AutoCloner

Multiple sequence alignment - TraesCS4D01G071800

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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	TraesCS4D01G071800	chr4D	100.000	3073	0	0	1	3073	46629318	46626246	0.000000e+00	5675.0
1	TraesCS4D01G071800	chr4D	94.222	2146	63	29	969	3071	47330153	47332280	0.000000e+00	3219.0
2	TraesCS4D01G071800	chr4D	92.423	937	46	11	984	1897	47322171	47323105	0.000000e+00	1314.0
3	TraesCS4D01G071800	chr4D	86.181	398	30	15	2694	3073	47324271	47324661	1.030000e-109	407.0
4	TraesCS4D01G071800	chr4D	83.953	430	28	19	2301	2693	47323804	47324229	1.040000e-99	374.0
5	TraesCS4D01G071800	chr4D	88.462	234	18	3	1897	2130	47323075	47323299	1.090000e-69	274.0
6	TraesCS4D01G071800	chr4D	95.000	80	4	0	2108	2187	47323728	47323807	3.220000e-25	126.0
7	TraesCS4D01G071800	chr4A	95.791	1188	35	5	1897	3073	552251090	552252273	0.000000e+00	1903.0
8	TraesCS4D01G071800	chr4A	89.669	1210	75	24	1897	3071	551137479	551136285	0.000000e+00	1496.0
9	TraesCS4D01G071800	chr4A	93.455	932	36	10	979	1897	551138368	551137449	0.000000e+00	1360.0
10	TraesCS4D01G071800	chr4A	89.263	773	45	15	1897	2633	533466277	533465507	0.000000e+00	933.0
11	TraesCS4D01G071800	chr4A	93.038	632	40	3	2	629	533474070	533473439	0.000000e+00	920.0
12	TraesCS4D01G071800	chr4A	90.644	652	40	9	1249	1889	533466896	533466255	0.000000e+00	846.0
13	TraesCS4D01G071800	chr4A	88.756	667	42	15	1241	1893	552250469	552251116	0.000000e+00	785.0
14	TraesCS4D01G071800	chr4A	88.629	598	27	16	689	1253	533473295	533472706	0.000000e+00	689.0
15	TraesCS4D01G071800	chr4A	93.750	384	23	1	244	626	552247236	552247619	2.660000e-160	575.0
16	TraesCS4D01G071800	chr4A	83.373	421	30	21	2301	2693	533464981	533464573	1.360000e-93	353.0
17	TraesCS4D01G071800	chr4A	87.973	291	25	3	1897	2187	533465258	533464978	4.910000e-88	335.0
18	TraesCS4D01G071800	chr4A	97.110	173	2	3	694	864	552247766	552247937	3.880000e-74	289.0
19	TraesCS4D01G071800	chr4A	92.593	54	4	0	888	941	552247931	552247984	9.140000e-11	78.7
20	TraesCS4D01G071800	chr4B	85.591	1742	121	52	967	2657	68954861	68956523	0.000000e+00	1707.0
21	TraesCS4D01G071800	chr4B	88.843	1210	88	25	1897	3073	68721443	68722638	0.000000e+00	1443.0
22	TraesCS4D01G071800	chr4B	86.858	1324	95	33	1060	2368	68125131	68123872	0.000000e+00	1408.0
23	TraesCS4D01G071800	chr4B	89.675	862	57	16	967	1813	68720580	68721424	0.000000e+00	1070.0
24	TraesCS4D01G071800	chr4B	88.601	386	27	13	2694	3073	68956615	68956989	1.300000e-123	453.0
25	TraesCS4D01G071800	chr4B	93.487	261	10	1	1345	1605	68718803	68719056	6.220000e-102	381.0
26	TraesCS4D01G071800	chr4B	91.034	290	13	8	1061	1350	68701182	68701458	2.240000e-101	379.0
27	TraesCS4D01G071800	chr4B	85.714	357	16	15	2368	2693	68123765	68123413	8.160000e-91	344.0
28	TraesCS4D01G071800	chr4B	86.688	308	19	14	2694	2984	68123371	68123069	3.820000e-84	322.0
29	TraesCS4D01G071800	chr4B	88.971	272	12	6	689	958	68125386	68125131	1.370000e-83	320.0
30	TraesCS4D01G071800	chr4B	92.118	203	15	1	423	625	68125739	68125538	5.020000e-73	285.0
31	TraesCS4D01G071800	chr4B	92.481	133	9	1	296	428	68131016	68130885	4.050000e-44	189.0

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	TraesCS4D01G071800	chr4D	46626246	46629318	3072	True	5675.000000	5675	100.000000	1	3073	1	chr4D.!!$R1	3072
1	TraesCS4D01G071800	chr4D	47330153	47332280	2127	False	3219.000000	3219	94.222000	969	3071	1	chr4D.!!$F1	2102
2	TraesCS4D01G071800	chr4D	47322171	47324661	2490	False	499.000000	1314	89.203800	984	3073	5	chr4D.!!$F2	2089
3	TraesCS4D01G071800	chr4A	551136285	551138368	2083	True	1428.000000	1496	91.562000	979	3071	2	chr4A.!!$R3	2092
4	TraesCS4D01G071800	chr4A	533472706	533474070	1364	True	804.500000	920	90.833500	2	1253	2	chr4A.!!$R2	1251
5	TraesCS4D01G071800	chr4A	552247236	552252273	5037	False	726.140000	1903	93.600000	244	3073	5	chr4A.!!$F1	2829
6	TraesCS4D01G071800	chr4A	533464573	533466896	2323	True	616.750000	933	87.813250	1249	2693	4	chr4A.!!$R1	1444
7	TraesCS4D01G071800	chr4B	68954861	68956989	2128	False	1080.000000	1707	87.096000	967	3073	2	chr4B.!!$F3	2106
8	TraesCS4D01G071800	chr4B	68718803	68722638	3835	False	964.666667	1443	90.668333	967	3073	3	chr4B.!!$F2	2106
9	TraesCS4D01G071800	chr4B	68123069	68125739	2670	True	535.800000	1408	88.069800	423	2984	5	chr4B.!!$R2	2561

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
187	191	0.107654	AAGACCGCAATAGCCACTCC	60.108	55.0	0.0	0.0	37.52	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2483	6162	0.321653	CCCACCAAGCCTGTCACTAC	60.322	60.0	0.0	0.0	0.0	2.73	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
28	29	7.065324	GTGGATAAACAAATGGACGTAGAATGA	59.935	37.037	0.00	0.00	0.00	2.57
73	75	6.532988	AACATACTAGTCTTCTCCTTCCAC	57.467	41.667	0.00	0.00	0.00	4.02
78	80	1.827969	AGTCTTCTCCTTCCACCGATG	59.172	52.381	0.00	0.00	0.00	3.84
135	139	2.622942	TCCAACTGCAAAGAAAAGCGAT	59.377	40.909	0.00	0.00	0.00	4.58
150	154	2.511600	GATACCTGCAAGCGCCGT	60.512	61.111	2.29	0.00	37.32	5.68
187	191	0.107654	AAGACCGCAATAGCCACTCC	60.108	55.000	0.00	0.00	37.52	3.85
306	311	0.108585	GGAGAACAGGTCAAGCCACA	59.891	55.000	0.00	0.00	40.61	4.17
349	354	1.947456	GAACTCACCTCACCAACAACC	59.053	52.381	0.00	0.00	0.00	3.77
354	359	0.750182	ACCTCACCAACAACCAACCG	60.750	55.000	0.00	0.00	0.00	4.44
477	482	0.392193	TCGTCGAGGTAGGGAGTGAC	60.392	60.000	4.85	0.00	0.00	3.67
495	500	1.276989	GACCGAATAGACCCCAACACA	59.723	52.381	0.00	0.00	0.00	3.72
525	530	1.605451	ACCCACCTCGTCGATGTCA	60.605	57.895	4.21	0.00	0.00	3.58
626	631	1.000612	GGAAGAGGAGGAGGACCGT	59.999	63.158	0.00	0.00	41.83	4.83
661	696	1.444836	TTTTTACCAGGATGTCGCCG	58.555	50.000	0.00	0.00	0.00	6.46
667	702	2.768344	AGGATGTCGCCGGGGAAT	60.768	61.111	24.36	17.77	0.00	3.01
668	703	1.458777	AGGATGTCGCCGGGGAATA	60.459	57.895	24.36	15.64	0.00	1.75
669	704	1.301479	GGATGTCGCCGGGGAATAC	60.301	63.158	24.36	15.19	0.00	1.89
670	705	1.444250	GATGTCGCCGGGGAATACA	59.556	57.895	24.36	17.92	0.00	2.29
672	707	1.274167	GATGTCGCCGGGGAATACATA	59.726	52.381	24.36	6.08	31.19	2.29
674	709	1.274167	TGTCGCCGGGGAATACATATC	59.726	52.381	24.36	8.65	0.00	1.63
676	711	0.902531	CGCCGGGGAATACATATCCT	59.097	55.000	14.46	0.00	37.14	3.24
677	712	1.278127	CGCCGGGGAATACATATCCTT	59.722	52.381	14.46	0.00	37.14	3.36
679	714	3.763057	GCCGGGGAATACATATCCTTTT	58.237	45.455	2.18	0.00	37.14	2.27
681	716	4.698780	GCCGGGGAATACATATCCTTTTAC	59.301	45.833	2.18	0.00	37.14	2.01
685	720	6.946009	CGGGGAATACATATCCTTTTACCATT	59.054	38.462	0.00	0.00	37.14	3.16
687	722	8.803235	GGGGAATACATATCCTTTTACCATTTC	58.197	37.037	0.00	0.00	37.14	2.17
847	943	8.928844	AGTTTTCACGTACATTTCTAAAATCG	57.071	30.769	0.00	0.00	0.00	3.34
946	1042	6.293955	GCACTTACCAATTTCTTACTTGCTCA	60.294	38.462	0.00	0.00	0.00	4.26
947	1043	7.648142	CACTTACCAATTTCTTACTTGCTCAA	58.352	34.615	0.00	0.00	0.00	3.02
948	1044	8.134895	CACTTACCAATTTCTTACTTGCTCAAA	58.865	33.333	0.00	0.00	0.00	2.69
2483	6162	7.541162	TCTGATGGTTGCAATTAAGATTTCTG	58.459	34.615	0.59	0.00	0.00	3.02
2503	6182	0.766674	TAGTGACAGGCTTGGTGGGT	60.767	55.000	0.00	0.00	0.00	4.51
2509	6188	3.074687	TGACAGGCTTGGTGGGTTTTATA	59.925	43.478	0.00	0.00	0.00	0.98
2678	7288	1.267806	GATGCTGTGTGTTGACAAGGG	59.732	52.381	0.00	0.00	32.49	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	4.957327	GGTGGAAGGAGAAGACTAGTATGT	59.043	45.833	0.00	0.00	0.00	2.29
52	53	4.036971	CGGTGGAAGGAGAAGACTAGTATG	59.963	50.000	0.00	0.00	0.00	2.39
73	75	1.157870	GGCGGTCAATGTACCATCGG	61.158	60.000	0.00	0.00	39.71	4.18
78	80	2.104253	CACCGGCGGTCAATGTACC	61.104	63.158	31.82	0.00	31.02	3.34
150	154	3.994392	GTCTTCAAAGCTTGGTATGACGA	59.006	43.478	0.00	0.00	0.00	4.20
187	191	8.001292	AGATTTATAATTCTTGTCTCAAGGGGG	58.999	37.037	9.18	0.00	0.00	5.40
216	220	0.450983	GCTCCAGCTGATGTTGCTTC	59.549	55.000	17.39	0.00	38.92	3.86
306	311	7.156876	TCAACATCTTCTTCTTTGTTGTTGT	57.843	32.000	12.68	0.00	45.65	3.32
349	354	1.000506	TCGAGGAGAGGTTTTCGGTTG	59.999	52.381	0.00	0.00	34.08	3.77
354	359	3.741856	GTGTCTTTCGAGGAGAGGTTTTC	59.258	47.826	1.27	0.00	0.00	2.29
477	482	1.677820	GGTGTGTTGGGGTCTATTCGG	60.678	57.143	0.00	0.00	0.00	4.30
495	500	2.747686	GTGGGTGGTGACGATGGT	59.252	61.111	0.00	0.00	0.00	3.55
525	530	3.117284	TCTTAGGTTTTTGCTTCCCTGGT	60.117	43.478	0.00	0.00	0.00	4.00
652	687	0.034896	ATGTATTCCCCGGCGACATC	59.965	55.000	9.30	0.00	0.00	3.06
655	690	1.405121	GGATATGTATTCCCCGGCGAC	60.405	57.143	9.30	0.00	0.00	5.19
656	691	0.899720	GGATATGTATTCCCCGGCGA	59.100	55.000	9.30	0.00	0.00	5.54
657	692	0.902531	AGGATATGTATTCCCCGGCG	59.097	55.000	0.00	0.00	0.00	6.46
659	694	5.221966	TGGTAAAAGGATATGTATTCCCCGG	60.222	44.000	0.00	0.00	0.00	5.73
660	695	5.871834	TGGTAAAAGGATATGTATTCCCCG	58.128	41.667	0.00	0.00	0.00	5.73
661	696	8.721133	AAATGGTAAAAGGATATGTATTCCCC	57.279	34.615	0.00	0.00	0.00	4.81
716	810	2.629051	GGGCCTACACTGTCACATAAC	58.371	52.381	0.84	0.00	0.00	1.89
876	972	6.704493	AGCATCTTCGTAAGTGAAAACTTGTA	59.296	34.615	1.42	0.00	39.48	2.41
965	1061	8.295288	AGTCGAATACATATCCTTTTACCGTAG	58.705	37.037	0.00	0.00	0.00	3.51
966	1062	8.169977	AGTCGAATACATATCCTTTTACCGTA	57.830	34.615	0.00	0.00	0.00	4.02
969	1065	8.658499	ACAAGTCGAATACATATCCTTTTACC	57.342	34.615	0.00	0.00	0.00	2.85
973	1069	7.472543	GCAAACAAGTCGAATACATATCCTTT	58.527	34.615	0.00	0.00	0.00	3.11
974	1070	6.238103	CGCAAACAAGTCGAATACATATCCTT	60.238	38.462	0.00	0.00	0.00	3.36
975	1071	5.234329	CGCAAACAAGTCGAATACATATCCT	59.766	40.000	0.00	0.00	0.00	3.24
976	1072	5.432157	CGCAAACAAGTCGAATACATATCC	58.568	41.667	0.00	0.00	0.00	2.59
977	1073	5.006358	ACCGCAAACAAGTCGAATACATATC	59.994	40.000	0.00	0.00	0.00	1.63
981	1793	2.485903	ACCGCAAACAAGTCGAATACA	58.514	42.857	0.00	0.00	0.00	2.29
997	1809	4.320690	TCGAATACGCGTATTTTATACCGC	59.679	41.667	36.92	23.38	42.53	5.68
2483	6162	0.321653	CCCACCAAGCCTGTCACTAC	60.322	60.000	0.00	0.00	0.00	2.73
2509	6188	9.768662	AGCAATCAGTTAAAAATTGATCACTTT	57.231	25.926	5.28	5.28	36.92	2.66
2710	7364	8.462016	GCTTAGACAACATGGATTGACTAAAAT	58.538	33.333	16.04	0.00	42.28	1.82
2916	7602	7.309920	TCCGATTTTGTTAGTGAAAATTAGGC	58.690	34.615	0.00	0.00	34.00	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.