AutoCloner

Multiple sequence alignment - TraesCS5D01G054300

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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	TraesCS5D01G054300	chr5D	100.000	2916	0	0	1	2916	51685051	51687966	0.000000e+00	5385
1	TraesCS5D01G054300	chr5D	91.188	749	54	5	2171	2910	81371627	81372372	0.000000e+00	1007
2	TraesCS5D01G054300	chr5D	90.438	753	50	12	2171	2916	435456353	435455616	0.000000e+00	972
3	TraesCS5D01G054300	chr5D	92.000	250	20	0	1	250	450172889	450172640	4.620000e-93	351
4	TraesCS5D01G054300	chr5A	94.058	1969	77	15	7	1960	40718881	40720824	0.000000e+00	2952
5	TraesCS5D01G054300	chr5A	91.866	209	17	0	1962	2170	40720859	40721067	2.840000e-75	292
6	TraesCS5D01G054300	chr5B	95.255	1728	58	8	248	1965	54701517	54703230	0.000000e+00	2715
7	TraesCS5D01G054300	chr5B	97.608	209	5	0	1962	2170	54703261	54703469	2.760000e-95	359
8	TraesCS5D01G054300	chr6D	92.339	744	50	5	2171	2911	105891290	105892029	0.000000e+00	1051
9	TraesCS5D01G054300	chr6D	92.032	251	20	0	1	251	265185681	265185931	1.290000e-93	353
10	TraesCS5D01G054300	chr4D	91.029	758	57	6	2167	2916	62708170	62707416	0.000000e+00	1013
11	TraesCS5D01G054300	chr4D	92.829	251	17	1	1	250	105123141	105122891	2.140000e-96	363
12	TraesCS5D01G054300	chr7D	90.837	753	59	5	2171	2916	205768418	205769167	0.000000e+00	1000
13	TraesCS5D01G054300	chr7D	89.509	753	58	14	2171	2916	565345045	565345783	0.000000e+00	933
14	TraesCS5D01G054300	chr7D	88.165	583	68	1	1338	1919	497046201	497045619	0.000000e+00	693
15	TraesCS5D01G054300	chr7D	80.515	272	36	8	858	1126	497046633	497046376	2.970000e-45	193
16	TraesCS5D01G054300	chr2D	90.106	758	58	9	2169	2916	262828478	262827728	0.000000e+00	968
17	TraesCS5D01G054300	chr2D	89.855	759	59	9	2169	2916	262936844	262936093	0.000000e+00	959
18	TraesCS5D01G054300	chr2A	89.509	753	70	5	2171	2916	7843560	7844310	0.000000e+00	944
19	TraesCS5D01G054300	chr7A	87.772	597	70	3	1325	1919	562303564	562302969	0.000000e+00	695
20	TraesCS5D01G054300	chr7B	87.500	592	70	4	1330	1919	525026161	525025572	0.000000e+00	680
21	TraesCS5D01G054300	chr7B	91.633	251	21	0	1	251	497083897	497083647	5.980000e-92	348
22	TraesCS5D01G054300	chr7B	77.053	414	59	18	787	1180	525026930	525026533	3.810000e-49	206
23	TraesCS5D01G054300	chr3B	87.587	572	68	3	1350	1919	46469335	46468765	0.000000e+00	660
24	TraesCS5D01G054300	chr3B	87.413	572	69	3	1350	1919	46613471	46612901	0.000000e+00	654
25	TraesCS5D01G054300	chr1D	92.800	250	18	0	1	250	473119054	473119303	2.140000e-96	363
26	TraesCS5D01G054300	chr6A	92.000	250	20	0	1	250	80727546	80727297	4.620000e-93	351
27	TraesCS5D01G054300	chr3D	91.633	251	21	0	1	251	586578946	586579196	5.980000e-92	348
28	TraesCS5D01G054300	chr3D	91.600	250	21	0	1	250	603703417	603703168	2.150000e-91	346
29	TraesCS5D01G054300	chrUn	88.073	109	13	0	1016	1124	187693345	187693237	2.360000e-26	130
30	TraesCS5D01G054300	chrUn	88.073	109	13	0	1016	1124	254192288	254192180	2.360000e-26	130
31	TraesCS5D01G054300	chrUn	87.156	109	14	0	1016	1124	110300727	110300619	1.100000e-24	124

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	TraesCS5D01G054300	chr5D	51685051	51687966	2915	False	5385	5385	100.0000	1	2916	1	chr5D.!!$F1	2915
1	TraesCS5D01G054300	chr5D	81371627	81372372	745	False	1007	1007	91.1880	2171	2910	1	chr5D.!!$F2	739
2	TraesCS5D01G054300	chr5D	435455616	435456353	737	True	972	972	90.4380	2171	2916	1	chr5D.!!$R1	745
3	TraesCS5D01G054300	chr5A	40718881	40721067	2186	False	1622	2952	92.9620	7	2170	2	chr5A.!!$F1	2163
4	TraesCS5D01G054300	chr5B	54701517	54703469	1952	False	1537	2715	96.4315	248	2170	2	chr5B.!!$F1	1922
5	TraesCS5D01G054300	chr6D	105891290	105892029	739	False	1051	1051	92.3390	2171	2911	1	chr6D.!!$F1	740
6	TraesCS5D01G054300	chr4D	62707416	62708170	754	True	1013	1013	91.0290	2167	2916	1	chr4D.!!$R1	749
7	TraesCS5D01G054300	chr7D	205768418	205769167	749	False	1000	1000	90.8370	2171	2916	1	chr7D.!!$F1	745
8	TraesCS5D01G054300	chr7D	565345045	565345783	738	False	933	933	89.5090	2171	2916	1	chr7D.!!$F2	745
9	TraesCS5D01G054300	chr7D	497045619	497046633	1014	True	443	693	84.3400	858	1919	2	chr7D.!!$R1	1061
10	TraesCS5D01G054300	chr2D	262827728	262828478	750	True	968	968	90.1060	2169	2916	1	chr2D.!!$R1	747
11	TraesCS5D01G054300	chr2D	262936093	262936844	751	True	959	959	89.8550	2169	2916	1	chr2D.!!$R2	747
12	TraesCS5D01G054300	chr2A	7843560	7844310	750	False	944	944	89.5090	2171	2916	1	chr2A.!!$F1	745
13	TraesCS5D01G054300	chr7A	562302969	562303564	595	True	695	695	87.7720	1325	1919	1	chr7A.!!$R1	594
14	TraesCS5D01G054300	chr7B	525025572	525026930	1358	True	443	680	82.2765	787	1919	2	chr7B.!!$R2	1132
15	TraesCS5D01G054300	chr3B	46468765	46469335	570	True	660	660	87.5870	1350	1919	1	chr3B.!!$R1	569
16	TraesCS5D01G054300	chr3B	46612901	46613471	570	True	654	654	87.4130	1350	1919	1	chr3B.!!$R2	569

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
276	281	0.390492	CAGATCATAGGCGGCTGTGA	59.610	55.0	34.24	34.24	0.0	3.58	F
277	282	0.390860	AGATCATAGGCGGCTGTGAC	59.609	55.0	34.72	26.93	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1567	1847	0.036164	TGGCACGGGGATGTATATGC	59.964	55.0	0.0	0.0	0.0	3.14	R
2187	2502	0.111061	TTGCCATGCCATAGCTAGGG	59.889	55.0	20.2	20.2	40.8	3.53	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
210	215	8.181573	TCAAACTTTGTGTAGATTGACTTTGAC	58.818	33.333	1.44	0.00	33.62	3.18
220	225	9.959749	TGTAGATTGACTTTGACCAAATTTTAC	57.040	29.630	0.00	0.00	0.00	2.01
223	228	8.474025	AGATTGACTTTGACCAAATTTTACACA	58.526	29.630	0.00	0.00	0.00	3.72
231	236	4.409187	ACCAAATTTTACACACGGGGTAT	58.591	39.130	0.00	0.00	0.00	2.73
235	240	7.030768	CCAAATTTTACACACGGGGTATAAAG	58.969	38.462	0.00	0.00	0.00	1.85
240	245	6.988622	TTACACACGGGGTATAAAGAAATG	57.011	37.500	0.00	0.00	0.00	2.32
244	249	4.472108	ACACGGGGTATAAAGAAATGGAGA	59.528	41.667	0.00	0.00	0.00	3.71
276	281	0.390492	CAGATCATAGGCGGCTGTGA	59.610	55.000	34.24	34.24	0.00	3.58
277	282	0.390860	AGATCATAGGCGGCTGTGAC	59.609	55.000	34.72	26.93	0.00	3.67
405	414	7.299246	AGGGTTTATATACATGAGCTAACGT	57.701	36.000	0.00	0.00	0.00	3.99
406	415	8.413309	AGGGTTTATATACATGAGCTAACGTA	57.587	34.615	0.00	0.00	0.00	3.57
407	416	8.521176	AGGGTTTATATACATGAGCTAACGTAG	58.479	37.037	0.00	0.00	0.00	3.51
450	459	4.745837	TTTTTACAAGCATGCAATTGCC	57.254	36.364	26.94	12.24	43.83	4.52
465	474	7.418840	TGCAATTGCCTTTTATGTTGTTTAG	57.581	32.000	26.94	0.00	41.18	1.85
468	477	8.341903	GCAATTGCCTTTTATGTTGTTTAGTTT	58.658	29.630	20.06	0.00	34.31	2.66
489	498	7.115414	AGTTTTAGGAGTAGGTAGTATGACGT	58.885	38.462	0.00	0.00	0.00	4.34
525	534	9.539825	AGATATGATGATGACTTCTGTTTACAC	57.460	33.333	0.00	0.00	0.00	2.90
532	541	6.481976	TGATGACTTCTGTTTACACGTCATTT	59.518	34.615	13.97	1.48	40.85	2.32
637	646	1.228769	TAGATAGCACCGCCCGGAT	60.229	57.895	14.44	0.00	38.96	4.18
762	780	3.550437	ACTTGGTGGAGCAGATACATC	57.450	47.619	0.00	0.00	0.00	3.06
849	867	7.441157	GTGACTATTTCAATCCGGTTGATCATA	59.559	37.037	16.70	14.52	45.77	2.15
885	909	4.402155	TGACTTGTCCTGTTTGCTCAAATT	59.598	37.500	0.00	0.00	32.36	1.82
910	934	2.094894	GCAGAAGTTCCATCATGTCACG	59.905	50.000	0.00	0.00	0.00	4.35
966	991	6.097839	AGCCAACTCCGACTATATAAGAACAA	59.902	38.462	0.00	0.00	0.00	2.83
1012	1037	1.198713	TCTCACAATGGCCTCCTCTC	58.801	55.000	3.32	0.00	0.00	3.20
1215	1252	3.740115	GTGGTCACACCTGAGTTATTGT	58.260	45.455	0.00	0.00	41.84	2.71
1309	1362	4.714632	ACCTTGTAAGCACAGTGTTACAT	58.285	39.130	20.24	10.00	38.58	2.29
1495	1775	5.144359	GTCACCAACATTAACGTCATCAAC	58.856	41.667	0.00	0.00	0.00	3.18
1564	1844	1.862602	GACCATTGGGCGTGAACACC	61.863	60.000	7.78	0.00	37.90	4.16
1567	1847	4.939368	TTGGGCGTGAACACCCCG	62.939	66.667	18.97	3.87	46.43	5.73
2126	2440	6.566197	AGTTCATGAGAAAACCAATGACTC	57.434	37.500	0.00	0.00	35.08	3.36
2163	2477	5.607939	TTCTGGGCACGATATTTAGAGAA	57.392	39.130	0.00	0.00	0.00	2.87
2180	2495	5.489792	AGAGAAATGCTTCACTAGTGGAA	57.510	39.130	22.48	13.77	31.53	3.53
2181	2496	5.869579	AGAGAAATGCTTCACTAGTGGAAA	58.130	37.500	22.48	9.69	31.53	3.13
2476	2798	8.877864	AAGTCTCAAATCCACAAAATATACCA	57.122	30.769	0.00	0.00	0.00	3.25
2479	2801	8.956426	GTCTCAAATCCACAAAATATACCAAGA	58.044	33.333	0.00	0.00	0.00	3.02
2591	2921	3.394674	TCTCACGCAACTTGTTATCCA	57.605	42.857	0.00	0.00	0.00	3.41
2604	2934	4.665833	TGTTATCCATGCGCTAACTAGT	57.334	40.909	9.73	0.00	0.00	2.57
2688	3018	2.295253	ATAGACTTTGCGGGTCTTCG	57.705	50.000	10.44	0.00	42.96	3.79
2752	3082	0.809385	GACTCGATCTCGGTGACCAA	59.191	55.000	1.11	0.00	40.29	3.67
2795	3126	5.877012	AGCTTCAATTTCTTATCGCAGAGAA	59.123	36.000	0.00	0.00	43.63	2.87
2818	3149	6.961360	ACGGAGTTATTGTCTATCATCTCA	57.039	37.500	0.00	0.00	37.78	3.27
2821	3152	7.231519	ACGGAGTTATTGTCTATCATCTCATCA	59.768	37.037	0.00	0.00	37.78	3.07
2883	3214	4.866508	TCATTGTACTCTCCTTTGACGT	57.133	40.909	0.00	0.00	0.00	4.34
2911	3242	2.267006	CGGCTGAGCATGTCCACT	59.733	61.111	6.82	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
190	195	7.397892	TTTGGTCAAAGTCAATCTACACAAA	57.602	32.000	0.00	0.00	0.00	2.83
210	215	6.512342	TTATACCCCGTGTGTAAAATTTGG	57.488	37.500	0.00	0.00	28.81	3.28
220	225	4.519213	TCCATTTCTTTATACCCCGTGTG	58.481	43.478	0.00	0.00	0.00	3.82
223	228	4.966805	TCTCTCCATTTCTTTATACCCCGT	59.033	41.667	0.00	0.00	0.00	5.28
231	236	5.126707	GGACGGTACTCTCTCCATTTCTTTA	59.873	44.000	0.00	0.00	0.00	1.85
235	240	2.223525	CGGACGGTACTCTCTCCATTTC	60.224	54.545	0.00	0.00	0.00	2.17
240	245	1.716826	CTGCGGACGGTACTCTCTCC	61.717	65.000	0.00	0.00	0.00	3.71
244	249	0.393944	TGATCTGCGGACGGTACTCT	60.394	55.000	0.00	0.00	0.00	3.24
271	276	6.201517	AGAATCGTGATTTTGTTTGTCACAG	58.798	36.000	5.70	0.00	41.69	3.66
276	281	9.191995	GGAATAAAGAATCGTGATTTTGTTTGT	57.808	29.630	0.00	0.00	0.00	2.83
277	282	9.410556	AGGAATAAAGAATCGTGATTTTGTTTG	57.589	29.630	0.00	0.00	0.00	2.93
317	324	7.829725	TGGATCATGTTCTCCACAATAAAAAG	58.170	34.615	9.41	0.00	39.50	2.27
405	414	7.886629	ATGGTACGTTCTCCAAGTATTACTA	57.113	36.000	10.03	0.00	37.27	1.82
406	415	6.786967	ATGGTACGTTCTCCAAGTATTACT	57.213	37.500	10.03	0.00	37.27	2.24
407	416	7.838771	AAATGGTACGTTCTCCAAGTATTAC	57.161	36.000	10.03	0.00	37.27	1.89
465	474	7.326968	ACGTCATACTACCTACTCCTAAAAC	57.673	40.000	0.00	0.00	0.00	2.43
468	477	9.935241	CTAATACGTCATACTACCTACTCCTAA	57.065	37.037	0.00	0.00	0.00	2.69
525	534	4.875544	ATGGTGGATAACGAAAATGACG	57.124	40.909	0.00	0.00	0.00	4.35
532	541	5.353123	GCTTGTAAGAATGGTGGATAACGAA	59.647	40.000	0.00	0.00	0.00	3.85
637	646	2.123033	TGCCATCTAGCCCGGCTA	60.123	61.111	18.39	18.39	46.39	3.93
762	780	9.976511	TCTCCTGTTTTCTTTATATACGTATGG	57.023	33.333	18.37	5.93	0.00	2.74
849	867	3.444388	GGACAAGTCAAGTACGAGAGGAT	59.556	47.826	2.29	0.00	0.00	3.24
885	909	3.943381	GACATGATGGAACTTCTGCATGA	59.057	43.478	17.83	0.00	35.99	3.07
966	991	2.367202	CCATGGAGGCGTGGGTAGT	61.367	63.158	5.56	0.00	0.00	2.73
1012	1037	0.391793	GCGAGGAGAAACAAGGAGGG	60.392	60.000	0.00	0.00	0.00	4.30
1214	1251	8.344831	TCAACATATAGCATGCAAAACTCATAC	58.655	33.333	21.98	0.00	0.00	2.39
1215	1252	8.449251	TCAACATATAGCATGCAAAACTCATA	57.551	30.769	21.98	0.43	0.00	2.15
1495	1775	0.895559	GGGTGTTGAGGCCAGGAAAG	60.896	60.000	5.01	0.00	0.00	2.62
1564	1844	0.391130	CACGGGGATGTATATGCGGG	60.391	60.000	0.00	0.00	0.00	6.13
1567	1847	0.036164	TGGCACGGGGATGTATATGC	59.964	55.000	0.00	0.00	0.00	3.14
1756	2036	0.312102	GGTTTTGGCTGCTGAGTGAC	59.688	55.000	0.00	0.00	0.00	3.67
1960	2241	6.573664	TGTCACGATTCAAAAGGAAATGAT	57.426	33.333	0.00	0.00	39.39	2.45
2126	2440	2.223735	CCCAGAAATAGCATGCAAGCAG	60.224	50.000	21.98	3.09	36.85	4.24
2187	2502	0.111061	TTGCCATGCCATAGCTAGGG	59.889	55.000	20.20	20.20	40.80	3.53
2494	2816	6.527057	AGGTAGTAGCAAACTAGTTACTGG	57.473	41.667	15.87	0.00	41.42	4.00
2557	2883	2.919859	GCGTGAGATGGATGATGATACG	59.080	50.000	0.00	0.00	0.00	3.06
2591	2921	4.563337	TCATCGTAACTAGTTAGCGCAT	57.437	40.909	15.68	13.01	0.00	4.73
2752	3082	0.610174	TCATCGACCAGAAGCAGCTT	59.390	50.000	7.60	7.60	0.00	3.74
2795	3126	6.961360	TGAGATGATAGACAATAACTCCGT	57.039	37.500	0.00	0.00	0.00	4.69
2809	3140	9.984190	CTGAAGAAAGAGAATGATGAGATGATA	57.016	33.333	0.00	0.00	0.00	2.15
2818	3149	5.486775	TGACTCCCTGAAGAAAGAGAATGAT	59.513	40.000	0.00	0.00	0.00	2.45
2821	3152	6.013032	TGAATGACTCCCTGAAGAAAGAGAAT	60.013	38.462	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.