AutoCloner

Multiple sequence alignment - TraesCS2D01G189700

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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	TraesCS2D01G189700	chr2D	100.000	2747	0	0	1	2747	133273994	133271248	0.000000e+00	5073.0
1	TraesCS2D01G189700	chr2A	94.806	2676	80	24	1	2648	141284419	141281775	0.000000e+00	4117.0
2	TraesCS2D01G189700	chr2A	94.444	108	6	0	2640	2747	240465855	240465962	1.690000e-37	167.0
3	TraesCS2D01G189700	chr2B	92.817	2673	124	30	1	2648	189746813	189744184	0.000000e+00	3810.0
4	TraesCS2D01G189700	chr2B	93.519	108	7	0	2640	2747	249527402	249527509	7.870000e-36	161.0
5	TraesCS2D01G189700	chr7D	94.444	108	6	0	2640	2747	379768978	379768871	1.690000e-37	167.0
6	TraesCS2D01G189700	chr7D	93.694	111	5	2	2639	2747	454079418	454079308	6.090000e-37	165.0
7	TraesCS2D01G189700	chr4B	95.238	105	4	1	2644	2747	178081268	178081164	6.090000e-37	165.0
8	TraesCS2D01G189700	chr6B	91.453	117	9	1	2632	2747	633056390	633056506	2.830000e-35	159.0
9	TraesCS2D01G189700	chr5D	89.683	126	11	2	2623	2747	230417016	230416892	2.830000e-35	159.0
10	TraesCS2D01G189700	chr3B	90.000	120	10	2	2628	2747	183594446	183594329	1.320000e-33	154.0
11	TraesCS2D01G189700	chr3A	82.143	168	18	9	2585	2747	616183550	616183710	1.720000e-27	134.0
12	TraesCS2D01G189700	chr5B	81.443	97	9	6	2585	2678	554917081	554916991	1.360000e-08	71.3
13	TraesCS2D01G189700	chr1D	81.443	97	9	7	2585	2678	132266411	132266321	1.360000e-08	71.3
14	TraesCS2D01G189700	chr6A	80.612	98	10	7	2585	2679	116144448	116144357	1.770000e-07	67.6

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	TraesCS2D01G189700	chr2D	133271248	133273994	2746	True	5073	5073	100.000	1	2747	1	chr2D.!!$R1	2746
1	TraesCS2D01G189700	chr2A	141281775	141284419	2644	True	4117	4117	94.806	1	2648	1	chr2A.!!$R1	2647
2	TraesCS2D01G189700	chr2B	189744184	189746813	2629	True	3810	3810	92.817	1	2648	1	chr2B.!!$R1	2647

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
419	445	1.848886	TTTTTCTCCCCTCCGCCCTC	61.849	60.000	0.0	0.0	0.00	4.3	F
967	997	2.402787	GAGGTAGGCGTCGTCGTC	59.597	66.667	0.0	0.0	42.44	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1449	1480	2.121832	TCGCCTTCTTCCCCCTGA	59.878	61.111	0.00	0.00	0.00	3.86	R
2411	2443	3.254166	CCATGATCCCGGCTTCATTTAAG	59.746	47.826	13.07	4.49	38.32	1.85	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
57	59	2.757868	TGCGGATTTATCTTTTGGGTGG	59.242	45.455	0.00	0.00	0.00	4.61
64	66	4.463050	TTATCTTTTGGGTGGTCAAGGT	57.537	40.909	0.00	0.00	0.00	3.50
66	68	3.955524	TCTTTTGGGTGGTCAAGGTAA	57.044	42.857	0.00	0.00	0.00	2.85
108	110	7.863375	CGTGAATGTGGGTAAAGAAAATTGTTA	59.137	33.333	0.00	0.00	0.00	2.41
109	111	9.705290	GTGAATGTGGGTAAAGAAAATTGTTAT	57.295	29.630	0.00	0.00	0.00	1.89
111	113	9.366216	GAATGTGGGTAAAGAAAATTGTTATCC	57.634	33.333	0.00	0.00	0.00	2.59
113	115	6.715718	TGTGGGTAAAGAAAATTGTTATCCGA	59.284	34.615	0.00	0.00	31.65	4.55
114	116	7.094549	TGTGGGTAAAGAAAATTGTTATCCGAG	60.095	37.037	0.00	0.00	31.65	4.63
115	117	7.120138	GTGGGTAAAGAAAATTGTTATCCGAGA	59.880	37.037	0.00	0.00	31.65	4.04
117	119	7.336176	GGGTAAAGAAAATTGTTATCCGAGAGT	59.664	37.037	0.00	0.00	0.00	3.24
118	120	8.388853	GGTAAAGAAAATTGTTATCCGAGAGTC	58.611	37.037	0.00	0.00	0.00	3.36
175	196	5.652994	TTATGGGTGTGGAAAATACAAGC	57.347	39.130	0.00	0.00	0.00	4.01
176	197	1.883275	TGGGTGTGGAAAATACAAGCG	59.117	47.619	0.00	0.00	0.00	4.68
217	243	7.732222	TGAACCCCTTGCAGAAATTAATAAT	57.268	32.000	0.00	0.00	0.00	1.28
218	244	8.144862	TGAACCCCTTGCAGAAATTAATAATT	57.855	30.769	0.00	0.00	0.00	1.40
219	245	9.261035	TGAACCCCTTGCAGAAATTAATAATTA	57.739	29.630	0.00	0.00	0.00	1.40
270	296	6.303259	GCGAAAGAAAACATACATGAACTCAC	59.697	38.462	0.00	0.00	0.00	3.51
368	394	2.125431	GATCCGGGCCGTCGAAAA	60.125	61.111	26.32	2.95	0.00	2.29
419	445	1.848886	TTTTTCTCCCCTCCGCCCTC	61.849	60.000	0.00	0.00	0.00	4.30
662	689	4.057428	GTCGCGTCCCTGCTGACT	62.057	66.667	5.77	0.00	36.32	3.41
963	993	3.674050	ATGGGGAGGTAGGCGTCGT	62.674	63.158	0.00	0.00	0.00	4.34
964	994	3.525545	GGGGAGGTAGGCGTCGTC	61.526	72.222	0.00	0.00	0.00	4.20
965	995	3.885521	GGGAGGTAGGCGTCGTCG	61.886	72.222	0.00	0.00	40.37	5.12
966	996	3.130160	GGAGGTAGGCGTCGTCGT	61.130	66.667	3.66	0.00	39.49	4.34
967	997	2.402787	GAGGTAGGCGTCGTCGTC	59.597	66.667	0.00	0.00	42.44	4.20
968	998	3.431683	GAGGTAGGCGTCGTCGTCG	62.432	68.421	7.53	7.53	46.96	5.12
1434	1465	2.829120	TGTCTTGTATGTGTCCGATCCA	59.171	45.455	0.00	0.00	0.00	3.41
1845	1877	6.349694	GCAGCTAGCTTTATCTTCAAAGGTTT	60.350	38.462	16.46	0.00	42.08	3.27
1979	2011	2.945447	ATCCATTGTTTGGTCATGCG	57.055	45.000	0.00	0.00	46.52	4.73
2327	2359	4.837896	TTGACACACTGTTCAAACAACA	57.162	36.364	0.00	0.00	38.66	3.33
2411	2443	6.583562	ACTAATCTTAGTGCATGGTACTTCC	58.416	40.000	1.87	0.00	42.13	3.46
2475	2507	5.486735	TCACAGAATTTCATTTGCCCATT	57.513	34.783	0.00	0.00	0.00	3.16
2490	2522	4.815269	TGCCCATTTTTCTGTTAAATCCG	58.185	39.130	0.00	0.00	0.00	4.18
2495	2527	5.925969	CCATTTTTCTGTTAAATCCGCAAGT	59.074	36.000	0.00	0.00	0.00	3.16
2513	2545	6.698766	CCGCAAGTATACTAACCGTTTATTCT	59.301	38.462	5.65	0.00	0.00	2.40
2561	2593	3.056179	CCTGTCCCTCTTGTTTCTCTCTC	60.056	52.174	0.00	0.00	0.00	3.20
2591	2623	1.001633	GGGGAGAAAACGTCACTGCTA	59.998	52.381	0.00	0.00	0.00	3.49
2594	2626	4.501071	GGGAGAAAACGTCACTGCTAATA	58.499	43.478	0.00	0.00	0.00	0.98
2632	2664	6.070481	TGTGATGTACCAACCTCATAGCTTTA	60.070	38.462	0.00	0.00	33.57	1.85
2658	2690	9.779951	ATATACCTATATTTTACTCCCTCCGTT	57.220	33.333	0.00	0.00	0.00	4.44
2659	2691	6.416631	ACCTATATTTTACTCCCTCCGTTC	57.583	41.667	0.00	0.00	0.00	3.95
2660	2692	5.306419	ACCTATATTTTACTCCCTCCGTTCC	59.694	44.000	0.00	0.00	0.00	3.62
2661	2693	5.543020	CCTATATTTTACTCCCTCCGTTCCT	59.457	44.000	0.00	0.00	0.00	3.36
2662	2694	6.723052	CCTATATTTTACTCCCTCCGTTCCTA	59.277	42.308	0.00	0.00	0.00	2.94
2663	2695	7.234166	CCTATATTTTACTCCCTCCGTTCCTAA	59.766	40.741	0.00	0.00	0.00	2.69
2664	2696	5.767277	ATTTTACTCCCTCCGTTCCTAAA	57.233	39.130	0.00	0.00	0.00	1.85
2665	2697	5.767277	TTTTACTCCCTCCGTTCCTAAAT	57.233	39.130	0.00	0.00	0.00	1.40
2666	2698	6.872585	TTTTACTCCCTCCGTTCCTAAATA	57.127	37.500	0.00	0.00	0.00	1.40
2667	2699	7.441903	TTTTACTCCCTCCGTTCCTAAATAT	57.558	36.000	0.00	0.00	0.00	1.28
2668	2700	8.551682	TTTTACTCCCTCCGTTCCTAAATATA	57.448	34.615	0.00	0.00	0.00	0.86
2669	2701	8.551682	TTTACTCCCTCCGTTCCTAAATATAA	57.448	34.615	0.00	0.00	0.00	0.98
2670	2702	6.667558	ACTCCCTCCGTTCCTAAATATAAG	57.332	41.667	0.00	0.00	0.00	1.73
2671	2703	6.141790	ACTCCCTCCGTTCCTAAATATAAGT	58.858	40.000	0.00	0.00	0.00	2.24
2672	2704	6.267242	ACTCCCTCCGTTCCTAAATATAAGTC	59.733	42.308	0.00	0.00	0.00	3.01
2673	2705	6.379579	TCCCTCCGTTCCTAAATATAAGTCT	58.620	40.000	0.00	0.00	0.00	3.24
2674	2706	6.842807	TCCCTCCGTTCCTAAATATAAGTCTT	59.157	38.462	0.00	0.00	0.00	3.01
2675	2707	7.346436	TCCCTCCGTTCCTAAATATAAGTCTTT	59.654	37.037	0.00	0.00	0.00	2.52
2676	2708	7.991460	CCCTCCGTTCCTAAATATAAGTCTTTT	59.009	37.037	0.00	0.00	0.00	2.27
2677	2709	9.392259	CCTCCGTTCCTAAATATAAGTCTTTTT	57.608	33.333	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	30	8.576442	CCCAAAAGATAAATCCGCATTAAGTAT	58.424	33.333	0.00	0.00	0.00	2.12
57	59	5.390567	CCACTATCGCAAACTTTACCTTGAC	60.391	44.000	0.00	0.00	0.00	3.18
64	66	2.413796	CACGCCACTATCGCAAACTTTA	59.586	45.455	0.00	0.00	0.00	1.85
66	68	0.796312	CACGCCACTATCGCAAACTT	59.204	50.000	0.00	0.00	0.00	2.66
108	110	4.500545	CGGATTTCATCTTGACTCTCGGAT	60.501	45.833	0.00	0.00	0.00	4.18
109	111	3.181486	CGGATTTCATCTTGACTCTCGGA	60.181	47.826	0.00	0.00	0.00	4.55
111	113	4.033990	TCGGATTTCATCTTGACTCTCG	57.966	45.455	0.00	0.00	0.00	4.04
113	115	5.667539	TTCTCGGATTTCATCTTGACTCT	57.332	39.130	0.00	0.00	0.00	3.24
114	116	6.727824	TTTTCTCGGATTTCATCTTGACTC	57.272	37.500	0.00	0.00	0.00	3.36
158	179	3.907894	TTCGCTTGTATTTTCCACACC	57.092	42.857	0.00	0.00	0.00	4.16
172	193	9.836076	GGTTCATTTAGTTACTTTTATTCGCTT	57.164	29.630	0.00	0.00	0.00	4.68
174	195	7.699391	GGGGTTCATTTAGTTACTTTTATTCGC	59.301	37.037	0.00	0.00	0.00	4.70
175	196	8.953313	AGGGGTTCATTTAGTTACTTTTATTCG	58.047	33.333	0.00	0.00	0.00	3.34
222	248	9.360093	TCGCCGTTTTCATCAATTTATTAATTT	57.640	25.926	0.00	0.00	31.63	1.82
226	252	8.237949	TCTTTCGCCGTTTTCATCAATTTATTA	58.762	29.630	0.00	0.00	0.00	0.98
229	255	6.003234	TCTTTCGCCGTTTTCATCAATTTA	57.997	33.333	0.00	0.00	0.00	1.40
270	296	1.152963	GTGGTCATTCGGGGATGGG	60.153	63.158	0.00	0.00	0.00	4.00
419	445	1.911702	GAAGAGGAAAGGGACGGGGG	61.912	65.000	0.00	0.00	0.00	5.40
472	499	3.541713	CGGGTAGGGCAGGAGCTC	61.542	72.222	4.71	4.71	43.44	4.09
587	614	2.826738	GAGCGCGAGAGGAGGAGT	60.827	66.667	12.10	0.00	0.00	3.85
693	720	4.130857	TGACTAGAAGCTCATACCTCGAG	58.869	47.826	5.13	5.13	0.00	4.04
965	995	4.057428	ACTCCAGCAGCGACCGAC	62.057	66.667	0.00	0.00	0.00	4.79
966	996	4.056125	CACTCCAGCAGCGACCGA	62.056	66.667	0.00	0.00	0.00	4.69
967	997	2.842394	AATCACTCCAGCAGCGACCG	62.842	60.000	0.00	0.00	0.00	4.79
968	998	0.674895	AAATCACTCCAGCAGCGACC	60.675	55.000	0.00	0.00	0.00	4.79
1354	1385	3.181967	CCTTGAGAAGCGCGTCCG	61.182	66.667	19.90	6.18	37.57	4.79
1449	1480	2.121832	TCGCCTTCTTCCCCCTGA	59.878	61.111	0.00	0.00	0.00	3.86
1602	1633	2.733671	CGCCGGCATCATATCAGCG	61.734	63.158	28.98	3.22	35.82	5.18
1979	2011	6.765915	AGAAATTGAAGAGTTAATCTGCCC	57.234	37.500	0.00	0.00	38.67	5.36
2029	2061	9.506018	TTCTATGACTCTGTTCATTCAAATTGA	57.494	29.630	0.00	0.00	37.42	2.57
2290	2322	8.320295	CAGTGTGTCAAAAACAATGATGTAAAC	58.680	33.333	0.00	0.00	44.24	2.01
2411	2443	3.254166	CCATGATCCCGGCTTCATTTAAG	59.746	47.826	13.07	4.49	38.32	1.85
2475	2507	8.556213	AGTATACTTGCGGATTTAACAGAAAA	57.444	30.769	0.00	0.00	0.00	2.29
2513	2545	3.826157	CTGGAAAACATGGCTGGTCTAAA	59.174	43.478	0.00	0.00	0.00	1.85
2561	2593	6.419710	GTGACGTTTTCTCCCCAAAAATTTAG	59.580	38.462	0.00	0.00	0.00	1.85
2632	2664	9.779951	AACGGAGGGAGTAAAATATAGGTATAT	57.220	33.333	0.00	0.00	0.00	0.86
2648	2680	6.494146	AGACTTATATTTAGGAACGGAGGGAG	59.506	42.308	0.00	0.00	0.00	4.30
2649	2681	6.379579	AGACTTATATTTAGGAACGGAGGGA	58.620	40.000	0.00	0.00	0.00	4.20
2650	2682	6.667558	AGACTTATATTTAGGAACGGAGGG	57.332	41.667	0.00	0.00	0.00	4.30
2651	2683	8.959705	AAAAGACTTATATTTAGGAACGGAGG	57.040	34.615	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.