTTTGG	57.508	42.857	15.65	3.45	0.00	3.28
4133	5350	5.774184	TGGATCAAATGAAGATGTCAACCAA	59.226	36.000	0.00	0.00	40.50	3.67
4174	5391	3.914312	TCAGTAGGAGAAACAGAAAGCG	58.086	45.455	0.00	0.00	0.00	4.68
4192	5409	2.159366	AGCGGTCAAGTAGTCATCTTCG	60.159	50.000	0.00	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.771577	TGAGAAACTTGAGGGTCTTCC	57.228	47.619	0.00	0.00	0.00	3.46
1	2	6.294231	GGAAAATGAGAAACTTGAGGGTCTTC	60.294	42.308	0.00	0.00	0.00	2.87
20	21	6.012113	TCATCACTTGGTCAATCTGGAAAAT	58.988	36.000	0.00	0.00	0.00	1.82
21	22	5.384336	TCATCACTTGGTCAATCTGGAAAA	58.616	37.500	0.00	0.00	0.00	2.29
22	23	4.984295	TCATCACTTGGTCAATCTGGAAA	58.016	39.130	0.00	0.00	0.00	3.13
74	75	1.537202	GATGGACTCAACTGCCACAAC	59.463	52.381	0.00	0.00	33.93	3.32
75	76	1.142667	TGATGGACTCAACTGCCACAA	59.857	47.619	0.00	0.00	33.93	3.33
76	77	0.764271	TGATGGACTCAACTGCCACA	59.236	50.000	0.00	0.00	33.93	4.17
93	117	2.753319	TCACTCCGTGGGTGATTGA	58.247	52.632	2.86	0.00	38.57	2.57
123	147	3.801307	AACCTCGACCCAACCTAAAAT	57.199	42.857	0.00	0.00	0.00	1.82
125	149	4.476628	GATAACCTCGACCCAACCTAAA	57.523	45.455	0.00	0.00	0.00	1.85
161	185	2.489722	GGAGGTTGATCAAAGCTTGGTC	59.510	50.000	10.35	0.73	46.56	4.02
183	207	4.335315	TCCAGTTGTCTGAAATGTGTGTTC	59.665	41.667	0.00	0.00	43.76	3.18
207	231	4.934075	ACGTGCATGCATCATATATGTC	57.066	40.909	25.64	5.57	0.00	3.06
259	477	9.071276	GTTGGTATGGATTGATGACAATAAGAT	57.929	33.333	0.00	0.00	45.30	2.40
261	479	7.012327	ACGTTGGTATGGATTGATGACAATAAG	59.988	37.037	0.00	0.00	45.30	1.73
291	509	4.649674	TCCGAGGAATCTAACTTGCTATGT	59.350	41.667	0.00	0.00	0.00	2.29
333	553	6.362016	CGAGTTATCTAAGATGCACTGATGTC	59.638	42.308	0.00	0.00	0.00	3.06
430	806	0.605589	CTGCTGACTTCCTCGTCCTT	59.394	55.000	0.00	0.00	32.97	3.36
481	859	1.449246	GAAGAGAGCACGCTGCCAT	60.449	57.895	0.00	0.00	46.52	4.40
518	902	2.117423	TGTCACGGAGGGCTCTGA	59.883	61.111	0.00	0.00	39.24	3.27
519	903	2.262915	GTGTCACGGAGGGCTCTG	59.737	66.667	0.00	0.00	41.63	3.35
520	904	2.997897	GGTGTCACGGAGGGCTCT	60.998	66.667	0.00	0.00	0.00	4.09
521	905	2.185310	ATTGGTGTCACGGAGGGCTC	62.185	60.000	0.00	0.00	0.00	4.70
712	1165	0.037605	GGTTGGTGTAGACCTGGACG	60.038	60.000	10.86	0.00	43.58	4.79
713	1166	0.323957	GGGTTGGTGTAGACCTGGAC	59.676	60.000	10.86	6.44	43.58	4.02
714	1167	1.189524	CGGGTTGGTGTAGACCTGGA	61.190	60.000	10.86	0.00	43.58	3.86
715	1168	1.295423	CGGGTTGGTGTAGACCTGG	59.705	63.158	10.86	0.00	43.58	4.45
716	1169	1.375523	GCGGGTTGGTGTAGACCTG	60.376	63.158	10.86	0.00	43.58	4.00
717	1170	1.535687	AGCGGGTTGGTGTAGACCT	60.536	57.895	10.86	0.00	43.58	3.85
718	1171	1.375523	CAGCGGGTTGGTGTAGACC	60.376	63.158	1.06	1.06	43.48	3.85
719	1172	4.278956	CAGCGGGTTGGTGTAGAC	57.721	61.111	0.00	0.00	41.21	2.59
733	1256	0.175989	GTAGGTAGGTGTGAGGCAGC	59.824	60.000	0.00	0.00	45.33	5.25
756	1293	1.953686	GGGATTAAATAGGCAGCGCAA	59.046	47.619	11.47	0.00	0.00	4.85
777	1314	1.308746	GGGAATGGAGGGAGGGGAA	60.309	63.158	0.00	0.00	0.00	3.97
910	1471	5.273208	TCTGGATTCTGGAAGTAAGCTAGT	58.727	41.667	0.00	0.00	33.76	2.57
1220	1782	3.626924	GCTCCACCCTGGTGTCGT	61.627	66.667	14.89	0.00	44.02	4.34
1374	1936	0.390124	GGATGAGCTCTCTCTGCAGG	59.610	60.000	15.13	4.77	40.03	4.85
1788	2385	1.078918	CTTCGTGCCATCTGGAGCA	60.079	57.895	0.00	0.00	37.39	4.26
2043	2640	3.323286	TCGATTTGCCCGGGGTGA	61.323	61.111	25.28	0.06	0.00	4.02
2112	2709	1.807573	CTCACCGAGCTTCTTCGCC	60.808	63.158	0.00	0.00	39.19	5.54
2221	2818	1.511305	GCTCGATCGACTTGGTGGA	59.489	57.895	15.15	0.00	0.00	4.02
2691	3288	3.903714	TCTTGACATTCTCCTCAAGGTGA	59.096	43.478	7.39	0.00	42.49	4.02
2760	3357	2.301870	GAGATGGCCATTGGTATCGGTA	59.698	50.000	21.84	0.00	0.00	4.02
3362	3982	3.373439	GGCAGCTCTAGAAGAACATTGTG	59.627	47.826	0.00	0.00	0.00	3.33
3590	4214	3.202829	AGGCACGAGTTTTACTTTCCA	57.797	42.857	0.00	0.00	0.00	3.53
3620	4244	6.829229	TTCAGAGAACTTATTACTGACCGA	57.171	37.500	0.00	0.00	37.34	4.69
3756	4382	8.630054	AGTTGAATAGCACCAAGTTAAACATA	57.370	30.769	0.00	0.00	0.00	2.29
3772	4398	4.110482	GCAGTGGTACGGTAGTTGAATAG	58.890	47.826	0.00	0.00	0.00	1.73
4023	5240	2.208132	ATGGTCAATGTACGCCCAAA	57.792	45.000	0.00	0.00	0.00	3.28
4024	5241	3.569194	ATATGGTCAATGTACGCCCAA	57.431	42.857	0.00	0.00	0.00	4.12
4027	5244	4.219944	TCTCCTATATGGTCAATGTACGCC	59.780	45.833	0.00	0.00	37.07	5.68
4133	5350	6.644347	ACTGAATTCGAGATTAGGACACAAT	58.356	36.000	10.61	0.00	0.00	2.71
4174	5391	4.174762	GGTTCGAAGATGACTACTTGACC	58.825	47.826	0.00	0.00	35.04	4.02
4239	5461	7.754851	ACACCGACTTTTAAGGAAATACAAT	57.245	32.000	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.