AutoCloner

Multiple sequence alignment - TraesCS3B01G064900

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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	TraesCS3B01G064900	chr3B	100.000	3071	0	0	1	3071	37969741	37972811	0.000000e+00	5672
1	TraesCS3B01G064900	chr3B	83.305	1749	180	60	512	2229	38793585	38795252	0.000000e+00	1509
2	TraesCS3B01G064900	chr3B	84.440	1054	103	28	1292	2320	38212450	38213467	0.000000e+00	981
3	TraesCS3B01G064900	chr3B	84.440	1054	103	28	1292	2320	38309783	38310800	0.000000e+00	981
4	TraesCS3B01G064900	chr3D	94.028	2361	89	30	1	2326	21792041	21794384	0.000000e+00	3531
5	TraesCS3B01G064900	chr3D	85.765	1398	137	35	949	2320	21888387	21889748	0.000000e+00	1423
6	TraesCS3B01G064900	chr3D	95.263	380	14	1	2357	2736	21794360	21794735	1.580000e-167	599
7	TraesCS3B01G064900	chr3D	98.492	199	3	0	2871	3069	21794730	21794928	4.870000e-93	351
8	TraesCS3B01G064900	chr3A	93.486	2364	107	17	1	2326	31558188	31560542	0.000000e+00	3469
9	TraesCS3B01G064900	chr3A	85.469	1397	142	36	942	2320	31603448	31604801	0.000000e+00	1399
10	TraesCS3B01G064900	chr3A	91.329	715	30	6	2357	3071	31560518	31561200	0.000000e+00	948
11	TraesCS3B01G064900	chrUn	84.548	1372	136	32	974	2320	336370768	336369448	0.000000e+00	1290
12	TraesCS3B01G064900	chrUn	84.475	1372	137	32	974	2320	336373434	336372114	0.000000e+00	1284
13	TraesCS3B01G064900	chrUn	84.440	1054	103	28	1292	2320	341538639	341537622	0.000000e+00	981
14	TraesCS3B01G064900	chrUn	84.440	1054	103	28	1292	2320	341541149	341540132	0.000000e+00	981
15	TraesCS3B01G064900	chr5A	86.122	1052	120	15	978	2022	665443631	665444663	0.000000e+00	1110
16	TraesCS3B01G064900	chr4B	86.161	1055	114	19	978	2022	616967490	616968522	0.000000e+00	1110
17	TraesCS3B01G064900	chr4D	85.266	1052	120	14	978	2022	484620758	484621781	0.000000e+00	1051
18	TraesCS3B01G064900	chr7D	89.506	162	16	1	893	1054	460319605	460319445	1.440000e-48	204

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	TraesCS3B01G064900	chr3B	37969741	37972811	3070	False	5672.000000	5672	100.000000	1	3071	1	chr3B.!!$F1	3070
1	TraesCS3B01G064900	chr3B	38793585	38795252	1667	False	1509.000000	1509	83.305000	512	2229	1	chr3B.!!$F4	1717
2	TraesCS3B01G064900	chr3B	38212450	38213467	1017	False	981.000000	981	84.440000	1292	2320	1	chr3B.!!$F2	1028
3	TraesCS3B01G064900	chr3B	38309783	38310800	1017	False	981.000000	981	84.440000	1292	2320	1	chr3B.!!$F3	1028
4	TraesCS3B01G064900	chr3D	21792041	21794928	2887	False	1493.666667	3531	95.927667	1	3069	3	chr3D.!!$F2	3068
5	TraesCS3B01G064900	chr3D	21888387	21889748	1361	False	1423.000000	1423	85.765000	949	2320	1	chr3D.!!$F1	1371
6	TraesCS3B01G064900	chr3A	31558188	31561200	3012	False	2208.500000	3469	92.407500	1	3071	2	chr3A.!!$F2	3070
7	TraesCS3B01G064900	chr3A	31603448	31604801	1353	False	1399.000000	1399	85.469000	942	2320	1	chr3A.!!$F1	1378
8	TraesCS3B01G064900	chrUn	336369448	336373434	3986	True	1287.000000	1290	84.511500	974	2320	2	chrUn.!!$R1	1346
9	TraesCS3B01G064900	chrUn	341537622	341541149	3527	True	981.000000	981	84.440000	1292	2320	2	chrUn.!!$R2	1028
10	TraesCS3B01G064900	chr5A	665443631	665444663	1032	False	1110.000000	1110	86.122000	978	2022	1	chr5A.!!$F1	1044
11	TraesCS3B01G064900	chr4B	616967490	616968522	1032	False	1110.000000	1110	86.161000	978	2022	1	chr4B.!!$F1	1044
12	TraesCS3B01G064900	chr4D	484620758	484621781	1023	False	1051.000000	1051	85.266000	978	2022	1	chr4D.!!$F1	1044

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
784	818	0.855995	TGCGAACACATGTGTACACG	59.144	50.000	30.75	30.53	44.13	4.49	F
1058	1098	1.305887	CCCAGTACTCTTCCGGGGT	60.306	63.158	0.00	0.00	32.88	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1782	6986	0.317160	AGCACGAGAACACGATGGAA	59.683	50.000	0.00	0.00	37.03	3.53	R
2197	7440	1.925185	GCAATCGGACTTAAGGACGAC	59.075	52.381	20.93	9.19	38.24	4.34	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
110	112	7.562135	TGGAGAAAACTACTCAGTGTTTACTT	58.438	34.615	5.98	0.00	32.01	2.24
112	114	8.976471	GGAGAAAACTACTCAGTGTTTACTTAC	58.024	37.037	5.98	0.00	32.01	2.34
230	259	9.948964	AATATTTTCTTTTGGCTTGCTAAGAAT	57.051	25.926	13.86	7.32	36.73	2.40
367	397	8.424918	AGAGCTAGTGTATTAACTGTGCATTAT	58.575	33.333	0.00	0.00	35.09	1.28
395	425	6.503524	TGAGAATTTAAGCAAACCAACTCAC	58.496	36.000	0.00	0.00	0.00	3.51
547	579	6.815089	TCAACATCCAAGTTGCTAAAACAAT	58.185	32.000	0.00	0.00	46.44	2.71
606	638	8.887264	AAACCACATGTAATATGGACCTTTTA	57.113	30.769	0.00	0.00	36.94	1.52
624	657	5.452078	TTTTAGAGGGTGCAAACATGAAG	57.548	39.130	0.00	0.00	0.00	3.02
632	666	3.128242	GGTGCAAACATGAAGATCTCCAG	59.872	47.826	0.00	0.00	0.00	3.86
639	673	3.455177	ACATGAAGATCTCCAGCATCACT	59.545	43.478	0.00	0.00	0.00	3.41
640	674	3.538634	TGAAGATCTCCAGCATCACTG	57.461	47.619	0.00	0.00	46.77	3.66
660	694	4.202111	ACTGCTTCAAATTTACCACCACAC	60.202	41.667	0.00	0.00	0.00	3.82
668	702	7.484975	TCAAATTTACCACCACACAAACTAAG	58.515	34.615	0.00	0.00	0.00	2.18
710	744	3.562141	TCCACTTCCACAAAATACGTGTG	59.438	43.478	0.00	0.00	44.90	3.82
715	749	2.032302	TCCACAAAATACGTGTGCACAC	59.968	45.455	35.04	35.04	44.13	3.82
768	802	9.237846	CACCACATTATCTATATATACACTGCG	57.762	37.037	0.00	0.00	0.00	5.18
784	818	0.855995	TGCGAACACATGTGTACACG	59.144	50.000	30.75	30.53	44.13	4.49
861	895	7.608153	TCTCATCGATCTTAACCTGTAAACAA	58.392	34.615	0.00	0.00	0.00	2.83
876	910	6.274157	TGTAAACAACCACAACACAAGAAT	57.726	33.333	0.00	0.00	0.00	2.40
1058	1098	1.305887	CCCAGTACTCTTCCGGGGT	60.306	63.158	0.00	0.00	32.88	4.95
1815	7019	3.672447	TGCTCGGCGTACGGTCAA	61.672	61.111	18.39	0.00	44.45	3.18
1981	7188	2.690452	CCGGAGAGAAGAGGGGGA	59.310	66.667	0.00	0.00	0.00	4.81
1986	7193	0.261696	GAGAGAAGAGGGGGAGAGCT	59.738	60.000	0.00	0.00	0.00	4.09
2118	7349	0.614979	TCCGGTTCTCCTCCCTCTTG	60.615	60.000	0.00	0.00	0.00	3.02
2197	7440	8.964420	TTTTATTCCTGAATTTTGCGTAGAAG	57.036	30.769	0.00	0.00	32.50	2.85
2202	7446	4.434330	CCTGAATTTTGCGTAGAAGTCGTC	60.434	45.833	0.36	0.00	0.00	4.20
2464	7724	7.990541	TGTTTCAATGAAGATTTGTTCACTG	57.009	32.000	0.00	0.00	39.25	3.66
2512	7772	8.335532	AGTACATAAGCAAGCAATAAGAAACA	57.664	30.769	0.00	0.00	0.00	2.83
2556	7816	5.767665	CCATACATCCGTGGAAAATTATGGA	59.232	40.000	16.21	0.00	37.72	3.41
2570	7830	8.854117	GGAAAATTATGGACATTGAGAGCTTAT	58.146	33.333	0.00	0.00	0.00	1.73
2617	7877	2.161855	TGCAGGTCATGGATTGTGTTC	58.838	47.619	0.00	0.00	0.00	3.18
2640	7900	4.406069	CACTCACATGGCTAAATTTGTCG	58.594	43.478	0.00	0.00	0.00	4.35
2729	7989	4.992951	TGGATATGATTGAACATCTCGCTG	59.007	41.667	0.00	0.00	0.00	5.18
2749	8009	4.142945	GCTGACACTAGATGCTTCAACTTG	60.143	45.833	0.00	0.00	0.00	3.16
2763	8023	7.755591	TGCTTCAACTTGATCATTCTTACATC	58.244	34.615	0.00	0.00	0.00	3.06
2909	8169	9.936759	AGATCTTGCTAGCTTAATTTATAGTCC	57.063	33.333	17.23	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	8.770438	TTTTTAGTCATGCACTTTGTTCTTTT	57.230	26.923	0.00	0.00	36.43	2.27
110	112	7.919091	GGTCATAGTCACTCATTCGTAAATGTA	59.081	37.037	0.00	0.00	42.46	2.29
112	114	6.756542	TGGTCATAGTCACTCATTCGTAAATG	59.243	38.462	0.00	0.00	43.10	2.32
115	117	5.907866	TGGTCATAGTCACTCATTCGTAA	57.092	39.130	0.00	0.00	0.00	3.18
367	397	8.177119	AGTTGGTTTGCTTAAATTCTCATACA	57.823	30.769	0.00	0.00	0.00	2.29
421	451	8.418597	AAATTAGCTTGGAGATATGCATGAAT	57.581	30.769	10.16	0.00	0.00	2.57
439	471	5.193679	ACCCACAGGAATGAGTAAATTAGC	58.806	41.667	0.00	0.00	36.73	3.09
441	473	7.777910	CCATAACCCACAGGAATGAGTAAATTA	59.222	37.037	0.00	0.00	34.13	1.40
481	513	6.475402	TCAATGTACTTGATGCATGTAGTACG	59.525	38.462	26.77	19.06	43.60	3.67
606	638	2.957402	TCTTCATGTTTGCACCCTCT	57.043	45.000	0.00	0.00	0.00	3.69
624	657	2.211806	GAAGCAGTGATGCTGGAGATC	58.788	52.381	3.09	0.00	45.54	2.75
632	666	4.622740	GTGGTAAATTTGAAGCAGTGATGC	59.377	41.667	0.00	0.00	0.00	3.91
639	673	3.701542	TGTGTGGTGGTAAATTTGAAGCA	59.298	39.130	0.00	0.00	0.00	3.91
640	674	4.314740	TGTGTGGTGGTAAATTTGAAGC	57.685	40.909	0.00	0.00	0.00	3.86
641	675	6.337356	AGTTTGTGTGGTGGTAAATTTGAAG	58.663	36.000	0.00	0.00	0.00	3.02
650	684	4.998672	GCATACTTAGTTTGTGTGGTGGTA	59.001	41.667	4.87	0.00	0.00	3.25
660	694	1.064060	GCTGGCGGCATACTTAGTTTG	59.936	52.381	13.85	0.00	41.35	2.93
710	744	2.541588	GGATGGATGCATTTACGTGTGC	60.542	50.000	0.00	13.38	41.61	4.57
715	749	6.969366	TCTATTTTGGATGGATGCATTTACG	58.031	36.000	0.00	0.00	0.00	3.18
765	799	0.855995	CGTGTACACATGTGTTCGCA	59.144	50.000	33.83	26.89	41.83	5.10
768	802	0.515564	GGGCGTGTACACATGTGTTC	59.484	55.000	34.66	28.97	41.83	3.18
784	818	1.678970	GAGGTGGTTGATGTGGGGC	60.679	63.158	0.00	0.00	0.00	5.80
861	895	3.951037	TGCTGTTATTCTTGTGTTGTGGT	59.049	39.130	0.00	0.00	0.00	4.16
876	910	9.353431	ACATATGGAAATAATGATGTGCTGTTA	57.647	29.630	7.80	0.00	0.00	2.41
1034	1074	1.783071	GGAAGAGTACTGGGAGGAGG	58.217	60.000	0.00	0.00	0.00	4.30
1623	6827	4.289245	CCGGTGGTGGTCGTCGTT	62.289	66.667	0.00	0.00	0.00	3.85
1782	6986	0.317160	AGCACGAGAACACGATGGAA	59.683	50.000	0.00	0.00	37.03	3.53
2118	7349	3.191162	TCATGCATGTAACAACCAGAAGC	59.809	43.478	25.43	0.00	0.00	3.86
2197	7440	1.925185	GCAATCGGACTTAAGGACGAC	59.075	52.381	20.93	9.19	38.24	4.34
2202	7446	4.191544	TCATTCTGCAATCGGACTTAAGG	58.808	43.478	7.53	0.00	0.00	2.69
2369	7629	9.312904	TGATGTGTCAAGATGATAGGACATATA	57.687	33.333	0.00	0.00	40.60	0.86
2370	7630	8.198807	TGATGTGTCAAGATGATAGGACATAT	57.801	34.615	0.00	0.00	42.35	1.78
2371	7631	7.601705	TGATGTGTCAAGATGATAGGACATA	57.398	36.000	0.00	0.00	41.73	2.29
2372	7632	6.490241	TGATGTGTCAAGATGATAGGACAT	57.510	37.500	0.00	0.00	41.73	3.06
2373	7633	5.937975	TGATGTGTCAAGATGATAGGACA	57.062	39.130	0.00	0.00	37.89	4.02
2374	7634	8.893219	TTATTGATGTGTCAAGATGATAGGAC	57.107	34.615	0.00	0.00	46.75	3.85
2464	7724	4.139786	TGCTGAAGGATATCAATTGGAGC	58.860	43.478	5.42	8.68	0.00	4.70
2540	7800	5.356751	TCTCAATGTCCATAATTTTCCACGG	59.643	40.000	0.00	0.00	0.00	4.94
2556	7816	8.743085	ATTTGTCATGTATAAGCTCTCAATGT	57.257	30.769	0.00	0.00	0.00	2.71
2570	7830	8.871862	GCAAGCAATTCAATTATTTGTCATGTA	58.128	29.630	0.00	0.00	34.32	2.29
2617	7877	4.672542	CGACAAATTTAGCCATGTGAGTGG	60.673	45.833	0.00	0.00	42.35	4.00
2729	7989	5.871524	TGATCAAGTTGAAGCATCTAGTGTC	59.128	40.000	10.14	0.00	0.00	3.67
2763	8023	8.765219	CACTCCTTTTCGGTATATGAAATACTG	58.235	37.037	4.54	0.00	35.43	2.74
2930	8190	8.677148	AAGTGCCGTAGATTGATGTAATATTT	57.323	30.769	0.00	0.00	0.00	1.40
2949	8209	6.529477	GCTTCTGATCATTTTAAAGAAGTGCC	59.471	38.462	15.81	1.82	43.68	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.