AutoCloner

Multiple sequence alignment - TraesCS5B01G172400

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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	TraesCS5B01G172400	chr5B	100.000	2240	0	0	1	2240	316625042	316622803	0.000000e+00	4137
1	TraesCS5B01G172400	chr5B	86.700	797	93	8	4	799	707354555	707355339	0.000000e+00	872
2	TraesCS5B01G172400	chr5B	86.375	800	104	5	1	799	707312585	707313380	0.000000e+00	869
3	TraesCS5B01G172400	chr5D	95.081	1423	47	11	826	2240	278468395	278466988	0.000000e+00	2218
4	TraesCS5B01G172400	chr5A	94.635	1342	47	7	899	2240	370096463	370097779	0.000000e+00	2056
5	TraesCS5B01G172400	chr5A	93.689	919	48	2	901	1819	370043312	370042404	0.000000e+00	1367
6	TraesCS5B01G172400	chr5A	90.049	412	25	6	1829	2240	370037019	370036624	9.170000e-144	520
7	TraesCS5B01G172400	chr3B	90.411	803	76	1	1	803	814145283	814146084	0.000000e+00	1055
8	TraesCS5B01G172400	chr4B	88.529	802	89	3	2	803	613828164	613827366	0.000000e+00	968
9	TraesCS5B01G172400	chr4B	86.912	787	98	3	14	799	637457695	637458477	0.000000e+00	878
10	TraesCS5B01G172400	chr2D	82.025	790	140	2	7	795	427980530	427979742	0.000000e+00	671
11	TraesCS5B01G172400	chr2D	80.637	754	144	2	43	795	572019846	572019094	1.150000e-162	582
12	TraesCS5B01G172400	chr7D	82.075	742	129	4	55	794	107012890	107012151	4.060000e-177	630
13	TraesCS5B01G172400	chr6D	80.657	791	149	4	7	795	70648560	70649348	5.290000e-171	610
14	TraesCS5B01G172400	chr6D	78.390	236	43	7	1421	1655	369661723	369661951	1.790000e-31	147
15	TraesCS5B01G172400	chr6A	79.661	236	40	7	1421	1655	510865537	510865765	1.780000e-36	163
16	TraesCS5B01G172400	chr6B	77.119	236	46	6	1421	1655	555293863	555294091	1.810000e-26	130

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	TraesCS5B01G172400	chr5B	316622803	316625042	2239	True	4137	4137	100.000	1	2240	1	chr5B.!!$R1	2239
1	TraesCS5B01G172400	chr5B	707354555	707355339	784	False	872	872	86.700	4	799	1	chr5B.!!$F2	795
2	TraesCS5B01G172400	chr5B	707312585	707313380	795	False	869	869	86.375	1	799	1	chr5B.!!$F1	798
3	TraesCS5B01G172400	chr5D	278466988	278468395	1407	True	2218	2218	95.081	826	2240	1	chr5D.!!$R1	1414
4	TraesCS5B01G172400	chr5A	370096463	370097779	1316	False	2056	2056	94.635	899	2240	1	chr5A.!!$F1	1341
5	TraesCS5B01G172400	chr5A	370042404	370043312	908	True	1367	1367	93.689	901	1819	1	chr5A.!!$R2	918
6	TraesCS5B01G172400	chr3B	814145283	814146084	801	False	1055	1055	90.411	1	803	1	chr3B.!!$F1	802
7	TraesCS5B01G172400	chr4B	613827366	613828164	798	True	968	968	88.529	2	803	1	chr4B.!!$R1	801
8	TraesCS5B01G172400	chr4B	637457695	637458477	782	False	878	878	86.912	14	799	1	chr4B.!!$F1	785
9	TraesCS5B01G172400	chr2D	427979742	427980530	788	True	671	671	82.025	7	795	1	chr2D.!!$R1	788
10	TraesCS5B01G172400	chr2D	572019094	572019846	752	True	582	582	80.637	43	795	1	chr2D.!!$R2	752
11	TraesCS5B01G172400	chr7D	107012151	107012890	739	True	630	630	82.075	55	794	1	chr7D.!!$R1	739
12	TraesCS5B01G172400	chr6D	70648560	70649348	788	False	610	610	80.657	7	795	1	chr6D.!!$F1	788

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
807	821	0.031178	GCACTTGCACTTGGACTTGG	59.969	55.0	0.0	0.0	41.59	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2094	2112	0.471591	TCCATTTGGGCAGCTGGTTT	60.472	50.0	17.12	0.0	36.21	3.27	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
68	71	1.407437	GCGACATCAGGATCTTTGGGT	60.407	52.381	0.00	0.00	0.00	4.51
131	145	3.365265	CGTTTGGGCAGCACCTCC	61.365	66.667	0.00	0.00	39.10	4.30
133	147	3.185203	TTTGGGCAGCACCTCCCT	61.185	61.111	0.00	0.00	43.04	4.20
134	148	2.777960	TTTGGGCAGCACCTCCCTT	61.778	57.895	0.00	0.00	43.04	3.95
227	241	2.027745	ACACGCAATCTTCATCCTCACT	60.028	45.455	0.00	0.00	0.00	3.41
292	306	1.256812	CCAAGCATTCGGAACCCTTT	58.743	50.000	0.00	0.00	0.00	3.11
332	346	2.507407	TGTGTTTCTTAGGGATGCCC	57.493	50.000	0.00	0.00	45.90	5.36
350	364	4.873810	TGCAGCCGCACACTGGTT	62.874	61.111	0.00	0.00	45.36	3.67
408	422	3.554232	CACGCACAGTGGCAGTAG	58.446	61.111	1.84	0.00	46.77	2.57
420	434	5.178061	CAGTGGCAGTAGTGTCATTGATAA	58.822	41.667	19.78	0.00	46.21	1.75
456	470	0.033504	ACTCGACTTCGCCATGTGTT	59.966	50.000	0.00	0.00	39.60	3.32
680	694	2.290641	CAGACAAAAGAAACCCTCACCG	59.709	50.000	0.00	0.00	0.00	4.94
701	715	2.498167	GAGATCGCACTGCCCATAATT	58.502	47.619	0.00	0.00	0.00	1.40
758	772	1.915769	AGAAGCGTGGCCCTCTTCT	60.916	57.895	19.51	19.51	41.01	2.85
761	775	0.890996	AAGCGTGGCCCTCTTCTTTG	60.891	55.000	0.00	0.00	0.00	2.77
795	809	1.341209	AGGGCTTAAACTTGCACTTGC	59.659	47.619	0.00	0.00	40.41	4.01
806	820	3.557207	GCACTTGCACTTGGACTTG	57.443	52.632	0.00	0.00	41.59	3.16
807	821	0.031178	GCACTTGCACTTGGACTTGG	59.969	55.000	0.00	0.00	41.59	3.61
808	822	1.679139	CACTTGCACTTGGACTTGGA	58.321	50.000	0.00	0.00	0.00	3.53
809	823	1.334869	CACTTGCACTTGGACTTGGAC	59.665	52.381	0.00	0.00	0.00	4.02
810	824	1.064758	ACTTGCACTTGGACTTGGACA	60.065	47.619	0.00	0.00	0.00	4.02
811	825	1.605710	CTTGCACTTGGACTTGGACAG	59.394	52.381	0.00	0.00	0.00	3.51
812	826	0.819259	TGCACTTGGACTTGGACAGC	60.819	55.000	0.00	0.00	0.00	4.40
813	827	0.819259	GCACTTGGACTTGGACAGCA	60.819	55.000	0.00	0.00	0.00	4.41
814	828	0.947244	CACTTGGACTTGGACAGCAC	59.053	55.000	0.00	0.00	0.00	4.40
815	829	0.532862	ACTTGGACTTGGACAGCACG	60.533	55.000	0.00	0.00	0.00	5.34
816	830	1.845809	CTTGGACTTGGACAGCACGC	61.846	60.000	0.00	0.00	0.00	5.34
817	831	2.280797	GGACTTGGACAGCACGCA	60.281	61.111	0.00	0.00	0.00	5.24
818	832	2.320587	GGACTTGGACAGCACGCAG	61.321	63.158	0.00	0.00	0.00	5.18
819	833	1.300931	GACTTGGACAGCACGCAGA	60.301	57.895	0.00	0.00	0.00	4.26
820	834	1.287730	GACTTGGACAGCACGCAGAG	61.288	60.000	0.00	0.00	0.00	3.35
821	835	1.301244	CTTGGACAGCACGCAGAGT	60.301	57.895	0.00	0.00	0.00	3.24
822	836	0.882042	CTTGGACAGCACGCAGAGTT	60.882	55.000	0.00	0.00	0.00	3.01
823	837	0.391228	TTGGACAGCACGCAGAGTTA	59.609	50.000	0.00	0.00	0.00	2.24
824	838	0.038251	TGGACAGCACGCAGAGTTAG	60.038	55.000	0.00	0.00	0.00	2.34
831	845	2.071688	CACGCAGAGTTAGTGCTCTT	57.928	50.000	0.00	0.00	42.69	2.85
1092	1110	3.114647	CTCCTCGTCGCCTTCGGAG	62.115	68.421	0.00	0.00	35.75	4.63
1419	1437	1.132643	GACGACACGTAGATGAAGCCT	59.867	52.381	0.00	0.00	41.37	4.58
1985	2003	6.210078	TCCAAAGTTAATTTAAGTTGCACCG	58.790	36.000	9.44	0.00	32.00	4.94
2008	2026	5.228635	CGCAATTTACTTTCATCTCATGTGC	59.771	40.000	0.00	0.00	0.00	4.57
2027	2045	3.862845	GTGCGAATGTTTCACCAAAAGTT	59.137	39.130	0.00	0.00	0.00	2.66
2031	2049	6.419413	TGCGAATGTTTCACCAAAAGTTAATC	59.581	34.615	0.00	0.00	0.00	1.75
2036	2054	6.674066	TGTTTCACCAAAAGTTAATCCGATC	58.326	36.000	0.00	0.00	0.00	3.69
2059	2077	3.813529	AACGCTCAACTATTGAACAGC	57.186	42.857	0.00	0.00	39.58	4.40
2066	2084	5.734498	GCTCAACTATTGAACAGCGTAAATG	59.266	40.000	0.00	0.00	39.58	2.32
2094	2112	6.014242	ACAGAAGAATGTGAGGTGACAGATAA	60.014	38.462	0.00	0.00	30.46	1.75
2120	2138	0.032813	CTGCCCAAATGGACCCAGAT	60.033	55.000	0.00	0.00	37.39	2.90
2128	2146	4.040217	CCAAATGGACCCAGATTTGAACAA	59.960	41.667	14.42	0.00	36.43	2.83
2129	2147	5.232463	CAAATGGACCCAGATTTGAACAAG	58.768	41.667	9.22	0.00	36.43	3.16
2133	2151	5.640147	TGGACCCAGATTTGAACAAGTATT	58.360	37.500	0.00	0.00	0.00	1.89
2199	2220	5.132897	TGCAATGTTGGTATTTGGTTCTC	57.867	39.130	0.00	0.00	0.00	2.87
2224	2245	3.188048	GCCTTCACAAGTGATCTGTCAAG	59.812	47.826	3.43	0.00	39.64	3.02
2226	2247	3.758755	TCACAAGTGATCTGTCAAGCT	57.241	42.857	0.00	0.00	35.80	3.74
2227	2248	3.396560	TCACAAGTGATCTGTCAAGCTG	58.603	45.455	0.00	0.00	35.80	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	117	4.999939	CCAAACGCGGTGGCAAGC	63.000	66.667	16.85	6.18	39.92	4.01
131	145	3.193479	GCTACCAAATCAAGGTGGAAAGG	59.807	47.826	0.00	0.00	39.74	3.11
133	147	3.161866	GGCTACCAAATCAAGGTGGAAA	58.838	45.455	0.00	0.00	39.74	3.13
134	148	2.378547	AGGCTACCAAATCAAGGTGGAA	59.621	45.455	0.00	0.00	39.74	3.53
227	241	3.664769	CTCATCAGGATGGGGCCA	58.335	61.111	4.39	0.00	39.24	5.36
292	306	0.037326	GTGTGAGGACCGCATCAAGA	60.037	55.000	0.00	0.00	36.47	3.02
344	358	1.303317	GGTCATGCCCGAAACCAGT	60.303	57.895	0.00	0.00	0.00	4.00
346	360	0.679640	GATGGTCATGCCCGAAACCA	60.680	55.000	4.34	4.34	45.32	3.67
347	361	1.714899	CGATGGTCATGCCCGAAACC	61.715	60.000	4.07	0.00	36.04	3.27
350	364	2.189257	CCGATGGTCATGCCCGAA	59.811	61.111	4.07	0.00	36.04	4.30
386	400	0.933097	CTGCCACTGTGCGTGATATC	59.067	55.000	1.29	0.00	46.81	1.63
420	434	5.414765	AGTCGAGTGGAAAACTTTTCTTGTT	59.585	36.000	12.88	0.00	40.07	2.83
434	448	1.215382	CATGGCGAAGTCGAGTGGA	59.785	57.895	4.59	0.00	43.02	4.02
456	470	1.757118	CTTCCCTTCTGCGGATCTGTA	59.243	52.381	2.89	0.00	0.00	2.74
618	632	1.003355	CCGAACTGCCAGTGGATGT	60.003	57.895	15.20	7.56	0.00	3.06
680	694	0.106708	TTATGGGCAGTGCGATCTCC	59.893	55.000	9.45	4.63	0.00	3.71
758	772	1.356270	CTTCTGCGTGCTGTGCAAA	59.644	52.632	0.00	0.00	42.70	3.68
761	775	3.730761	CCCTTCTGCGTGCTGTGC	61.731	66.667	0.00	0.00	0.00	4.57
795	809	0.947244	GTGCTGTCCAAGTCCAAGTG	59.053	55.000	0.00	0.00	0.00	3.16
799	813	2.280797	GCGTGCTGTCCAAGTCCA	60.281	61.111	0.00	0.00	0.00	4.02
801	815	1.287730	CTCTGCGTGCTGTCCAAGTC	61.288	60.000	0.00	0.00	0.00	3.01
802	816	1.301244	CTCTGCGTGCTGTCCAAGT	60.301	57.895	0.00	0.00	0.00	3.16
803	817	0.882042	AACTCTGCGTGCTGTCCAAG	60.882	55.000	0.00	0.00	0.00	3.61
804	818	0.391228	TAACTCTGCGTGCTGTCCAA	59.609	50.000	0.00	0.00	0.00	3.53
805	819	0.038251	CTAACTCTGCGTGCTGTCCA	60.038	55.000	0.00	0.00	0.00	4.02
806	820	0.038159	ACTAACTCTGCGTGCTGTCC	60.038	55.000	0.00	0.00	0.00	4.02
807	821	1.063806	CACTAACTCTGCGTGCTGTC	58.936	55.000	0.00	0.00	0.00	3.51
808	822	3.201342	CACTAACTCTGCGTGCTGT	57.799	52.632	0.00	0.00	0.00	4.40
811	825	1.937108	AAGAGCACTAACTCTGCGTGC	60.937	52.381	5.55	5.55	46.38	5.34
812	826	2.071688	AAGAGCACTAACTCTGCGTG	57.928	50.000	0.00	0.00	46.38	5.34
813	827	2.416162	GCTAAGAGCACTAACTCTGCGT	60.416	50.000	0.00	0.00	46.38	5.24
814	828	2.189342	GCTAAGAGCACTAACTCTGCG	58.811	52.381	0.00	0.00	46.38	5.18
821	835	7.118390	GAGACAAATCTTTGCTAAGAGCACTAA	59.882	37.037	15.63	0.00	43.14	2.24
822	836	6.591834	GAGACAAATCTTTGCTAAGAGCACTA	59.408	38.462	15.63	0.00	43.14	2.74
823	837	5.411053	GAGACAAATCTTTGCTAAGAGCACT	59.589	40.000	15.63	10.03	43.14	4.40
824	838	5.180117	TGAGACAAATCTTTGCTAAGAGCAC	59.820	40.000	15.63	6.14	43.14	4.40
831	845	5.562696	CGCCTTTTGAGACAAATCTTTGCTA	60.563	40.000	2.63	0.00	41.79	3.49
836	850	3.004734	CACCGCCTTTTGAGACAAATCTT	59.995	43.478	0.00	0.00	34.34	2.40
919	937	2.396160	ACGTCAGTCAGTCGTGTAAC	57.604	50.000	0.00	0.00	40.37	2.50
1092	1110	3.200593	CCGCTGCTCATGCTGTCC	61.201	66.667	0.00	0.00	39.81	4.02
1419	1437	2.363795	ATCAGCCGGACCGAGGAA	60.364	61.111	17.49	0.00	0.00	3.36
1755	1773	2.357034	ACCCGCTACAACACGCTG	60.357	61.111	0.00	0.00	0.00	5.18
1886	1904	2.586357	GGGACTGGAAGATCGCGC	60.586	66.667	0.00	0.00	37.43	6.86
1985	2003	5.228635	CGCACATGAGATGAAAGTAAATTGC	59.771	40.000	0.00	0.00	0.00	3.56
2008	2026	6.087555	CGGATTAACTTTTGGTGAAACATTCG	59.912	38.462	0.00	0.00	39.98	3.34
2027	2045	2.933906	GTTGAGCGTTTGGATCGGATTA	59.066	45.455	0.00	0.00	32.36	1.75
2031	2049	2.004583	TAGTTGAGCGTTTGGATCGG	57.995	50.000	0.00	0.00	32.36	4.18
2036	2054	4.466828	CTGTTCAATAGTTGAGCGTTTGG	58.533	43.478	2.85	0.00	42.91	3.28
2059	2077	6.401474	CCTCACATTCTTCTGTCACATTTACG	60.401	42.308	0.00	0.00	0.00	3.18
2066	2084	3.743396	GTCACCTCACATTCTTCTGTCAC	59.257	47.826	0.00	0.00	0.00	3.67
2094	2112	0.471591	TCCATTTGGGCAGCTGGTTT	60.472	50.000	17.12	0.00	36.21	3.27
2199	2220	2.082231	CAGATCACTTGTGAAGGCCAG	58.918	52.381	5.01	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.