AutoCloner

Multiple sequence alignment - TraesCS7B01G490100

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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	TraesCS7B01G490100	chr7B	100.000	2768	0	0	1	2768	743708481	743711248	0.000000e+00	5112.0
1	TraesCS7B01G490100	chr7B	97.485	2107	43	2	672	2768	744269010	744271116	0.000000e+00	3589.0
2	TraesCS7B01G490100	chr7B	89.456	2115	151	25	668	2766	744331156	744329098	0.000000e+00	2604.0
3	TraesCS7B01G490100	chr7B	86.355	1517	168	20	668	2156	744239227	744240732	0.000000e+00	1618.0
4	TraesCS7B01G490100	chr7B	83.945	1171	158	21	982	2134	744339396	744338238	0.000000e+00	1094.0
5	TraesCS7B01G490100	chr7B	81.037	1292	204	29	999	2280	645403210	645401950	0.000000e+00	990.0
6	TraesCS7B01G490100	chr7B	97.430	467	7	3	1	467	744268527	744268988	0.000000e+00	791.0
7	TraesCS7B01G490100	chr7B	80.682	704	64	32	1	670	744000089	743999424	5.360000e-132	481.0
8	TraesCS7B01G490100	chr7B	90.506	316	19	5	668	974	743999575	743999262	9.230000e-110	407.0
9	TraesCS7B01G490100	chr7B	97.315	149	3	1	523	670	744269010	744269158	4.580000e-63	252.0
10	TraesCS7B01G490100	chr7B	99.275	138	0	1	668	805	743708999	743709135	5.920000e-62	248.0
11	TraesCS7B01G490100	chr7B	99.275	138	0	1	519	655	743709148	743709285	5.920000e-62	248.0
12	TraesCS7B01G490100	chr7B	100.000	132	0	0	1	132	744238607	744238738	7.660000e-61	244.0
13	TraesCS7B01G490100	chr7B	83.936	249	12	3	444	664	744239126	744239374	2.160000e-51	213.0
14	TraesCS7B01G490100	chr7B	93.548	62	3	1	465	526	744331236	744331176	1.060000e-14	91.6
15	TraesCS7B01G490100	chr7A	87.679	1956	163	37	668	2588	736008673	736006761	0.000000e+00	2206.0
16	TraesCS7B01G490100	chr7A	81.071	1289	212	22	999	2280	671427319	671426056	0.000000e+00	1000.0
17	TraesCS7B01G490100	chr7A	93.333	60	4	0	2705	2764	736006745	736006686	3.800000e-14	89.8
18	TraesCS7B01G490100	chrUn	86.563	1414	110	30	1371	2768	330873721	330875070	0.000000e+00	1485.0
19	TraesCS7B01G490100	chrUn	87.915	993	80	11	1371	2348	219093787	219092820	0.000000e+00	1133.0
20	TraesCS7B01G490100	chrUn	85.330	409	24	13	2361	2768	409760664	409761037	9.290000e-105	390.0
21	TraesCS7B01G490100	chr3B	87.988	1307	92	25	1463	2768	778534317	778535559	0.000000e+00	1483.0
22	TraesCS7B01G490100	chr7D	89.953	1075	88	11	999	2057	632033222	632034292	0.000000e+00	1369.0
23	TraesCS7B01G490100	chr7D	83.942	1370	185	16	802	2155	632079481	632080831	0.000000e+00	1279.0
24	TraesCS7B01G490100	chr7D	82.438	1173	178	11	906	2054	555047227	555048395	0.000000e+00	1000.0
25	TraesCS7B01G490100	chr7D	76.923	572	53	31	1	530	632078893	632079427	4.580000e-63	252.0

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	TraesCS7B01G490100	chr7B	743708481	743711248	2767	False	1869.333333	5112	99.516667	1	2768	3	chr7B.!!$F1	2767
1	TraesCS7B01G490100	chr7B	744268527	744271116	2589	False	1544.000000	3589	97.410000	1	2768	3	chr7B.!!$F3	2767
2	TraesCS7B01G490100	chr7B	744329098	744331236	2138	True	1347.800000	2604	91.502000	465	2766	2	chr7B.!!$R4	2301
3	TraesCS7B01G490100	chr7B	744338238	744339396	1158	True	1094.000000	1094	83.945000	982	2134	1	chr7B.!!$R2	1152
4	TraesCS7B01G490100	chr7B	645401950	645403210	1260	True	990.000000	990	81.037000	999	2280	1	chr7B.!!$R1	1281
5	TraesCS7B01G490100	chr7B	744238607	744240732	2125	False	691.666667	1618	90.097000	1	2156	3	chr7B.!!$F2	2155
6	TraesCS7B01G490100	chr7B	743999262	744000089	827	True	444.000000	481	85.594000	1	974	2	chr7B.!!$R3	973
7	TraesCS7B01G490100	chr7A	736006686	736008673	1987	True	1147.900000	2206	90.506000	668	2764	2	chr7A.!!$R2	2096
8	TraesCS7B01G490100	chr7A	671426056	671427319	1263	True	1000.000000	1000	81.071000	999	2280	1	chr7A.!!$R1	1281
9	TraesCS7B01G490100	chrUn	330873721	330875070	1349	False	1485.000000	1485	86.563000	1371	2768	1	chrUn.!!$F1	1397
10	TraesCS7B01G490100	chrUn	219092820	219093787	967	True	1133.000000	1133	87.915000	1371	2348	1	chrUn.!!$R1	977
11	TraesCS7B01G490100	chr3B	778534317	778535559	1242	False	1483.000000	1483	87.988000	1463	2768	1	chr3B.!!$F1	1305
12	TraesCS7B01G490100	chr7D	632033222	632034292	1070	False	1369.000000	1369	89.953000	999	2057	1	chr7D.!!$F2	1058
13	TraesCS7B01G490100	chr7D	555047227	555048395	1168	False	1000.000000	1000	82.438000	906	2054	1	chr7D.!!$F1	1148
14	TraesCS7B01G490100	chr7D	632078893	632080831	1938	False	765.500000	1279	80.432500	1	2155	2	chr7D.!!$F3	2154

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
623	771	0.178998	CCAATCCCTCCATGCTCCAG	60.179	60.0	0.0	0.0	0.00	3.86	F
629	777	0.179051	CCTCCATGCTCCAGCTCTTC	60.179	60.0	0.0	0.0	42.66	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1638	1840	3.120792	CTCGTCGTTGAAGACCTTTTGA	58.879	45.455	0.0	0.0	37.85	2.69	R
2405	2609	6.336566	TGAGATAGAAACTTGCACTCAGATC	58.663	40.000	0.0	0.0	0.00	2.75	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
152	181	2.489073	CCCACCTGCTTAAGTTTCACCT	60.489	50.000	4.02	0.00	0.00	4.00
219	255	5.298527	GGTAGTTGTTGCTTAAGTTTCACCT	59.701	40.000	4.02	2.07	0.00	4.00
379	500	1.418342	GCGCATGAGGCAAAAGCATG	61.418	55.000	0.30	0.00	45.17	4.06
600	748	1.818959	GCTGTGGCATTGCTTCCCAA	61.819	55.000	8.82	0.00	38.54	4.12
601	749	0.680618	CTGTGGCATTGCTTCCCAAA	59.319	50.000	8.82	0.00	36.92	3.28
602	750	1.276989	CTGTGGCATTGCTTCCCAAAT	59.723	47.619	8.82	0.00	36.92	2.32
603	751	2.496871	CTGTGGCATTGCTTCCCAAATA	59.503	45.455	8.82	0.00	36.92	1.40
604	752	2.233431	TGTGGCATTGCTTCCCAAATAC	59.767	45.455	8.82	0.00	36.92	1.89
605	753	1.830477	TGGCATTGCTTCCCAAATACC	59.170	47.619	8.82	0.00	36.92	2.73
606	754	1.830477	GGCATTGCTTCCCAAATACCA	59.170	47.619	8.82	0.00	36.92	3.25
607	755	2.235898	GGCATTGCTTCCCAAATACCAA	59.764	45.455	8.82	0.00	36.92	3.67
608	756	3.118298	GGCATTGCTTCCCAAATACCAAT	60.118	43.478	8.82	0.00	36.92	3.16
609	757	4.122046	GCATTGCTTCCCAAATACCAATC	58.878	43.478	0.16	0.00	36.92	2.67
610	758	4.696455	CATTGCTTCCCAAATACCAATCC	58.304	43.478	0.00	0.00	36.92	3.01
611	759	2.745968	TGCTTCCCAAATACCAATCCC	58.254	47.619	0.00	0.00	0.00	3.85
612	760	2.314549	TGCTTCCCAAATACCAATCCCT	59.685	45.455	0.00	0.00	0.00	4.20
613	761	2.959030	GCTTCCCAAATACCAATCCCTC	59.041	50.000	0.00	0.00	0.00	4.30
614	762	3.566351	CTTCCCAAATACCAATCCCTCC	58.434	50.000	0.00	0.00	0.00	4.30
615	763	2.579100	TCCCAAATACCAATCCCTCCA	58.421	47.619	0.00	0.00	0.00	3.86
616	764	3.138518	TCCCAAATACCAATCCCTCCAT	58.861	45.455	0.00	0.00	0.00	3.41
617	765	3.117169	TCCCAAATACCAATCCCTCCATG	60.117	47.826	0.00	0.00	0.00	3.66
618	766	2.629617	CCAAATACCAATCCCTCCATGC	59.370	50.000	0.00	0.00	0.00	4.06
619	767	3.569491	CAAATACCAATCCCTCCATGCT	58.431	45.455	0.00	0.00	0.00	3.79
620	768	3.515602	AATACCAATCCCTCCATGCTC	57.484	47.619	0.00	0.00	0.00	4.26
621	769	1.140312	TACCAATCCCTCCATGCTCC	58.860	55.000	0.00	0.00	0.00	4.70
622	770	0.920763	ACCAATCCCTCCATGCTCCA	60.921	55.000	0.00	0.00	0.00	3.86
623	771	0.178998	CCAATCCCTCCATGCTCCAG	60.179	60.000	0.00	0.00	0.00	3.86
624	772	0.822532	CAATCCCTCCATGCTCCAGC	60.823	60.000	0.00	0.00	42.50	4.85
625	773	0.992431	AATCCCTCCATGCTCCAGCT	60.992	55.000	0.00	0.00	42.66	4.24
626	774	1.417288	ATCCCTCCATGCTCCAGCTC	61.417	60.000	0.00	0.00	42.66	4.09
627	775	2.071262	CCCTCCATGCTCCAGCTCT	61.071	63.158	0.00	0.00	42.66	4.09
628	776	1.633915	CCCTCCATGCTCCAGCTCTT	61.634	60.000	0.00	0.00	42.66	2.85
629	777	0.179051	CCTCCATGCTCCAGCTCTTC	60.179	60.000	0.00	0.00	42.66	2.87
630	778	0.179051	CTCCATGCTCCAGCTCTTCC	60.179	60.000	0.00	0.00	42.66	3.46
631	779	1.153005	CCATGCTCCAGCTCTTCCC	60.153	63.158	0.00	0.00	42.66	3.97
632	780	1.153005	CATGCTCCAGCTCTTCCCC	60.153	63.158	0.00	0.00	42.66	4.81
633	781	1.617536	ATGCTCCAGCTCTTCCCCA	60.618	57.895	0.00	0.00	42.66	4.96
634	782	1.633915	ATGCTCCAGCTCTTCCCCAG	61.634	60.000	0.00	0.00	42.66	4.45
635	783	2.588989	CTCCAGCTCTTCCCCAGC	59.411	66.667	0.00	0.00	37.12	4.85
636	784	2.203983	TCCAGCTCTTCCCCAGCA	60.204	61.111	0.00	0.00	39.56	4.41
637	785	2.045536	CCAGCTCTTCCCCAGCAC	60.046	66.667	0.00	0.00	39.56	4.40
638	786	2.600729	CCAGCTCTTCCCCAGCACT	61.601	63.158	0.00	0.00	39.56	4.40
639	787	1.376942	CAGCTCTTCCCCAGCACTG	60.377	63.158	0.00	0.00	39.56	3.66
640	788	2.749441	GCTCTTCCCCAGCACTGC	60.749	66.667	0.00	0.00	36.82	4.40
641	789	2.045536	CTCTTCCCCAGCACTGCC	60.046	66.667	0.00	0.00	0.00	4.85
642	790	2.853542	TCTTCCCCAGCACTGCCA	60.854	61.111	0.00	0.00	0.00	4.92
643	791	2.207501	CTCTTCCCCAGCACTGCCAT	62.208	60.000	0.00	0.00	0.00	4.40
644	792	1.751927	CTTCCCCAGCACTGCCATC	60.752	63.158	0.00	0.00	0.00	3.51
645	793	3.626996	TTCCCCAGCACTGCCATCG	62.627	63.158	0.00	0.00	0.00	3.84
647	795	4.790962	CCCAGCACTGCCATCGCT	62.791	66.667	0.00	0.00	36.10	4.93
648	796	3.200593	CCAGCACTGCCATCGCTC	61.201	66.667	0.00	0.00	32.48	5.03
649	797	3.200593	CAGCACTGCCATCGCTCC	61.201	66.667	0.00	0.00	32.48	4.70
650	798	4.479993	AGCACTGCCATCGCTCCC	62.480	66.667	0.00	0.00	35.36	4.30
681	829	0.998727	CGTCCGCTTTGCTTTGCTTC	60.999	55.000	0.00	0.00	0.00	3.86
682	830	0.312102	GTCCGCTTTGCTTTGCTTCT	59.688	50.000	0.00	0.00	0.00	2.85
684	832	0.595095	CCGCTTTGCTTTGCTTCTCT	59.405	50.000	0.00	0.00	0.00	3.10
690	838	1.376553	GCTTTGCTTCTCTCCGCCT	60.377	57.895	0.00	0.00	0.00	5.52
704	852	1.376609	CCGCCTGATGCTTTACCCAC	61.377	60.000	0.00	0.00	38.05	4.61
710	858	0.463833	GATGCTTTACCCACCTCCGG	60.464	60.000	0.00	0.00	0.00	5.14
724	872	2.813908	CCGGCTGCCAACGAGTAC	60.814	66.667	20.29	0.00	0.00	2.73
726	874	2.436115	GGCTGCCAACGAGTACCC	60.436	66.667	15.17	0.00	0.00	3.69
727	875	2.663196	GCTGCCAACGAGTACCCT	59.337	61.111	0.00	0.00	0.00	4.34
766	914	3.138518	TCCCAAATACCAATCCCTCCAT	58.861	45.455	0.00	0.00	0.00	3.41
1146	1315	2.028385	GGACCTTAAGAACTTCCTCGCA	60.028	50.000	3.36	0.00	0.00	5.10
1251	1420	2.183811	CTCGACCTCTGCCAGCTG	59.816	66.667	6.78	6.78	0.00	4.24
1254	1423	1.004560	CGACCTCTGCCAGCTGAAA	60.005	57.895	17.39	1.14	0.00	2.69
1318	1487	2.125773	CAATCCCTTGCTCTTCTGCT	57.874	50.000	0.00	0.00	0.00	4.24
1329	1498	0.615331	TCTTCTGCTTGCGGAATCCT	59.385	50.000	16.01	0.00	0.00	3.24
1638	1840	4.021925	GGCAAGACCACCCTCGCT	62.022	66.667	0.00	0.00	38.86	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
345	413	2.945984	CGCACGCCAAATGACAGT	59.054	55.556	0.00	0.00	0.00	3.55
426	547	5.759059	TGAACAGAAGAGGGCATTGATATT	58.241	37.500	0.00	0.00	0.00	1.28
600	748	2.108952	GGAGCATGGAGGGATTGGTATT	59.891	50.000	0.00	0.00	0.00	1.89
601	749	1.707427	GGAGCATGGAGGGATTGGTAT	59.293	52.381	0.00	0.00	0.00	2.73
602	750	1.140312	GGAGCATGGAGGGATTGGTA	58.860	55.000	0.00	0.00	0.00	3.25
603	751	0.920763	TGGAGCATGGAGGGATTGGT	60.921	55.000	0.00	0.00	0.00	3.67
604	752	0.178998	CTGGAGCATGGAGGGATTGG	60.179	60.000	0.00	0.00	0.00	3.16
605	753	0.822532	GCTGGAGCATGGAGGGATTG	60.823	60.000	0.00	0.00	41.59	2.67
606	754	0.992431	AGCTGGAGCATGGAGGGATT	60.992	55.000	0.65	0.00	45.16	3.01
607	755	1.385631	AGCTGGAGCATGGAGGGAT	60.386	57.895	0.65	0.00	45.16	3.85
608	756	2.041762	AGCTGGAGCATGGAGGGA	59.958	61.111	0.65	0.00	45.16	4.20
609	757	1.633915	AAGAGCTGGAGCATGGAGGG	61.634	60.000	0.00	0.00	45.16	4.30
610	758	0.179051	GAAGAGCTGGAGCATGGAGG	60.179	60.000	0.00	0.00	45.16	4.30
611	759	0.179051	GGAAGAGCTGGAGCATGGAG	60.179	60.000	0.00	0.00	45.16	3.86
612	760	1.630126	GGGAAGAGCTGGAGCATGGA	61.630	60.000	0.00	0.00	45.16	3.41
613	761	1.153005	GGGAAGAGCTGGAGCATGG	60.153	63.158	0.00	0.00	45.16	3.66
614	762	1.153005	GGGGAAGAGCTGGAGCATG	60.153	63.158	0.00	0.00	45.16	4.06
615	763	1.617536	TGGGGAAGAGCTGGAGCAT	60.618	57.895	0.00	0.00	45.16	3.79
616	764	2.203983	TGGGGAAGAGCTGGAGCA	60.204	61.111	0.00	0.00	45.16	4.26
617	765	2.588989	CTGGGGAAGAGCTGGAGC	59.411	66.667	0.00	0.00	42.49	4.70
618	766	2.296365	TGCTGGGGAAGAGCTGGAG	61.296	63.158	0.00	0.00	37.35	3.86
619	767	2.203983	TGCTGGGGAAGAGCTGGA	60.204	61.111	0.00	0.00	37.35	3.86
620	768	2.045536	GTGCTGGGGAAGAGCTGG	60.046	66.667	0.00	0.00	37.35	4.85
621	769	1.376942	CAGTGCTGGGGAAGAGCTG	60.377	63.158	0.00	0.00	37.35	4.24
622	770	3.076092	CAGTGCTGGGGAAGAGCT	58.924	61.111	0.00	0.00	37.35	4.09
623	771	2.749441	GCAGTGCTGGGGAAGAGC	60.749	66.667	8.18	0.00	36.95	4.09
624	772	2.045536	GGCAGTGCTGGGGAAGAG	60.046	66.667	16.11	0.00	0.00	2.85
625	773	2.202236	GATGGCAGTGCTGGGGAAGA	62.202	60.000	16.11	0.00	0.00	2.87
626	774	1.751927	GATGGCAGTGCTGGGGAAG	60.752	63.158	16.11	0.00	0.00	3.46
627	775	2.356278	GATGGCAGTGCTGGGGAA	59.644	61.111	16.11	0.00	0.00	3.97
628	776	4.100084	CGATGGCAGTGCTGGGGA	62.100	66.667	16.11	0.00	0.00	4.81
630	778	4.790962	AGCGATGGCAGTGCTGGG	62.791	66.667	16.11	3.45	43.41	4.45
631	779	3.200593	GAGCGATGGCAGTGCTGG	61.201	66.667	19.40	0.00	43.41	4.85
632	780	3.200593	GGAGCGATGGCAGTGCTG	61.201	66.667	19.40	4.02	43.41	4.41
633	781	4.479993	GGGAGCGATGGCAGTGCT	62.480	66.667	16.11	15.16	43.41	4.40
660	808	2.429069	CAAAGCAAAGCGGACGGC	60.429	61.111	0.00	0.00	44.05	5.68
661	809	2.406452	AAGCAAAGCAAAGCGGACGG	62.406	55.000	0.00	0.00	35.48	4.79
662	810	0.998727	GAAGCAAAGCAAAGCGGACG	60.999	55.000	0.00	0.00	35.48	4.79
663	811	0.312102	AGAAGCAAAGCAAAGCGGAC	59.688	50.000	0.00	0.00	35.48	4.79
690	838	0.251916	CGGAGGTGGGTAAAGCATCA	59.748	55.000	0.00	0.00	0.00	3.07
710	858	1.741770	CAGGGTACTCGTTGGCAGC	60.742	63.158	0.00	0.00	0.00	5.25
724	872	2.283388	AATGCCACAGCCACAGGG	60.283	61.111	0.00	0.00	38.69	4.45
726	874	1.812686	AAGCAATGCCACAGCCACAG	61.813	55.000	0.00	0.00	38.69	3.66
727	875	1.808531	GAAGCAATGCCACAGCCACA	61.809	55.000	0.00	0.00	38.69	4.17
766	914	2.203983	TGGGGAAGAGCTGGAGCA	60.204	61.111	0.00	0.00	45.16	4.26
1146	1315	4.040217	GTGATGTTCCTCCTATCAGCATCT	59.960	45.833	0.00	0.00	34.22	2.90
1251	1420	1.936547	CCACGCTTCTCCATAGCTTTC	59.063	52.381	0.00	0.00	36.49	2.62
1254	1423	1.826024	CCCACGCTTCTCCATAGCT	59.174	57.895	0.00	0.00	36.49	3.32
1257	1426	1.344953	ATGGCCCACGCTTCTCCATA	61.345	55.000	0.00	0.00	35.90	2.74
1329	1498	1.471501	CCGATCTCACGAGCATGGAAA	60.472	52.381	0.00	0.00	35.09	3.13
1638	1840	3.120792	CTCGTCGTTGAAGACCTTTTGA	58.879	45.455	0.00	0.00	37.85	2.69
2405	2609	6.336566	TGAGATAGAAACTTGCACTCAGATC	58.663	40.000	0.00	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.