AutoCloner

Multiple sequence alignment - TraesCS2D01G597700

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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	TraesCS2D01G597700	chr2D	100.000	2951	0	0	1	2951	650075890	650078840	0.000000e+00	5450.0
1	TraesCS2D01G597700	chr2D	82.000	400	39	20	33	416	650212598	650212980	2.860000e-80	309.0
2	TraesCS2D01G597700	chr2A	93.090	1317	68	9	387	1686	774832232	774830922	0.000000e+00	1906.0
3	TraesCS2D01G597700	chr2A	94.428	1041	21	5	1932	2951	774816579	774815555	0.000000e+00	1567.0
4	TraesCS2D01G597700	chr2A	77.062	885	138	42	996	1849	619809166	619808316	1.610000e-122	449.0
5	TraesCS2D01G597700	chr2A	88.104	269	24	5	65	329	774840387	774840123	2.210000e-81	313.0
6	TraesCS2D01G597700	chr2A	80.270	370	38	20	65	420	774810149	774809801	2.270000e-61	246.0
7	TraesCS2D01G597700	chr2A	96.528	144	2	1	1667	1810	774829076	774828936	4.920000e-58	235.0
8	TraesCS2D01G597700	chr2A	98.333	120	2	0	1806	1925	774816935	774816816	8.290000e-51	211.0
9	TraesCS2D01G597700	chr2B	94.160	1250	61	4	664	1907	786102236	786103479	0.000000e+00	1893.0
10	TraesCS2D01G597700	chr2B	86.635	1040	104	7	1932	2951	786103711	786104735	0.000000e+00	1118.0
11	TraesCS2D01G597700	chr2B	89.686	669	47	11	25	677	786060556	786061218	0.000000e+00	833.0
12	TraesCS2D01G597700	chr2B	91.667	216	16	1	158	371	786123477	786123692	6.180000e-77	298.0
13	TraesCS2D01G597700	chr3B	75.190	919	149	48	954	1834	723456632	723457509	7.780000e-96	361.0
14	TraesCS2D01G597700	chr4A	88.199	161	11	4	2618	2777	699609013	699608860	5.020000e-43	185.0
15	TraesCS2D01G597700	chr4A	82.063	223	19	5	2634	2856	572560709	572560910	1.410000e-38	171.0
16	TraesCS2D01G597700	chr1A	81.154	260	21	7	2618	2870	582640333	582640571	1.810000e-42	183.0
17	TraesCS2D01G597700	chr7A	80.478	251	26	11	2618	2867	696906820	696906592	1.410000e-38	171.0
18	TraesCS2D01G597700	chr5A	85.542	83	12	0	2618	2700	708749268	708749350	1.460000e-13	87.9

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	TraesCS2D01G597700	chr2D	650075890	650078840	2950	False	5450.0	5450	100.0000	1	2951	1	chr2D.!!$F1	2950
1	TraesCS2D01G597700	chr2A	774828936	774832232	3296	True	1070.5	1906	94.8090	387	1810	2	chr2A.!!$R5	1423
2	TraesCS2D01G597700	chr2A	774815555	774816935	1380	True	889.0	1567	96.3805	1806	2951	2	chr2A.!!$R4	1145
3	TraesCS2D01G597700	chr2A	619808316	619809166	850	True	449.0	449	77.0620	996	1849	1	chr2A.!!$R1	853
4	TraesCS2D01G597700	chr2B	786102236	786104735	2499	False	1505.5	1893	90.3975	664	2951	2	chr2B.!!$F3	2287
5	TraesCS2D01G597700	chr2B	786060556	786061218	662	False	833.0	833	89.6860	25	677	1	chr2B.!!$F1	652
6	TraesCS2D01G597700	chr3B	723456632	723457509	877	False	361.0	361	75.1900	954	1834	1	chr3B.!!$F1	880

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
79	80	0.175989	GAACTCCAGATCCCGTCACC	59.824	60.0	0.0	0.0	0.0	4.02	F
185	189	0.182775	ACACTCCAAGCGTTTTCCCT	59.817	50.0	0.0	0.0	0.0	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1930	3892	0.449388	CACAATCCTTCTTCGGCTGC	59.551	55.0	0.00	0.0	0.0	5.25	R
2058	4255	0.868406	CAGTTCAAGCACCGGAAGAC	59.132	55.0	9.46	0.0	0.0	3.01	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
42	43	2.593978	CCTCTACCGAGTCCCCGA	59.406	66.667	0.00	0.00	35.43	5.14
60	61	2.159707	CCGACAATTAAACAGCGTCCAG	60.160	50.000	0.00	0.00	0.00	3.86
61	62	2.734606	CGACAATTAAACAGCGTCCAGA	59.265	45.455	0.00	0.00	0.00	3.86
62	63	3.185594	CGACAATTAAACAGCGTCCAGAA	59.814	43.478	0.00	0.00	0.00	3.02
63	64	4.464112	GACAATTAAACAGCGTCCAGAAC	58.536	43.478	0.00	0.00	0.00	3.01
64	65	4.134563	ACAATTAAACAGCGTCCAGAACT	58.865	39.130	0.00	0.00	0.00	3.01
79	80	0.175989	GAACTCCAGATCCCGTCACC	59.824	60.000	0.00	0.00	0.00	4.02
85	86	0.249073	CAGATCCCGTCACCGATGTC	60.249	60.000	0.00	0.00	35.63	3.06
86	87	1.067582	GATCCCGTCACCGATGTCC	59.932	63.158	0.00	0.00	35.63	4.02
161	165	3.050703	CGACCTTGCATCGCTTACT	57.949	52.632	0.00	0.00	31.96	2.24
162	166	0.647410	CGACCTTGCATCGCTTACTG	59.353	55.000	0.00	0.00	31.96	2.74
163	167	1.009829	GACCTTGCATCGCTTACTGG	58.990	55.000	0.00	0.00	0.00	4.00
185	189	0.182775	ACACTCCAAGCGTTTTCCCT	59.817	50.000	0.00	0.00	0.00	4.20
187	191	0.182775	ACTCCAAGCGTTTTCCCTGT	59.817	50.000	0.00	0.00	0.00	4.00
192	196	1.029681	AAGCGTTTTCCCTGTGAACC	58.970	50.000	0.00	0.00	31.05	3.62
222	227	0.958382	GCAGTAATCGTGGGGTGCAA	60.958	55.000	0.00	0.00	0.00	4.08
224	229	2.091541	CAGTAATCGTGGGGTGCAAAT	58.908	47.619	0.00	0.00	0.00	2.32
232	237	2.119029	GGGGTGCAAATAGCCGGTC	61.119	63.158	1.90	0.00	44.83	4.79
264	270	3.070576	GCGAAATGCTGCCCCCTT	61.071	61.111	0.00	0.00	41.73	3.95
276	282	3.168292	CTGCCCCCTTTGAAGAAGAAAT	58.832	45.455	0.00	0.00	0.00	2.17
286	292	7.256286	CCTTTGAAGAAGAAATTATGCTCCTG	58.744	38.462	0.00	0.00	0.00	3.86
287	293	5.824904	TGAAGAAGAAATTATGCTCCTGC	57.175	39.130	0.00	0.00	40.20	4.85
299	305	0.599558	GCTCCTGCATTTGCTGTTCA	59.400	50.000	3.94	0.00	42.66	3.18
320	326	4.436998	GGTCGGTGCCTGTCCTCG	62.437	72.222	0.00	0.00	0.00	4.63
328	334	1.374758	GCCTGTCCTCGTTGTCCAG	60.375	63.158	0.00	0.00	0.00	3.86
580	596	7.542824	TGTTTTGTCACTTAACTAAAACTTGGC	59.457	33.333	0.00	0.00	40.20	4.52
644	660	4.374843	TTCATTGCCTTTTCCATCATCG	57.625	40.909	0.00	0.00	0.00	3.84
685	702	4.890581	ACCTGATGATGTGAGTAGAGTACC	59.109	45.833	0.00	0.00	0.00	3.34
747	768	0.790814	GTGAGGAGAAGAAAACGCGG	59.209	55.000	12.47	0.00	0.00	6.46
771	795	4.998051	AGAGAGATAAGAGGGATGAGGTC	58.002	47.826	0.00	0.00	0.00	3.85
804	828	1.133009	AGTGGAGTGACTGAGAAGGGT	60.133	52.381	0.00	0.00	0.00	4.34
819	843	3.198853	AGAAGGGTTGTGAGGAGATAAGC	59.801	47.826	0.00	0.00	0.00	3.09
841	865	0.387878	GATGTGGAGGCGAGCGATAG	60.388	60.000	0.00	0.00	0.00	2.08
977	1004	4.923871	CACAGTAGTATCCAACACAGACAC	59.076	45.833	0.00	0.00	0.00	3.67
1041	1078	2.553268	GTGCTTGCAGTGCTCGTC	59.447	61.111	17.60	3.63	0.00	4.20
1228	1289	2.188817	ACCTACCCATCGAGAGCTTTT	58.811	47.619	0.00	0.00	0.00	2.27
1518	1585	1.000896	GCTGCCCAAGGGTGTATGT	60.001	57.895	7.05	0.00	37.65	2.29
1925	3887	1.229625	AGCCATCTCCACCACCTCA	60.230	57.895	0.00	0.00	0.00	3.86
1926	3888	0.842030	AGCCATCTCCACCACCTCAA	60.842	55.000	0.00	0.00	0.00	3.02
1928	3890	0.391661	CCATCTCCACCACCTCAACG	60.392	60.000	0.00	0.00	0.00	4.10
1930	3892	0.898320	ATCTCCACCACCTCAACGAG	59.102	55.000	0.00	0.00	0.00	4.18
2019	4216	0.598419	GGCTGCTTTGCAACTGAACC	60.598	55.000	0.00	0.00	38.41	3.62
2296	4493	0.607489	GCTCCCACAGTGACTGCATT	60.607	55.000	13.37	0.00	34.37	3.56
2325	4522	2.131972	TGATGACGGAACACTCAAACG	58.868	47.619	0.00	0.00	0.00	3.60
2360	4557	3.550820	TGCAAGTGCTCTTCTGGTTTTA	58.449	40.909	4.69	0.00	42.66	1.52
2406	4620	6.266168	TGGATGCACAGGTATTTTAACTTG	57.734	37.500	0.00	0.00	33.01	3.16
2646	4871	7.732025	TCTATTCTTAAATAGTCGCATCCCAA	58.268	34.615	5.38	0.00	43.28	4.12
2695	4920	3.946606	TGTCACATCATCAAGTCATGCT	58.053	40.909	0.00	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	4.134563	AGTTCTGGACGCTGTTTAATTGT	58.865	39.130	0.00	0.00	0.00	2.71
60	61	0.175989	GGTGACGGGATCTGGAGTTC	59.824	60.000	0.00	0.00	0.00	3.01
61	62	2.287829	GGTGACGGGATCTGGAGTT	58.712	57.895	0.00	0.00	0.00	3.01
62	63	4.035843	GGTGACGGGATCTGGAGT	57.964	61.111	0.00	0.00	0.00	3.85
86	87	1.266124	GCACGAAAAAGGCCGAAACG	61.266	55.000	0.00	3.89	0.00	3.60
158	162	0.320374	CGCTTGGAGTGTTCCCAGTA	59.680	55.000	0.00	0.00	43.33	2.74
160	164	0.535102	AACGCTTGGAGTGTTCCCAG	60.535	55.000	1.31	0.00	44.85	4.45
161	165	1.529796	AACGCTTGGAGTGTTCCCA	59.470	52.632	1.31	0.00	44.85	4.37
162	166	4.475527	AACGCTTGGAGTGTTCCC	57.524	55.556	1.31	0.00	44.85	3.97
192	196	3.074412	ACGATTACTGCAAAACCAGGAG	58.926	45.455	0.00	0.00	37.16	3.69
222	227	0.185175	GGGGATTTGGACCGGCTATT	59.815	55.000	0.00	0.00	0.00	1.73
224	229	2.380285	GGGGGATTTGGACCGGCTA	61.380	63.158	0.00	0.00	0.00	3.93
255	261	2.292828	TTCTTCTTCAAAGGGGGCAG	57.707	50.000	0.00	0.00	0.00	4.85
258	264	5.423290	AGCATAATTTCTTCTTCAAAGGGGG	59.577	40.000	0.00	0.00	0.00	5.40
264	270	6.199937	GCAGGAGCATAATTTCTTCTTCAA	57.800	37.500	0.00	0.00	41.58	2.69
286	292	0.593128	ACCGAGTGAACAGCAAATGC	59.407	50.000	0.00	0.00	42.49	3.56
287	293	1.136252	CGACCGAGTGAACAGCAAATG	60.136	52.381	0.00	0.00	0.00	2.32
288	294	1.148310	CGACCGAGTGAACAGCAAAT	58.852	50.000	0.00	0.00	0.00	2.32
295	301	2.737376	GGCACCGACCGAGTGAAC	60.737	66.667	12.71	4.04	37.42	3.18
299	305	3.681835	GACAGGCACCGACCGAGT	61.682	66.667	0.00	0.00	33.69	4.18
320	326	4.083271	GGCAAAACTATCTGACTGGACAAC	60.083	45.833	0.00	0.00	0.00	3.32
328	334	7.801716	TTGTATATGGGCAAAACTATCTGAC	57.198	36.000	0.00	0.00	0.00	3.51
378	386	8.554528	CACAGTCTTATAACATAAATGAGGCAG	58.445	37.037	0.00	0.00	0.00	4.85
409	417	3.075884	TGTGCCGTGTAAACTAAATCCC	58.924	45.455	0.00	0.00	0.00	3.85
631	647	5.106197	TGTTTGGATGACGATGATGGAAAAG	60.106	40.000	0.00	0.00	0.00	2.27
644	660	5.790593	TCAGGTAGTACTTGTTTGGATGAC	58.209	41.667	11.74	0.00	0.00	3.06
685	702	0.246635	CCCCGCCTGTTAGATATCCG	59.753	60.000	0.00	0.00	0.00	4.18
747	768	4.202673	ACCTCATCCCTCTTATCTCTCTCC	60.203	50.000	0.00	0.00	0.00	3.71
782	806	1.548269	CCTTCTCAGTCACTCCACTCC	59.452	57.143	0.00	0.00	0.00	3.85
783	807	1.548269	CCCTTCTCAGTCACTCCACTC	59.452	57.143	0.00	0.00	0.00	3.51
784	808	1.133009	ACCCTTCTCAGTCACTCCACT	60.133	52.381	0.00	0.00	0.00	4.00
785	809	1.343069	ACCCTTCTCAGTCACTCCAC	58.657	55.000	0.00	0.00	0.00	4.02
786	810	1.694150	CAACCCTTCTCAGTCACTCCA	59.306	52.381	0.00	0.00	0.00	3.86
804	828	3.776969	ACATCAGGCTTATCTCCTCACAA	59.223	43.478	0.00	0.00	0.00	3.33
819	843	2.202987	GCTCGCCTCCACATCAGG	60.203	66.667	0.00	0.00	0.00	3.86
1105	1142	5.244178	ACGGATAAGGTATCTCATCAACCTC	59.756	44.000	0.00	0.00	42.86	3.85
1228	1289	6.068010	ACAGGTTGTTGGAATCAAAGATGTA	58.932	36.000	0.00	0.00	34.28	2.29
1907	3869	0.842030	TTGAGGTGGTGGAGATGGCT	60.842	55.000	0.00	0.00	0.00	4.75
1925	3887	1.374758	CCTTCTTCGGCTGCTCGTT	60.375	57.895	0.00	0.00	0.00	3.85
1926	3888	1.608717	ATCCTTCTTCGGCTGCTCGT	61.609	55.000	0.00	0.00	0.00	4.18
1928	3890	1.012841	CAATCCTTCTTCGGCTGCTC	58.987	55.000	0.00	0.00	0.00	4.26
1930	3892	0.449388	CACAATCCTTCTTCGGCTGC	59.551	55.000	0.00	0.00	0.00	5.25
2019	4216	6.073873	GGCTCGAAGACATTTGAGATAGAATG	60.074	42.308	9.02	0.00	46.23	2.67
2058	4255	0.868406	CAGTTCAAGCACCGGAAGAC	59.132	55.000	9.46	0.00	0.00	3.01
2311	4508	2.288030	ACCTAGACGTTTGAGTGTTCCG	60.288	50.000	0.00	0.00	0.00	4.30
2325	4522	1.067071	ACTTGCAGCGGTAACCTAGAC	60.067	52.381	0.00	0.00	0.00	2.59
2431	4645	8.019652	AGAACTCTAGAATTTGTATATCCCCCT	58.980	37.037	0.00	0.00	0.00	4.79
2641	4866	6.789268	TGAAGAGGAAAATTAGACATTGGGA	58.211	36.000	0.00	0.00	0.00	4.37
2646	4871	7.177216	TGTTGCATGAAGAGGAAAATTAGACAT	59.823	33.333	0.00	0.00	0.00	3.06
2776	5001	9.863845	AGTTAAGCAAAAACTAAGTTAAGCAAA	57.136	25.926	0.00	0.00	35.44	3.68
2777	5002	9.863845	AAGTTAAGCAAAAACTAAGTTAAGCAA	57.136	25.926	0.00	0.00	36.17	3.91
2846	5071	6.096846	CCCGAGGAATCCTGTTAAAAATGAAT	59.903	38.462	6.50	0.00	31.76	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.