AutoCloner

Multiple sequence alignment - TraesCS2A01G220200

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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	TraesCS2A01G220200	chr2A	100.000	2825	0	0	1	2825	207655656	207652832	0.000000e+00	5217.0
1	TraesCS2A01G220200	chr2A	84.839	310	31	12	403	709	162429031	162428735	5.920000e-77	298.0
2	TraesCS2A01G220200	chr2A	80.473	338	52	11	379	708	502932121	502932452	2.170000e-61	246.0
3	TraesCS2A01G220200	chr2A	77.136	398	60	23	15	401	209097661	209097284	4.770000e-48	202.0
4	TraesCS2A01G220200	chr2D	95.070	1420	34	8	707	2093	194047311	194045895	0.000000e+00	2202.0
5	TraesCS2A01G220200	chr2D	94.721	663	16	5	2162	2822	194045894	194045249	0.000000e+00	1013.0
6	TraesCS2A01G220200	chr2D	90.909	66	5	1	2621	2685	631943465	631943400	1.390000e-13	87.9
7	TraesCS2A01G220200	chr2B	95.874	1236	37	7	872	2093	249670112	249668877	0.000000e+00	1988.0
8	TraesCS2A01G220200	chr2B	92.486	692	49	3	5	695	16902224	16902913	0.000000e+00	987.0
9	TraesCS2A01G220200	chr2B	96.089	179	7	0	707	885	249670315	249670137	2.750000e-75	292.0
10	TraesCS2A01G220200	chr2B	83.974	312	41	8	401	707	99495350	99495657	9.900000e-75	291.0
11	TraesCS2A01G220200	chr2B	95.000	80	3	1	2111	2189	249668887	249668808	1.060000e-24	124.0
12	TraesCS2A01G220200	chr7D	94.342	707	37	1	5	708	571485683	571484977	0.000000e+00	1081.0
13	TraesCS2A01G220200	chr7D	76.108	406	70	20	2	398	22390347	22389960	1.340000e-43	187.0
14	TraesCS2A01G220200	chr7D	76.650	394	50	27	15	401	384050780	384050422	2.240000e-41	180.0
15	TraesCS2A01G220200	chr7D	75.250	400	64	24	15	401	547273748	547274125	1.050000e-34	158.0
16	TraesCS2A01G220200	chr4A	90.537	708	48	9	2	708	704470085	704470774	0.000000e+00	918.0
17	TraesCS2A01G220200	chr4A	82.748	313	40	10	403	709	703778891	703778587	1.670000e-67	267.0
18	TraesCS2A01G220200	chr4A	81.962	316	40	15	403	710	690143108	690143414	4.670000e-63	252.0
19	TraesCS2A01G220200	chr4A	86.441	59	7	1	2624	2681	157876064	157876006	2.350000e-06	63.9
20	TraesCS2A01G220200	chr5D	80.401	699	79	33	15	708	564217114	564216469	1.970000e-131	479.0
21	TraesCS2A01G220200	chr6B	83.871	310	38	10	401	705	279085504	279085806	4.610000e-73	285.0
22	TraesCS2A01G220200	chr6B	81.703	317	44	11	401	711	279085818	279086126	4.670000e-63	252.0
23	TraesCS2A01G220200	chr6B	76.098	410	61	25	1	398	16604108	16604492	2.240000e-41	180.0
24	TraesCS2A01G220200	chr6B	76.111	360	63	12	19	375	674372610	674372271	1.740000e-37	167.0
25	TraesCS2A01G220200	chr3B	74.859	708	117	39	19	711	10723272	10723933	6.000000e-67	265.0
26	TraesCS2A01G220200	chr3D	77.005	374	61	20	29	398	371340676	371340324	1.030000e-44	191.0
27	TraesCS2A01G220200	chr3D	75.773	388	76	14	15	398	421605263	421605636	2.240000e-41	180.0
28	TraesCS2A01G220200	chr3D	80.500	200	34	3	199	398	474116615	474116809	6.310000e-32	148.0
29	TraesCS2A01G220200	chr3A	80.833	240	38	4	159	398	492185458	492185227	6.220000e-42	182.0
30	TraesCS2A01G220200	chr3A	79.508	244	41	5	159	401	492057861	492057626	6.260000e-37	165.0
31	TraesCS2A01G220200	chr1D	93.750	64	3	1	2623	2685	8461601	8461664	8.330000e-16	95.3
32	TraesCS2A01G220200	chr1D	100.000	40	0	0	2009	2048	7895621	7895660	1.090000e-09	75.0
33	TraesCS2A01G220200	chr1D	93.333	45	1	2	2623	2666	434323150	434323193	6.530000e-07	65.8
34	TraesCS2A01G220200	chr1B	92.188	64	2	3	2621	2683	1956911	1956850	1.390000e-13	87.9
35	TraesCS2A01G220200	chr6D	96.078	51	1	1	2623	2672	469577578	469577528	6.490000e-12	82.4
36	TraesCS2A01G220200	chr1A	88.060	67	6	2	2623	2687	99618589	99618523	8.390000e-11	78.7
37	TraesCS2A01G220200	chr7B	85.484	62	8	1	2623	2683	707023827	707023888	2.350000e-06	63.9

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	TraesCS2A01G220200	chr2A	207652832	207655656	2824	True	5217.000000	5217	100.000000	1	2825	1	chr2A.!!$R2	2824
1	TraesCS2A01G220200	chr2D	194045249	194047311	2062	True	1607.500000	2202	94.895500	707	2822	2	chr2D.!!$R2	2115
2	TraesCS2A01G220200	chr2B	16902224	16902913	689	False	987.000000	987	92.486000	5	695	1	chr2B.!!$F1	690
3	TraesCS2A01G220200	chr2B	249668808	249670315	1507	True	801.333333	1988	95.654333	707	2189	3	chr2B.!!$R1	1482
4	TraesCS2A01G220200	chr7D	571484977	571485683	706	True	1081.000000	1081	94.342000	5	708	1	chr7D.!!$R3	703
5	TraesCS2A01G220200	chr4A	704470085	704470774	689	False	918.000000	918	90.537000	2	708	1	chr4A.!!$F2	706
6	TraesCS2A01G220200	chr5D	564216469	564217114	645	True	479.000000	479	80.401000	15	708	1	chr5D.!!$R1	693
7	TraesCS2A01G220200	chr6B	279085504	279086126	622	False	268.500000	285	82.787000	401	711	2	chr6B.!!$F2	310
8	TraesCS2A01G220200	chr3B	10723272	10723933	661	False	265.000000	265	74.859000	19	711	1	chr3B.!!$F1	692

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	End Stability	Orientation
159	168	0.669318	GAATGAGTCCACGAACGCCA	60.669	55.0	0.00	5.69	F
244	253	1.755179	CCCTGGCATTCTCGAACATT	58.245	50.0	0.00	2.71	F
1148	1584	1.325355	CAAGGGGCCTCATATTGCAG	58.675	55.0	4.79	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1128	1564	0.630673	TGCAATATGAGGCCCCTTGT	59.369	50.000	3.16	R
1583	2033	1.133025	GGCACAAGATCCACAATTCCG	59.867	52.381	4.30	R
2684	3141	0.465460	ACGTGCAAAGTCATGGGTGT	60.465	50.000	4.16	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
159	168	0.669318	GAATGAGTCCACGAACGCCA	60.669	55.000	0.00	0.00	0.00	5.69
183	192	2.762043	TGGCGATCCGATGACCCA	60.762	61.111	0.00	0.00	34.14	4.51
244	253	1.755179	CCCTGGCATTCTCGAACATT	58.245	50.000	0.00	0.00	0.00	2.71
334	370	3.457749	TGTGGATGTGTATGCCCATAAGA	59.542	43.478	0.00	0.00	0.00	2.10
376	412	7.849804	TTGTTGTATTAGGAAGCTTCTGATC	57.150	36.000	25.05	9.23	0.00	2.92
381	417	2.663826	AGGAAGCTTCTGATCGTCAC	57.336	50.000	25.05	5.98	0.00	3.67
553	628	5.806654	ATTAAATCAACACCTGCCAAAGT	57.193	34.783	0.00	0.00	0.00	2.66
567	643	5.016051	TGCCAAAGTAAGCATGAAACAAA	57.984	34.783	0.00	0.00	33.08	2.83
669	1059	2.083167	AGCGGACGAAAATAAACCGA	57.917	45.000	0.00	0.00	45.31	4.69
688	1078	3.257624	CCGAAGTACCAGACTACCAACTT	59.742	47.826	0.00	0.00	37.44	2.66
752	1142	5.047943	GCTACGCAAGATAAAGATAGGGAGA	60.048	44.000	0.00	0.00	43.62	3.71
891	1319	3.587061	TCTCTCTCTCTCTCTCCTGTGTT	59.413	47.826	0.00	0.00	0.00	3.32
938	1366	6.006449	TCTTTGCAAAGCTATTCCTTCTTCT	58.994	36.000	30.35	0.00	35.99	2.85
994	1422	4.002906	TCTGCTTTACCCTACACACAAG	57.997	45.455	0.00	0.00	0.00	3.16
1148	1584	1.325355	CAAGGGGCCTCATATTGCAG	58.675	55.000	4.79	0.00	0.00	4.41
1413	1861	8.172352	TGTATGTAGTTGGTGTTAATTTTGCT	57.828	30.769	0.00	0.00	0.00	3.91
1621	2073	6.978343	TGTGCCTACATAGTTGTCAATAAC	57.022	37.500	0.00	0.00	37.28	1.89
1719	2171	1.412710	GATGCGGTGATGGAAGGAGTA	59.587	52.381	0.00	0.00	0.00	2.59
1895	2351	5.984233	CGAATCTTGTCGGAATTGGATTA	57.016	39.130	0.00	0.00	37.37	1.75
2090	2546	7.121974	ACAACTGTATTTCATTCTGTCTTCG	57.878	36.000	0.00	0.00	0.00	3.79
2093	2549	4.574892	TGTATTTCATTCTGTCTTCGGCA	58.425	39.130	0.00	0.00	0.00	5.69
2094	2550	4.631377	TGTATTTCATTCTGTCTTCGGCAG	59.369	41.667	0.00	0.00	35.43	4.85
2095	2551	1.442769	TTCATTCTGTCTTCGGCAGC	58.557	50.000	0.00	0.00	34.21	5.25
2096	2552	0.610174	TCATTCTGTCTTCGGCAGCT	59.390	50.000	0.00	0.00	34.21	4.24
2097	2553	1.002430	TCATTCTGTCTTCGGCAGCTT	59.998	47.619	0.00	0.00	34.21	3.74
2098	2554	1.808945	CATTCTGTCTTCGGCAGCTTT	59.191	47.619	0.00	0.00	34.21	3.51
2099	2555	1.967319	TTCTGTCTTCGGCAGCTTTT	58.033	45.000	0.00	0.00	34.21	2.27
2100	2556	1.512926	TCTGTCTTCGGCAGCTTTTC	58.487	50.000	0.00	0.00	34.21	2.29
2101	2557	0.519077	CTGTCTTCGGCAGCTTTTCC	59.481	55.000	0.00	0.00	0.00	3.13
2102	2558	0.179032	TGTCTTCGGCAGCTTTTCCA	60.179	50.000	0.00	0.00	0.00	3.53
2103	2559	0.951558	GTCTTCGGCAGCTTTTCCAA	59.048	50.000	0.00	0.00	0.00	3.53
2104	2560	1.336755	GTCTTCGGCAGCTTTTCCAAA	59.663	47.619	0.00	0.00	0.00	3.28
2105	2561	2.028130	TCTTCGGCAGCTTTTCCAAAA	58.972	42.857	0.00	0.00	0.00	2.44
2106	2562	2.428890	TCTTCGGCAGCTTTTCCAAAAA	59.571	40.909	0.00	0.00	0.00	1.94
2143	2599	7.845066	GCTACTAGCTTATTAACAACCAACT	57.155	36.000	0.00	0.00	38.45	3.16
2144	2600	7.685594	GCTACTAGCTTATTAACAACCAACTG	58.314	38.462	0.00	0.00	38.45	3.16
2145	2601	7.333672	GCTACTAGCTTATTAACAACCAACTGT	59.666	37.037	0.00	0.00	38.45	3.55
2146	2602	7.435068	ACTAGCTTATTAACAACCAACTGTG	57.565	36.000	0.00	0.00	0.00	3.66
2147	2603	6.996282	ACTAGCTTATTAACAACCAACTGTGT	59.004	34.615	0.00	0.00	0.00	3.72
2149	2605	7.811117	AGCTTATTAACAACCAACTGTGTTA	57.189	32.000	0.00	0.00	0.00	2.41
2150	2606	8.404107	AGCTTATTAACAACCAACTGTGTTAT	57.596	30.769	0.00	0.00	0.00	1.89
2254	2711	7.512992	AGAACAAAATCTACTAGATGGATGGG	58.487	38.462	0.00	0.00	34.65	4.00
2255	2712	6.831664	ACAAAATCTACTAGATGGATGGGT	57.168	37.500	0.00	0.00	34.65	4.51
2270	2727	4.597507	TGGATGGGTTTCTACTGGATATCC	59.402	45.833	15.39	15.39	33.81	2.59
2321	2778	5.772393	AAGAGGTGATGTGGTACCAAATA	57.228	39.130	18.00	7.37	39.46	1.40
2395	2852	6.662234	CGTCCAGGGATATAACATAAGTCCTA	59.338	42.308	0.00	0.00	0.00	2.94
2398	2855	6.436532	CCAGGGATATAACATAAGTCCTACGT	59.563	42.308	0.00	0.00	0.00	3.57
2483	2940	1.312371	TTGTTTCCATAGCGGCTGGC	61.312	55.000	13.86	0.00	44.05	4.85
2581	3038	0.914644	ACCATCCATGAGTGGGTCAG	59.085	55.000	17.26	0.00	46.06	3.51
2609	3066	5.944007	GCCAAACTTTCCCTCTGTTAATCTA	59.056	40.000	0.00	0.00	0.00	1.98
2619	3076	6.497259	TCCCTCTGTTAATCTATACACCCATC	59.503	42.308	0.00	0.00	0.00	3.51
2635	3092	2.417339	CATCACTTATGGCTGCATGC	57.583	50.000	11.82	11.82	41.94	4.06
2636	3093	1.679153	CATCACTTATGGCTGCATGCA	59.321	47.619	21.29	21.29	45.15	3.96
2637	3094	2.061509	TCACTTATGGCTGCATGCAT	57.938	45.000	22.97	9.00	45.15	3.96
2638	3095	1.951602	TCACTTATGGCTGCATGCATC	59.048	47.619	22.97	17.75	45.15	3.91
2639	3096	0.949397	ACTTATGGCTGCATGCATCG	59.051	50.000	22.97	12.00	45.15	3.84
2640	3097	1.232119	CTTATGGCTGCATGCATCGA	58.768	50.000	22.97	15.35	45.15	3.59
2641	3098	1.810755	CTTATGGCTGCATGCATCGAT	59.189	47.619	22.97	21.43	45.15	3.59
2642	3099	1.900245	TATGGCTGCATGCATCGATT	58.100	45.000	22.97	7.71	45.15	3.34
2643	3100	0.313987	ATGGCTGCATGCATCGATTG	59.686	50.000	22.97	9.56	45.15	2.67
2644	3101	0.748729	TGGCTGCATGCATCGATTGA	60.749	50.000	22.97	0.00	45.15	2.57
2645	3102	0.596577	GGCTGCATGCATCGATTGAT	59.403	50.000	22.97	0.00	45.15	2.57
2727	3184	7.413328	CGTGCTATTGAAATCATGAAGAACAGA	60.413	37.037	0.00	0.00	0.00	3.41
2740	3197	6.137794	TGAAGAACAGATCGAGTTATCTCC	57.862	41.667	6.58	0.00	37.40	3.71
2822	3281	9.118300	GAATAGATTGTGGATAATCATGGATCC	57.882	37.037	4.20	4.20	41.85	3.36
2823	3282	5.824421	AGATTGTGGATAATCATGGATCCC	58.176	41.667	9.90	9.83	40.94	3.85
2824	3283	5.314039	AGATTGTGGATAATCATGGATCCCA	59.686	40.000	9.90	11.53	40.94	4.37

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.476074	GTGGTCGTCGTTCGTAACAA	58.524	50.000	0.00	0.00	40.80	2.83
3	4	0.384230	GTCGTGGTCGTCGTTCGTAA	60.384	55.000	0.00	0.00	40.80	3.18
159	168	0.318699	CATCGGATCGCCACGTACAT	60.319	55.000	0.00	0.00	0.00	2.29
244	253	0.250858	CTGGGCCTGATGTCAACACA	60.251	55.000	4.53	0.00	36.78	3.72
367	403	7.640852	TCTACTATTAAGTGACGATCAGAAGC	58.359	38.462	0.00	0.00	36.36	3.86
567	643	8.599624	ACCCAAATGTCATTAAATGAGAGATT	57.400	30.769	0.00	0.00	40.53	2.40
583	970	9.374711	TCCTTCTCTTATTAAAAACCCAAATGT	57.625	29.630	0.00	0.00	0.00	2.71
617	1004	1.074090	TCTCACCACCCTTCCCACA	60.074	57.895	0.00	0.00	0.00	4.17
651	1038	2.158254	ACTTCGGTTTATTTTCGTCCGC	59.842	45.455	0.00	0.00	40.81	5.54
669	1059	4.527427	GGAGAAGTTGGTAGTCTGGTACTT	59.473	45.833	0.00	0.00	39.80	2.24
752	1142	2.795329	CTGGCCGGCCTAATCAATAAT	58.205	47.619	43.34	0.00	36.94	1.28
891	1319	5.398236	AGAGAGACAGCCTGGCTTATATAA	58.602	41.667	20.79	0.00	34.53	0.98
938	1366	5.551233	ACTACAAGCTGTGCTTCTATGAAA	58.449	37.500	1.45	0.00	46.77	2.69
1128	1564	0.630673	TGCAATATGAGGCCCCTTGT	59.369	50.000	0.00	0.00	0.00	3.16
1148	1584	2.840651	TCCTCCTCCTCCTGATCAAAAC	59.159	50.000	0.00	0.00	0.00	2.43
1358	1806	7.447545	ACTCCAAGGACTTGTCTAATTTTAACC	59.552	37.037	10.81	0.00	38.85	2.85
1583	2033	1.133025	GGCACAAGATCCACAATTCCG	59.867	52.381	0.00	0.00	0.00	4.30
1621	2073	5.922544	CCTTCATGCAAGAAAAACTAACAGG	59.077	40.000	5.79	0.00	33.29	4.00
1895	2351	8.893219	GAAATTTTGAAGGAATTTCAGGAAGT	57.107	30.769	14.18	0.00	46.01	3.01
1986	2442	7.619302	ACTGTATGTTTTGGTCAATTATCCCAT	59.381	33.333	0.00	0.00	0.00	4.00
2103	2559	7.371126	GCTAGTAGCTGAAGACAGAATTTTT	57.629	36.000	15.16	0.00	46.03	1.94
2104	2560	6.976636	GCTAGTAGCTGAAGACAGAATTTT	57.023	37.500	15.16	0.00	46.03	1.82
2254	2711	4.232091	TGAGGGGGATATCCAGTAGAAAC	58.768	47.826	23.27	3.08	37.91	2.78
2255	2712	4.569676	TGAGGGGGATATCCAGTAGAAA	57.430	45.455	23.27	0.00	37.91	2.52
2270	2727	2.823747	CACCATATGCATGAATGAGGGG	59.176	50.000	10.16	3.21	33.67	4.79
2369	2826	5.148651	ACTTATGTTATATCCCTGGACGC	57.851	43.478	0.00	0.00	0.00	5.19
2395	2852	5.172934	ACAACATATATTCACCACGAACGT	58.827	37.500	0.00	0.00	36.12	3.99
2398	2855	5.984725	AGGACAACATATATTCACCACGAA	58.015	37.500	0.00	0.00	38.22	3.85
2483	2940	2.747436	TCATGCTGATAAGCTAGTGCG	58.253	47.619	3.06	0.00	45.42	5.34
2568	3025	0.883833	GGCAAACTGACCCACTCATG	59.116	55.000	0.00	0.00	0.00	3.07
2581	3038	2.430694	ACAGAGGGAAAGTTTGGCAAAC	59.569	45.455	30.67	30.67	41.69	2.93
2619	3076	1.334689	CGATGCATGCAGCCATAAGTG	60.335	52.381	28.76	10.20	44.83	3.16
2636	3093	1.598962	CGGCCCTGCATCAATCGAT	60.599	57.895	0.00	0.00	0.00	3.59
2637	3094	2.203056	CGGCCCTGCATCAATCGA	60.203	61.111	0.00	0.00	0.00	3.59
2638	3095	3.282157	CCGGCCCTGCATCAATCG	61.282	66.667	0.00	0.00	0.00	3.34
2639	3096	2.908940	CCCGGCCCTGCATCAATC	60.909	66.667	0.00	0.00	0.00	2.67
2640	3097	4.528039	CCCCGGCCCTGCATCAAT	62.528	66.667	0.00	0.00	0.00	2.57
2646	3103	4.581093	GATAACCCCCGGCCCTGC	62.581	72.222	0.00	0.00	0.00	4.85
2683	3140	1.202710	ACGTGCAAAGTCATGGGTGTA	60.203	47.619	0.00	0.00	0.00	2.90
2684	3141	0.465460	ACGTGCAAAGTCATGGGTGT	60.465	50.000	0.00	0.00	0.00	4.16
2759	3218	7.208064	TGCTTACTCCTATAAACCCTGAATT	57.792	36.000	0.00	0.00	0.00	2.17
2793	3252	8.447200	TCCATGATTATCCACAATCTATTCCAA	58.553	33.333	0.00	0.00	36.16	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.