AutoCloner

Multiple sequence alignment - TraesCS3D01G123500

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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	TraesCS3D01G123500	chr3D	100.000	4020	0	0	698	4717	81363762	81367781	0.000000e+00	7424.0
1	TraesCS3D01G123500	chr3D	100.000	464	0	0	1	464	81363065	81363528	0.000000e+00	857.0
2	TraesCS3D01G123500	chr3B	94.467	4012	143	28	713	4683	127289562	127293535	0.000000e+00	6106.0
3	TraesCS3D01G123500	chr3B	94.624	465	15	6	1	464	127288879	127289334	0.000000e+00	712.0
4	TraesCS3D01G123500	chr3B	94.624	93	2	1	4140	4229	44750959	44751051	1.770000e-29	141.0
5	TraesCS3D01G123500	chr3B	95.455	88	2	2	4129	4216	765013528	765013443	6.360000e-29	139.0
6	TraesCS3D01G123500	chr3B	89.423	104	10	1	2999	3102	452550763	452550865	3.830000e-26	130.0
7	TraesCS3D01G123500	chr3A	94.089	4060	164	35	698	4717	95527254	95531277	0.000000e+00	6098.0
8	TraesCS3D01G123500	chr3A	94.681	470	18	4	1	464	95526768	95527236	0.000000e+00	723.0
9	TraesCS3D01G123500	chr3A	95.000	60	2	1	4219	4277	95530712	95530771	5.030000e-15	93.5
10	TraesCS3D01G123500	chr3A	97.826	46	1	0	4232	4277	95530654	95530699	3.910000e-11	80.5
11	TraesCS3D01G123500	chr1D	82.322	939	158	5	1165	2096	115578017	115577080	0.000000e+00	808.0
12	TraesCS3D01G123500	chr1D	90.090	111	5	5	4124	4229	447863704	447863813	6.360000e-29	139.0
13	TraesCS3D01G123500	chr1A	81.896	939	162	5	1165	2096	126858358	126857421	0.000000e+00	785.0
14	TraesCS3D01G123500	chr5D	94.792	96	5	0	3015	3110	278275197	278275102	2.940000e-32	150.0
15	TraesCS3D01G123500	chr1B	95.556	90	2	2	4130	4219	661504151	661504238	4.920000e-30	143.0
16	TraesCS3D01G123500	chr7D	92.784	97	6	1	3005	3100	289566341	289566437	6.360000e-29	139.0
17	TraesCS3D01G123500	chr7A	92.857	98	4	2	4130	4224	719589476	719589379	6.360000e-29	139.0
18	TraesCS3D01G123500	chr6B	92.632	95	6	1	3013	3107	216509755	216509848	8.230000e-28	135.0
19	TraesCS3D01G123500	chr6B	91.089	101	6	3	4120	4219	171735003	171735101	2.960000e-27	134.0
20	TraesCS3D01G123500	chr4B	90.385	104	9	1	2999	3102	24837398	24837296	8.230000e-28	135.0
21	TraesCS3D01G123500	chr2D	94.318	88	5	0	3016	3103	53145727	53145814	8.230000e-28	135.0
22	TraesCS3D01G123500	chr2D	88.288	111	10	3	3005	3115	574413520	574413627	3.830000e-26	130.0
23	TraesCS3D01G123500	chr5A	91.837	98	4	3	4136	4230	331942339	331942243	2.960000e-27	134.0
24	TraesCS3D01G123500	chr7B	91.000	100	6	3	3014	3112	398380287	398380190	1.070000e-26	132.0
25	TraesCS3D01G123500	chr7B	89.189	111	5	6	4124	4229	483787839	483787731	1.070000e-26	132.0

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	TraesCS3D01G123500	chr3D	81363065	81367781	4716	False	4140.50	7424	100.0000	1	4717	2	chr3D.!!$F1	4716
1	TraesCS3D01G123500	chr3B	127288879	127293535	4656	False	3409.00	6106	94.5455	1	4683	2	chr3B.!!$F3	4682
2	TraesCS3D01G123500	chr3A	95526768	95531277	4509	False	1748.75	6098	95.3990	1	4717	4	chr3A.!!$F1	4716
3	TraesCS3D01G123500	chr1D	115577080	115578017	937	True	808.00	808	82.3220	1165	2096	1	chr1D.!!$R1	931
4	TraesCS3D01G123500	chr1A	126857421	126858358	937	True	785.00	785	81.8960	1165	2096	1	chr1A.!!$R1	931

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
736	942	0.318275	TTTTTGGCGGTGCGTTCATC	60.318	50.0	0.0	0.0	0.00	2.92	F
2431	2646	1.102154	CCGATGCACCTTTTATGCCA	58.898	50.0	0.0	0.0	42.69	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2518	2739	1.688197	ACCAATTGCACCAGAACCAAG	59.312	47.619	0.00	0.0	0.00	3.61	R
4332	4660	0.032540	CAACAGCTGCCAAAAGGGAC	59.967	55.000	15.27	0.0	40.01	4.46	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
121	124	2.094494	TCATCGTCTCTGCAAGGAGAAC	60.094	50.000	7.20	2.48	42.95	3.01
124	127	2.300152	TCGTCTCTGCAAGGAGAACAAT	59.700	45.455	7.20	0.00	42.95	2.71
134	137	4.156739	GCAAGGAGAACAATTTACCAGGAG	59.843	45.833	0.00	0.00	0.00	3.69
135	138	4.576330	AGGAGAACAATTTACCAGGAGG	57.424	45.455	0.00	0.00	42.21	4.30
136	139	4.175962	AGGAGAACAATTTACCAGGAGGA	58.824	43.478	0.00	0.00	38.69	3.71
148	154	0.977395	CAGGAGGAGGAAAGAACCGT	59.023	55.000	0.00	0.00	34.73	4.83
196	202	2.359107	CCCCATGATCGGATGGCG	60.359	66.667	6.56	0.00	41.59	5.69
736	942	0.318275	TTTTTGGCGGTGCGTTCATC	60.318	50.000	0.00	0.00	0.00	2.92
888	1097	4.616181	GCAAGGTGCGTCTTTTACATAT	57.384	40.909	0.00	0.00	31.71	1.78
908	1117	7.576236	ACATATAATTTCTGCGAGGAATTTCG	58.424	34.615	7.45	0.00	43.23	3.46
1056	1265	1.304282	GCTGAAATCTGGCCCTGGA	59.696	57.895	0.00	0.00	0.00	3.86
1290	1502	2.930562	AGGAAGCGGCAGGTCCTT	60.931	61.111	12.51	0.00	0.00	3.36
1689	1904	2.253452	CGCAAGGCTGTGAGCAAC	59.747	61.111	0.00	0.00	44.75	4.17
1830	2045	1.867233	CTATGGAAAGCGTTGATCCCG	59.133	52.381	0.00	0.00	32.01	5.14
2280	2495	6.356556	TGGTAGGAAGTTATCATCACCATTG	58.643	40.000	0.00	0.00	30.11	2.82
2337	2552	8.568794	GGTCCATTCTATTGCTTATTTTAGGTC	58.431	37.037	0.00	0.00	0.00	3.85
2414	2629	1.808411	AGTGTTACTTGCATGGTCCG	58.192	50.000	4.44	0.00	0.00	4.79
2431	2646	1.102154	CCGATGCACCTTTTATGCCA	58.898	50.000	0.00	0.00	42.69	4.92
2432	2647	1.682854	CCGATGCACCTTTTATGCCAT	59.317	47.619	0.00	0.00	42.69	4.40
2433	2648	2.884012	CCGATGCACCTTTTATGCCATA	59.116	45.455	0.00	0.00	42.69	2.74
2434	2649	3.058016	CCGATGCACCTTTTATGCCATAG	60.058	47.826	0.00	0.00	42.69	2.23
2435	2650	3.565482	CGATGCACCTTTTATGCCATAGT	59.435	43.478	0.00	0.00	42.69	2.12
2436	2651	4.319766	CGATGCACCTTTTATGCCATAGTC	60.320	45.833	0.00	0.00	42.69	2.59
2512	2732	1.947456	GGACCAAACACCTCAGTTGTC	59.053	52.381	0.00	0.00	0.00	3.18
2518	2739	0.249911	ACACCTCAGTTGTCGCCTTC	60.250	55.000	0.00	0.00	0.00	3.46
2649	2870	4.422073	TCTTATATCTGGGTGGTTGCAG	57.578	45.455	0.00	0.00	0.00	4.41
2799	3020	6.650807	GGTCATGTCATGGTACGAATTATGAT	59.349	38.462	12.90	0.00	32.76	2.45
3011	3249	6.595326	TCAGTGATTGGCATTGACTACTAAAG	59.405	38.462	1.26	0.00	38.19	1.85
3071	3309	4.067972	ACACCACACTAGTGTCGAAAAT	57.932	40.909	25.63	6.85	45.13	1.82
3072	3310	3.807622	ACACCACACTAGTGTCGAAAATG	59.192	43.478	25.63	15.03	45.13	2.32
3075	3313	3.498397	CCACACTAGTGTCGAAAATGCTT	59.502	43.478	25.63	0.00	44.39	3.91
3167	3406	7.931015	TTATGTATACTGTCTTCTCCCCATT	57.069	36.000	4.17	0.00	0.00	3.16
3181	3420	7.840716	TCTTCTCCCCATTGATTTTCATGTTAT	59.159	33.333	0.00	0.00	0.00	1.89
3313	3555	9.620259	TTTGGCCAAGTTATTTGTTAAGATTTT	57.380	25.926	19.48	0.00	34.87	1.82
3314	3556	9.620259	TTGGCCAAGTTATTTGTTAAGATTTTT	57.380	25.926	16.05	0.00	34.87	1.94
3437	3679	3.566322	CCCAAAACCGTCAAGTGATTGTA	59.434	43.478	0.00	0.00	0.00	2.41
3555	3797	1.107114	GGACGAGAGATTGCTCCTGA	58.893	55.000	0.00	0.00	42.30	3.86
3737	3988	1.068748	CACGGGTCCGAATATACTCCG	60.069	57.143	16.90	0.00	42.83	4.63
4103	4354	3.764434	TGCCAGGTTCACTTGTTTGTTTA	59.236	39.130	0.00	0.00	0.00	2.01
4143	4394	6.980978	TCTCTAACAGCATATGCAAGTTACTC	59.019	38.462	27.74	3.23	45.16	2.59
4144	4395	6.049149	TCTAACAGCATATGCAAGTTACTCC	58.951	40.000	27.74	2.62	45.16	3.85
4145	4396	3.545703	ACAGCATATGCAAGTTACTCCC	58.454	45.455	28.62	0.00	45.16	4.30
4157	4408	5.567423	GCAAGTTACTCCCTCCGTAAACTAA	60.567	44.000	0.00	0.00	0.00	2.24
4166	4417	7.039853	ACTCCCTCCGTAAACTAATATAAGAGC	60.040	40.741	0.00	0.00	0.00	4.09
4294	4622	3.201290	CCATGAGCAATGTGGAGTAGAC	58.799	50.000	0.00	0.00	34.94	2.59
4313	4641	1.348036	ACGGAGGAAGAAAACAGGAGG	59.652	52.381	0.00	0.00	0.00	4.30
4332	4660	3.552875	AGGTGCTGGAATCTCATGAATG	58.447	45.455	0.00	0.00	0.00	2.67
4629	4960	2.770164	GCCTGAGCTTGAGTTTCCTA	57.230	50.000	0.00	0.00	35.50	2.94
4647	4979	5.099042	TCCTATTGTTTGGAGGCTACTTC	57.901	43.478	0.00	0.00	0.00	3.01
4675	5007	3.893753	AGCTGAGCTCCCTATAAGAGA	57.106	47.619	12.15	0.00	30.62	3.10
4683	5015	3.258123	GCTCCCTATAAGAGAAGCCTCAG	59.742	52.174	4.06	0.00	41.87	3.35
4684	5016	3.235200	TCCCTATAAGAGAAGCCTCAGC	58.765	50.000	0.00	0.00	41.87	4.26
4702	5034	3.365265	CCTCAAGGCGCCAACCAC	61.365	66.667	31.54	0.00	0.00	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
121	124	5.179452	TCTTTCCTCCTCCTGGTAAATTG	57.821	43.478	0.00	0.00	34.23	2.32
124	127	3.329814	GGTTCTTTCCTCCTCCTGGTAAA	59.670	47.826	0.00	0.00	34.23	2.01
134	137	1.269936	TGTCGAACGGTTCTTTCCTCC	60.270	52.381	17.94	0.28	0.00	4.30
135	138	2.144482	TGTCGAACGGTTCTTTCCTC	57.856	50.000	17.94	3.87	0.00	3.71
136	139	2.607631	TTGTCGAACGGTTCTTTCCT	57.392	45.000	17.94	0.00	0.00	3.36
148	154	1.573829	GCAGCCGTTGGATTGTCGAA	61.574	55.000	0.00	0.00	0.00	3.71
192	198	2.032634	GTTCGGTTCATCTGCGCCA	61.033	57.895	4.18	0.00	0.00	5.69
196	202	1.359459	GGACGGTTCGGTTCATCTGC	61.359	60.000	0.00	0.00	0.00	4.26
310	320	4.115199	GGGCGCAGAAGTGGGGAT	62.115	66.667	10.83	0.00	37.11	3.85
736	942	1.076332	GACGGATCAAGAACCAACGG	58.924	55.000	0.00	0.00	0.00	4.44
1290	1502	0.253894	TGGAGTCGACGAGGGACATA	59.746	55.000	10.46	0.00	36.87	2.29
1536	1751	3.323979	ACGAACTGTCCACATACTTCCTT	59.676	43.478	0.00	0.00	0.00	3.36
2280	2495	5.909610	CAGCTTTGCAACTACTCTACAAAAC	59.090	40.000	0.00	0.00	30.51	2.43
2337	2552	6.367422	AGAACAAGCAGATTCTTCGACTAAAG	59.633	38.462	0.00	0.00	30.88	1.85
2414	2629	4.580167	TGACTATGGCATAAAAGGTGCATC	59.420	41.667	8.79	0.00	44.25	3.91
2466	2686	5.241728	ACTTTAGCCAACAAGGAATGAGTTC	59.758	40.000	0.00	0.00	41.22	3.01
2512	2732	1.856265	GCACCAGAACCAAGAAGGCG	61.856	60.000	0.00	0.00	43.14	5.52
2518	2739	1.688197	ACCAATTGCACCAGAACCAAG	59.312	47.619	0.00	0.00	0.00	3.61
2649	2870	5.299279	TGAGGATTTCACCTTTTTGTGACTC	59.701	40.000	0.00	0.00	44.55	3.36
2799	3020	4.590647	TCTGATTTATTTGGGTGGTTGCAA	59.409	37.500	0.00	0.00	0.00	4.08
2940	3178	7.780271	TGAGCTATCAAAGGATGTTCTCTACTA	59.220	37.037	0.00	0.00	34.89	1.82
3011	3249	2.822707	TGGGACAGAGGGAGTAGTAC	57.177	55.000	0.00	0.00	0.00	2.73
3053	3291	4.024048	AAAGCATTTTCGACACTAGTGTGG	60.024	41.667	32.51	29.41	41.53	4.17
3071	3309	5.514136	CCCTCCGTCCCATAATATAAAAGCA	60.514	44.000	0.00	0.00	0.00	3.91
3072	3310	4.941873	CCCTCCGTCCCATAATATAAAAGC	59.058	45.833	0.00	0.00	0.00	3.51
3075	3313	5.408824	ACTCCCTCCGTCCCATAATATAAA	58.591	41.667	0.00	0.00	0.00	1.40
3083	3322	1.145325	CTAGTACTCCCTCCGTCCCAT	59.855	57.143	0.00	0.00	0.00	4.00
3266	3508	0.320247	ACTGCAAGAGAAGACCTGCG	60.320	55.000	0.00	0.00	37.43	5.18
3437	3679	2.365617	CAGAGCTGGGTATACGATTGGT	59.634	50.000	0.00	0.00	0.00	3.67
3610	3852	0.467384	CTCCCATGTGAGCCTTCGAT	59.533	55.000	0.00	0.00	0.00	3.59
3737	3988	3.529835	AAGCAAGGGAAGGTGGGGC	62.530	63.158	0.00	0.00	0.00	5.80
4083	4334	6.142818	TCATAAACAAACAAGTGAACCTGG	57.857	37.500	0.00	0.00	0.00	4.45
4103	4354	5.809001	TGTTAGAGAAGGCATCTTGTTCAT	58.191	37.500	0.00	0.00	38.96	2.57
4143	4394	6.091437	CGCTCTTATATTAGTTTACGGAGGG	58.909	44.000	0.00	0.00	0.00	4.30
4144	4395	6.675987	ACGCTCTTATATTAGTTTACGGAGG	58.324	40.000	0.00	0.00	0.00	4.30
4145	4396	8.571461	AAACGCTCTTATATTAGTTTACGGAG	57.429	34.615	0.00	0.00	31.14	4.63
4210	4461	9.886132	GAATCTCAATAAAAGGTACTCCTGTAA	57.114	33.333	0.00	0.00	44.35	2.41
4211	4462	9.042450	TGAATCTCAATAAAAGGTACTCCTGTA	57.958	33.333	0.00	0.00	44.35	2.74
4212	4463	7.824779	GTGAATCTCAATAAAAGGTACTCCTGT	59.175	37.037	0.00	0.00	44.35	4.00
4213	4464	8.043710	AGTGAATCTCAATAAAAGGTACTCCTG	58.956	37.037	0.00	0.00	44.35	3.86
4294	4622	1.348036	ACCTCCTGTTTTCTTCCTCCG	59.652	52.381	0.00	0.00	0.00	4.63
4313	4641	3.314635	GGACATTCATGAGATTCCAGCAC	59.685	47.826	11.74	0.00	0.00	4.40
4332	4660	0.032540	CAACAGCTGCCAAAAGGGAC	59.967	55.000	15.27	0.00	40.01	4.46
4626	4957	4.843728	TGAAGTAGCCTCCAAACAATAGG	58.156	43.478	0.00	0.00	0.00	2.57
4675	5007	3.085223	CCTTGAGGGCTGAGGCTT	58.915	61.111	5.84	0.00	38.73	4.35
4684	5016	4.659172	TGGTTGGCGCCTTGAGGG	62.659	66.667	29.70	0.00	35.18	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.