AutoCloner

Multiple sequence alignment - TraesCS3B01G435300

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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	TraesCS3B01G435300	chr3B	100.000	2549	0	0	1	2549	673607972	673605424	0.000000e+00	4708
1	TraesCS3B01G435300	chr3B	94.810	2004	79	5	552	2549	46395682	46393698	0.000000e+00	3101
2	TraesCS3B01G435300	chr3B	94.364	2005	89	7	552	2549	108092314	108090327	0.000000e+00	3055
3	TraesCS3B01G435300	chr3B	93.098	2014	96	15	543	2549	330378552	330380529	0.000000e+00	2909
4	TraesCS3B01G435300	chr3B	93.716	557	30	4	1	553	437718487	437719042	0.000000e+00	830
5	TraesCS3B01G435300	chr3B	90.026	391	24	2	552	942	13424069	13424444	2.280000e-135	492
6	TraesCS3B01G435300	chr4A	95.055	2002	74	8	554	2549	705529252	705527270	0.000000e+00	3125
7	TraesCS3B01G435300	chr1B	94.786	2014	82	13	543	2549	581717571	581715574	0.000000e+00	3116
8	TraesCS3B01G435300	chr1B	94.750	2000	82	9	554	2549	520844119	520842139	0.000000e+00	3090
9	TraesCS3B01G435300	chr1B	94.389	2014	84	9	544	2549	671392199	671394191	0.000000e+00	3066
10	TraesCS3B01G435300	chr1B	93.383	2010	98	14	547	2549	663786487	663788468	0.000000e+00	2942
11	TraesCS3B01G435300	chr1B	93.682	554	34	1	1	553	307930863	307930310	0.000000e+00	828
12	TraesCS3B01G435300	chr1B	93.671	553	33	2	1	552	357102784	357103335	0.000000e+00	826
13	TraesCS3B01G435300	chr7B	94.661	2004	82	8	553	2549	720989191	720987206	0.000000e+00	3085
14	TraesCS3B01G435300	chr7B	94.795	1979	77	8	578	2549	708943230	708941271	0.000000e+00	3061
15	TraesCS3B01G435300	chr7B	94.139	546	31	1	9	553	422943337	422942792	0.000000e+00	830
16	TraesCS3B01G435300	chr7B	93.190	558	36	2	1	557	290176882	290176326	0.000000e+00	819
17	TraesCS3B01G435300	chr2B	94.511	2004	85	11	552	2549	692955895	692957879	0.000000e+00	3068
18	TraesCS3B01G435300	chr2B	93.863	554	33	1	1	553	234482532	234481979	0.000000e+00	833
19	TraesCS3B01G435300	chr2B	93.321	554	36	1	1	553	384682245	384681692	0.000000e+00	817
20	TraesCS3B01G435300	chr4B	94.173	2008	83	17	553	2549	372353118	372351134	0.000000e+00	3029
21	TraesCS3B01G435300	chr5B	93.744	2014	90	14	543	2549	269389463	269391447	0.000000e+00	2988
22	TraesCS3B01G435300	chr5B	93.028	2008	89	9	549	2549	129114113	129116076	0.000000e+00	2885
23	TraesCS3B01G435300	chr5B	93.252	1645	74	16	554	2192	317969015	317970628	0.000000e+00	2388
24	TraesCS3B01G435300	chr5B	91.282	390	31	1	553	942	680910065	680909679	1.740000e-146	529
25	TraesCS3B01G435300	chr6B	93.369	558	30	6	1	553	638361138	638361693	0.000000e+00	819
26	TraesCS3B01G435300	chr6B	93.321	554	35	2	1	553	230689286	230689838	0.000000e+00	817
27	TraesCS3B01G435300	chr6B	90.513	390	22	7	554	942	658367388	658367013	3.790000e-138	501

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	TraesCS3B01G435300	chr3B	673605424	673607972	2548	True	4708	4708	100.000	1	2549	1	chr3B.!!$R3	2548
1	TraesCS3B01G435300	chr3B	46393698	46395682	1984	True	3101	3101	94.810	552	2549	1	chr3B.!!$R1	1997
2	TraesCS3B01G435300	chr3B	108090327	108092314	1987	True	3055	3055	94.364	552	2549	1	chr3B.!!$R2	1997
3	TraesCS3B01G435300	chr3B	330378552	330380529	1977	False	2909	2909	93.098	543	2549	1	chr3B.!!$F2	2006
4	TraesCS3B01G435300	chr3B	437718487	437719042	555	False	830	830	93.716	1	553	1	chr3B.!!$F3	552
5	TraesCS3B01G435300	chr4A	705527270	705529252	1982	True	3125	3125	95.055	554	2549	1	chr4A.!!$R1	1995
6	TraesCS3B01G435300	chr1B	581715574	581717571	1997	True	3116	3116	94.786	543	2549	1	chr1B.!!$R3	2006
7	TraesCS3B01G435300	chr1B	520842139	520844119	1980	True	3090	3090	94.750	554	2549	1	chr1B.!!$R2	1995
8	TraesCS3B01G435300	chr1B	671392199	671394191	1992	False	3066	3066	94.389	544	2549	1	chr1B.!!$F3	2005
9	TraesCS3B01G435300	chr1B	663786487	663788468	1981	False	2942	2942	93.383	547	2549	1	chr1B.!!$F2	2002
10	TraesCS3B01G435300	chr1B	307930310	307930863	553	True	828	828	93.682	1	553	1	chr1B.!!$R1	552
11	TraesCS3B01G435300	chr1B	357102784	357103335	551	False	826	826	93.671	1	552	1	chr1B.!!$F1	551
12	TraesCS3B01G435300	chr7B	720987206	720989191	1985	True	3085	3085	94.661	553	2549	1	chr7B.!!$R4	1996
13	TraesCS3B01G435300	chr7B	708941271	708943230	1959	True	3061	3061	94.795	578	2549	1	chr7B.!!$R3	1971
14	TraesCS3B01G435300	chr7B	422942792	422943337	545	True	830	830	94.139	9	553	1	chr7B.!!$R2	544
15	TraesCS3B01G435300	chr7B	290176326	290176882	556	True	819	819	93.190	1	557	1	chr7B.!!$R1	556
16	TraesCS3B01G435300	chr2B	692955895	692957879	1984	False	3068	3068	94.511	552	2549	1	chr2B.!!$F1	1997
17	TraesCS3B01G435300	chr2B	234481979	234482532	553	True	833	833	93.863	1	553	1	chr2B.!!$R1	552
18	TraesCS3B01G435300	chr2B	384681692	384682245	553	True	817	817	93.321	1	553	1	chr2B.!!$R2	552
19	TraesCS3B01G435300	chr4B	372351134	372353118	1984	True	3029	3029	94.173	553	2549	1	chr4B.!!$R1	1996
20	TraesCS3B01G435300	chr5B	269389463	269391447	1984	False	2988	2988	93.744	543	2549	1	chr5B.!!$F2	2006
21	TraesCS3B01G435300	chr5B	129114113	129116076	1963	False	2885	2885	93.028	549	2549	1	chr5B.!!$F1	2000
22	TraesCS3B01G435300	chr5B	317969015	317970628	1613	False	2388	2388	93.252	554	2192	1	chr5B.!!$F3	1638
23	TraesCS3B01G435300	chr6B	638361138	638361693	555	False	819	819	93.369	1	553	1	chr6B.!!$F2	552
24	TraesCS3B01G435300	chr6B	230689286	230689838	552	False	817	817	93.321	1	553	1	chr6B.!!$F1	552

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
304	305	0.033504	AACATGAGACGTTCAGCCGT	59.966	50.0	0.0	0.0	45.18	5.68	F
589	591	0.462047	GCCCTTAGTGGTGTCCATCG	60.462	60.0	0.0	0.0	35.28	3.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1261	1304	0.809241	GTCTTGGCCAGAGCATCGAG	60.809	60.0	5.11	0.0	42.67	4.04	R
2352	2613	0.771127	TCAACCTTCCAACCCTCCAG	59.229	55.0	0.00	0.0	0.00	3.86	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
53	54	2.422519	GCATCAGTGTCATCCCTGGATT	60.423	50.000	0.00	0.00	31.62	3.01
72	73	1.890876	TGGTAATGCTGACACACACC	58.109	50.000	0.00	0.00	0.00	4.16
73	74	1.141858	TGGTAATGCTGACACACACCA	59.858	47.619	0.00	0.00	36.26	4.17
122	123	8.541133	TTCAATCACACACTTATTACATCGAA	57.459	30.769	0.00	0.00	0.00	3.71
184	185	8.171164	GCTGAAGGCCATCTAAACTAAATAAT	57.829	34.615	9.78	0.00	34.27	1.28
218	219	5.419542	TCGAAGGTAAATGAGTCCATCAAG	58.580	41.667	0.00	0.00	42.53	3.02
244	245	1.402968	CGGCATAGCTGAGTGCAAAAT	59.597	47.619	18.26	0.00	45.94	1.82
247	248	4.438608	CGGCATAGCTGAGTGCAAAATAAA	60.439	41.667	18.26	0.00	45.94	1.40
256	257	6.662414	TGAGTGCAAAATAAAGACCTATCG	57.338	37.500	0.00	0.00	0.00	2.92
267	268	3.644884	AGACCTATCGCACCTTATTCG	57.355	47.619	0.00	0.00	0.00	3.34
269	270	3.383825	AGACCTATCGCACCTTATTCGTT	59.616	43.478	0.00	0.00	0.00	3.85
274	275	3.853831	TCGCACCTTATTCGTTGTCTA	57.146	42.857	0.00	0.00	0.00	2.59
298	299	2.408050	AGTCTGCAACATGAGACGTTC	58.592	47.619	0.00	0.00	42.93	3.95
299	300	2.135139	GTCTGCAACATGAGACGTTCA	58.865	47.619	0.00	0.00	40.85	3.18
300	301	2.156504	GTCTGCAACATGAGACGTTCAG	59.843	50.000	0.00	0.00	39.68	3.02
301	302	0.867746	TGCAACATGAGACGTTCAGC	59.132	50.000	0.00	0.00	39.68	4.26
303	304	0.439985	CAACATGAGACGTTCAGCCG	59.560	55.000	0.00	0.00	39.68	5.52
304	305	0.033504	AACATGAGACGTTCAGCCGT	59.966	50.000	0.00	0.00	45.18	5.68
305	306	0.885879	ACATGAGACGTTCAGCCGTA	59.114	50.000	0.00	0.00	41.98	4.02
319	321	3.706055	CCGTATAGGCCAGCACATT	57.294	52.632	5.01	0.00	0.00	2.71
445	447	6.387041	AGCTAGTTTTTCCCTACAACAAAC	57.613	37.500	0.00	0.00	0.00	2.93
496	498	6.897413	AGTTGCCCAATATTTGAGAAGGTAAT	59.103	34.615	0.00	0.00	0.00	1.89
503	505	7.561356	CCAATATTTGAGAAGGTAATCCCAACT	59.439	37.037	0.00	0.00	34.66	3.16
519	521	6.603940	TCCCAACTCAAATCCCAATTAAAG	57.396	37.500	0.00	0.00	0.00	1.85
539	541	8.657387	TTAAAGGTATCATCATTGACCCAAAA	57.343	30.769	0.00	0.00	33.85	2.44
540	542	7.552050	AAAGGTATCATCATTGACCCAAAAA	57.448	32.000	0.00	0.00	33.85	1.94
589	591	0.462047	GCCCTTAGTGGTGTCCATCG	60.462	60.000	0.00	0.00	35.28	3.84
638	640	1.144913	TGCTCAGTTTTGCCCCTAGTT	59.855	47.619	0.00	0.00	0.00	2.24
719	721	1.299976	CCTTACAGGTGGGACCAGC	59.700	63.158	12.42	12.42	41.95	4.85
760	762	4.059459	CAGACCGTTGCACGCGTC	62.059	66.667	9.86	5.12	40.91	5.19
811	813	3.935315	GCATAGAGCCATTGAGCATAGA	58.065	45.455	0.00	0.00	37.23	1.98
812	814	3.933955	GCATAGAGCCATTGAGCATAGAG	59.066	47.826	0.00	0.00	37.23	2.43
813	815	2.547299	AGAGCCATTGAGCATAGAGC	57.453	50.000	0.00	0.00	46.19	4.09
849	855	1.855295	TATTAGTGGGCGACAGTGGA	58.145	50.000	1.61	0.00	33.87	4.02
851	857	2.167398	TTAGTGGGCGACAGTGGAGC	62.167	60.000	1.61	0.00	33.87	4.70
888	894	4.007644	CAGGGCGCTGACCACAGA	62.008	66.667	25.55	0.00	46.03	3.41
897	903	1.543607	CTGACCACAGAGAGAGAGCA	58.456	55.000	0.00	0.00	46.03	4.26
1134	1140	1.375523	ACCGAGGAACCACAATCGC	60.376	57.895	0.00	0.00	33.94	4.58
1170	1176	3.448660	GCAGCAAGAATGGGGTAAGAATT	59.551	43.478	0.00	0.00	0.00	2.17
1197	1203	4.236147	CAATTGCATCATTTTCGTGGTCA	58.764	39.130	0.00	0.00	0.00	4.02
1261	1304	3.311966	GTGACATGCTTCTTTCTTTGGC	58.688	45.455	0.00	0.00	0.00	4.52
1517	1763	1.202651	AGGTATGGTAATCGCACTGGC	60.203	52.381	0.00	0.00	0.00	4.85
1749	2001	8.593945	ATTATTCCAGAGCCAAACAATTAAGA	57.406	30.769	0.00	0.00	0.00	2.10
2167	2426	3.319198	GGCTGGGGACTCGAACCA	61.319	66.667	9.91	4.55	0.00	3.67
2216	2475	2.493030	GCGCTGGTAACCGCTAGA	59.507	61.111	0.00	0.00	46.14	2.43
2352	2613	6.660887	TTCCTTTGTTTTGCACTGAAATTC	57.339	33.333	0.00	0.00	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	1.890876	GGTGTGTGTCAGCATTACCA	58.109	50.000	0.00	0.00	43.22	3.25
72	73	9.751542	AAACTCTGTTATAATTCCTCGAGTATG	57.248	33.333	12.31	0.00	30.99	2.39
73	74	9.968870	GAAACTCTGTTATAATTCCTCGAGTAT	57.031	33.333	12.31	5.15	30.99	2.12
138	139	6.883756	TCAGCCATGATACTTTTGTGTAATCA	59.116	34.615	0.00	0.00	0.00	2.57
179	180	3.065371	CCTTCGAAGCTTCCGCAATTATT	59.935	43.478	19.99	0.00	39.10	1.40
184	185	0.319083	TACCTTCGAAGCTTCCGCAA	59.681	50.000	19.99	9.94	39.10	4.85
218	219	0.108138	ACTCAGCTATGCCGTTGGAC	60.108	55.000	0.00	0.00	0.00	4.02
244	245	5.068198	ACGAATAAGGTGCGATAGGTCTTTA	59.932	40.000	0.00	0.00	0.00	1.85
247	248	2.957006	ACGAATAAGGTGCGATAGGTCT	59.043	45.455	0.00	0.00	0.00	3.85
256	257	6.098017	ACTACTTAGACAACGAATAAGGTGC	58.902	40.000	0.00	0.00	32.05	5.01
267	268	5.926542	TCATGTTGCAGACTACTTAGACAAC	59.073	40.000	0.00	0.00	37.14	3.32
269	270	5.476945	TCTCATGTTGCAGACTACTTAGACA	59.523	40.000	0.00	0.00	0.00	3.41
274	275	3.005897	ACGTCTCATGTTGCAGACTACTT	59.994	43.478	9.77	0.00	37.49	2.24
301	302	1.202639	TCAATGTGCTGGCCTATACGG	60.203	52.381	3.32	0.00	0.00	4.02
303	304	5.392380	GCATATTCAATGTGCTGGCCTATAC	60.392	44.000	11.65	0.04	43.11	1.47
304	305	4.701651	GCATATTCAATGTGCTGGCCTATA	59.298	41.667	11.65	0.00	43.11	1.31
305	306	3.508793	GCATATTCAATGTGCTGGCCTAT	59.491	43.478	11.65	0.00	43.11	2.57
319	321	4.191544	GTGTAACTCTGCCAGCATATTCA	58.808	43.478	0.00	0.00	0.00	2.57
427	429	8.631676	TTTATTCGTTTGTTGTAGGGAAAAAC	57.368	30.769	0.00	0.00	0.00	2.43
468	470	5.404466	TTCTCAAATATTGGGCAACTTGG	57.596	39.130	0.00	0.00	0.00	3.61
496	498	5.483583	CCTTTAATTGGGATTTGAGTTGGGA	59.516	40.000	0.00	0.00	0.00	4.37
503	505	9.659135	ATGATGATACCTTTAATTGGGATTTGA	57.341	29.630	0.00	0.00	0.00	2.69
546	548	9.192642	GGCAAAAGGATAATTAACCCTACTTAA	57.807	33.333	8.09	0.00	0.00	1.85
547	549	7.781219	GGGCAAAAGGATAATTAACCCTACTTA	59.219	37.037	8.09	0.00	31.84	2.24
548	550	6.610020	GGGCAAAAGGATAATTAACCCTACTT	59.390	38.462	8.09	4.22	31.84	2.24
549	551	6.068438	AGGGCAAAAGGATAATTAACCCTACT	60.068	38.462	8.09	0.00	43.36	2.57
550	552	6.134055	AGGGCAAAAGGATAATTAACCCTAC	58.866	40.000	8.09	1.34	43.36	3.18
767	769	2.686835	GGCTCTCTGCTGGGTCCT	60.687	66.667	0.00	0.00	42.39	3.85
801	803	1.083806	CGCAACGGCTCTATGCTCAA	61.084	55.000	0.00	0.00	42.39	3.02
802	804	1.519234	CGCAACGGCTCTATGCTCA	60.519	57.895	0.00	0.00	42.39	4.26
803	805	2.240500	CCGCAACGGCTCTATGCTC	61.241	63.158	0.00	0.00	41.17	4.26
804	806	2.202932	CCGCAACGGCTCTATGCT	60.203	61.111	0.00	0.00	41.17	3.79
805	807	3.272334	CCCGCAACGGCTCTATGC	61.272	66.667	0.00	0.00	46.86	3.14
806	808	2.173669	CACCCGCAACGGCTCTATG	61.174	63.158	0.00	0.00	46.86	2.23
807	809	2.186903	CACCCGCAACGGCTCTAT	59.813	61.111	0.00	0.00	46.86	1.98
808	810	3.307906	ACACCCGCAACGGCTCTA	61.308	61.111	0.00	0.00	46.86	2.43
809	811	4.988598	CACACCCGCAACGGCTCT	62.989	66.667	0.00	0.00	46.86	4.09
814	816	1.295792	AATATAGCACACCCGCAACG	58.704	50.000	0.00	0.00	0.00	4.10
815	817	3.247648	CACTAATATAGCACACCCGCAAC	59.752	47.826	0.00	0.00	0.00	4.17
849	855	2.236223	CTCTGTCGCCATGGTCAGCT	62.236	60.000	14.67	0.00	0.00	4.24
851	857	0.179116	CTCTCTGTCGCCATGGTCAG	60.179	60.000	14.67	18.10	0.00	3.51
873	879	3.655810	CTCTCTGTGGTCAGCGCCC	62.656	68.421	2.29	0.00	41.10	6.13
886	892	0.810648	CGTGCTCTTGCTCTCTCTCT	59.189	55.000	0.00	0.00	40.48	3.10
888	894	0.525761	GTCGTGCTCTTGCTCTCTCT	59.474	55.000	0.00	0.00	40.48	3.10
897	903	2.029073	CACCACCGTCGTGCTCTT	59.971	61.111	0.00	0.00	38.79	2.85
942	948	0.980231	CCTCCACAGCTAGCTTCCCT	60.980	60.000	16.46	0.00	0.00	4.20
1085	1091	3.417275	CTCCGATCAACGCTCGCCT	62.417	63.158	0.00	0.00	41.07	5.52
1170	1176	2.677325	CGAAAATGATGCAATTGCCCCA	60.677	45.455	26.94	22.79	41.18	4.96
1197	1203	3.012518	CAACCGATTGCTCAAAGATCCT	58.987	45.455	0.00	0.00	0.00	3.24
1261	1304	0.809241	GTCTTGGCCAGAGCATCGAG	60.809	60.000	5.11	0.00	42.67	4.04
1362	1607	1.118838	CGCCCTCCATCTCTTCTTCT	58.881	55.000	0.00	0.00	0.00	2.85
1453	1699	4.440112	GCAAATGGGTATTGGTAGTGCTTC	60.440	45.833	0.00	0.00	0.00	3.86
1517	1763	9.357652	CCTTTCCATACATTTTCAACATTACAG	57.642	33.333	0.00	0.00	0.00	2.74
1700	1948	9.834628	AATTCATTGCATTTCATTGATCAAAAC	57.165	25.926	13.09	0.00	35.67	2.43
1990	2243	2.593436	CCACGCGGTCTTGGGTTT	60.593	61.111	12.47	0.00	32.02	3.27
2216	2475	3.554934	TGTCAAACTCTTGCCATCTGTT	58.445	40.909	0.00	0.00	32.14	3.16
2352	2613	0.771127	TCAACCTTCCAACCCTCCAG	59.229	55.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.