AutoCloner

Multiple sequence alignment - TraesCS5D01G061100

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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	TraesCS5D01G061100	chr5D	100.000	3525	0	0	1	3525	57989862	57993386	0.000000e+00	6510.0
1	TraesCS5D01G061100	chr5D	86.392	316	33	7	2232	2546	58118637	58118943	1.570000e-88	337.0
2	TraesCS5D01G061100	chr5D	78.723	423	59	21	1242	1649	58117439	58117845	1.620000e-63	254.0
3	TraesCS5D01G061100	chr5D	84.615	208	29	1	1916	2123	58118065	58118269	1.660000e-48	204.0
4	TraesCS5D01G061100	chr5A	95.709	2843	94	12	702	3522	46001044	46003880	0.000000e+00	4549.0
5	TraesCS5D01G061100	chr5A	93.094	695	47	1	2829	3522	46050956	46051650	0.000000e+00	1016.0
6	TraesCS5D01G061100	chr5A	78.549	648	98	29	1838	2472	46418911	46419530	4.270000e-104	388.0
7	TraesCS5D01G061100	chr5A	79.387	587	70	29	1242	1793	46491818	46492388	2.000000e-97	366.0
8	TraesCS5D01G061100	chr5A	86.084	309	33	8	2239	2546	46492706	46493005	1.220000e-84	324.0
9	TraesCS5D01G061100	chr5B	93.724	1418	59	14	821	2236	62938935	62940324	0.000000e+00	2098.0
10	TraesCS5D01G061100	chr5B	85.991	1085	104	27	2238	3302	62940405	62941461	0.000000e+00	1118.0
11	TraesCS5D01G061100	chr5B	91.271	653	26	12	1	652	62914502	62915124	0.000000e+00	861.0
12	TraesCS5D01G061100	chr5B	78.886	1364	176	62	1242	2546	63254444	63255754	0.000000e+00	821.0
13	TraesCS5D01G061100	chr5B	91.875	160	10	2	652	809	62917162	62917320	1.650000e-53	220.0
14	TraesCS5D01G061100	chr4A	94.575	977	46	7	2356	3328	564653898	564652925	0.000000e+00	1504.0
15	TraesCS5D01G061100	chr4A	96.117	206	8	0	3317	3522	564650311	564650106	1.570000e-88	337.0
16	TraesCS5D01G061100	chrUn	78.428	649	97	26	1838	2472	379638672	379639291	1.990000e-102	383.0
17	TraesCS5D01G061100	chrUn	87.500	72	8	1	2922	2992	64208752	64208823	8.110000e-12	82.4
18	TraesCS5D01G061100	chrUn	97.222	36	1	0	2838	2873	64208738	64208703	1.060000e-05	62.1
19	TraesCS5D01G061100	chr6B	88.119	202	22	2	2793	2992	531792642	531792441	4.550000e-59	239.0

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	TraesCS5D01G061100	chr5D	57989862	57993386	3524	False	6510.0	6510	100.000000	1	3525	1	chr5D.!!$F1	3524
1	TraesCS5D01G061100	chr5D	58117439	58118943	1504	False	265.0	337	83.243333	1242	2546	3	chr5D.!!$F2	1304
2	TraesCS5D01G061100	chr5A	46001044	46003880	2836	False	4549.0	4549	95.709000	702	3522	1	chr5A.!!$F1	2820
3	TraesCS5D01G061100	chr5A	46050956	46051650	694	False	1016.0	1016	93.094000	2829	3522	1	chr5A.!!$F2	693
4	TraesCS5D01G061100	chr5A	46418911	46419530	619	False	388.0	388	78.549000	1838	2472	1	chr5A.!!$F3	634
5	TraesCS5D01G061100	chr5A	46491818	46493005	1187	False	345.0	366	82.735500	1242	2546	2	chr5A.!!$F4	1304
6	TraesCS5D01G061100	chr5B	62938935	62941461	2526	False	1608.0	2098	89.857500	821	3302	2	chr5B.!!$F3	2481
7	TraesCS5D01G061100	chr5B	63254444	63255754	1310	False	821.0	821	78.886000	1242	2546	1	chr5B.!!$F1	1304
8	TraesCS5D01G061100	chr5B	62914502	62917320	2818	False	540.5	861	91.573000	1	809	2	chr5B.!!$F2	808
9	TraesCS5D01G061100	chr4A	564650106	564653898	3792	True	920.5	1504	95.346000	2356	3522	2	chr4A.!!$R1	1166
10	TraesCS5D01G061100	chrUn	379638672	379639291	619	False	383.0	383	78.428000	1838	2472	1	chrUn.!!$F2	634

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
185	187	0.040067	GTCGTTGCCAAGCCTTTCTG	60.040	55.0	0.00	0.0	0.00	3.02	F
647	649	0.541863	AAGAGGTGAATGGGCCTACG	59.458	55.0	4.53	0.0	34.81	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1788	3883	0.535335	TAGGACCGACAGCATTGACC	59.465	55.0	0.0	0.0	0.00	4.02	R
2605	5018	0.322816	GAGCTGGGTTCAGGCATTGA	60.323	55.0	0.0	0.0	41.19	2.57	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
72	74	6.530567	CGCAAGTTCTTACATATTCGTGAAA	58.469	36.000	0.00	0.00	0.00	2.69
73	75	7.012943	CGCAAGTTCTTACATATTCGTGAAAA	58.987	34.615	0.00	0.00	0.00	2.29
163	165	2.366837	TGGCATCCCATCCTCCGT	60.367	61.111	0.00	0.00	35.79	4.69
164	166	2.111878	GGCATCCCATCCTCCGTG	59.888	66.667	0.00	0.00	0.00	4.94
165	167	2.592861	GCATCCCATCCTCCGTGC	60.593	66.667	0.00	0.00	0.00	5.34
166	168	2.280389	CATCCCATCCTCCGTGCG	60.280	66.667	0.00	0.00	0.00	5.34
167	169	2.764128	ATCCCATCCTCCGTGCGT	60.764	61.111	0.00	0.00	0.00	5.24
168	170	2.797278	ATCCCATCCTCCGTGCGTC	61.797	63.158	0.00	0.00	0.00	5.19
169	171	4.873129	CCCATCCTCCGTGCGTCG	62.873	72.222	0.00	0.00	39.52	5.12
170	172	4.129737	CCATCCTCCGTGCGTCGT	62.130	66.667	0.00	0.00	37.94	4.34
171	173	2.126071	CATCCTCCGTGCGTCGTT	60.126	61.111	0.00	0.00	37.94	3.85
172	174	2.126071	ATCCTCCGTGCGTCGTTG	60.126	61.111	0.00	0.00	37.94	4.10
176	178	4.893601	TCCGTGCGTCGTTGCCAA	62.894	61.111	0.00	0.00	37.94	4.52
177	179	4.368808	CCGTGCGTCGTTGCCAAG	62.369	66.667	0.00	0.00	37.94	3.61
179	181	4.683334	GTGCGTCGTTGCCAAGCC	62.683	66.667	0.00	0.00	0.00	4.35
180	182	4.927782	TGCGTCGTTGCCAAGCCT	62.928	61.111	0.00	0.00	0.00	4.58
185	187	0.040067	GTCGTTGCCAAGCCTTTCTG	60.040	55.000	0.00	0.00	0.00	3.02
226	228	2.772739	CCCAAGGCAAGATCGACTG	58.227	57.895	0.00	0.00	0.00	3.51
243	245	3.252215	CGACTGGTATGAGGTTTGCAAAA	59.748	43.478	14.67	0.00	0.00	2.44
245	247	5.564651	CGACTGGTATGAGGTTTGCAAAAAT	60.565	40.000	14.67	5.17	0.00	1.82
247	249	5.990996	ACTGGTATGAGGTTTGCAAAAATTG	59.009	36.000	14.67	0.00	0.00	2.32
463	465	1.411977	CAGATCACACTCCTGCCTAGG	59.588	57.143	3.67	3.67	46.06	3.02
491	493	4.612932	GCTTGGAGCAAAGTTATCAGAG	57.387	45.455	0.00	0.00	41.89	3.35
562	564	7.016170	TGCATAGCATAGACCTAACCTATGAAA	59.984	37.037	19.90	11.19	43.69	2.69
570	572	7.130681	AGACCTAACCTATGAAAAGATCCAG	57.869	40.000	0.00	0.00	0.00	3.86
571	573	6.674419	AGACCTAACCTATGAAAAGATCCAGT	59.326	38.462	0.00	0.00	0.00	4.00
572	574	7.182930	AGACCTAACCTATGAAAAGATCCAGTT	59.817	37.037	0.00	0.00	0.00	3.16
573	575	8.388656	ACCTAACCTATGAAAAGATCCAGTTA	57.611	34.615	0.00	0.00	0.00	2.24
574	576	8.832735	ACCTAACCTATGAAAAGATCCAGTTAA	58.167	33.333	0.00	0.00	0.00	2.01
575	577	9.331282	CCTAACCTATGAAAAGATCCAGTTAAG	57.669	37.037	0.00	0.00	0.00	1.85
589	591	8.047310	AGATCCAGTTAAGTTAAATACCCAGTG	58.953	37.037	0.00	0.00	0.00	3.66
594	596	4.929146	AAGTTAAATACCCAGTGCTCCT	57.071	40.909	0.00	0.00	0.00	3.69
613	615	7.651704	GTGCTCCTAATCAAATAGAGAACTCTC	59.348	40.741	7.65	0.52	40.93	3.20
626	628	6.672266	AGAGAACTCTCAGTAATTGTTCCA	57.328	37.500	9.34	0.00	45.21	3.53
647	649	0.541863	AAGAGGTGAATGGGCCTACG	59.458	55.000	4.53	0.00	34.81	3.51
678	2718	1.957877	GTAGAGGAGATCGACCCTTGG	59.042	57.143	8.07	0.00	31.84	3.61
874	2933	1.668151	GAGTGGACGTGTGCCTTCC	60.668	63.158	0.00	0.00	0.00	3.46
983	3043	2.419011	ATTAAGCCACCACCACGCCA	62.419	55.000	0.00	0.00	0.00	5.69
1505	3573	2.225091	ACAGATTCCCAAGGTGATGCAA	60.225	45.455	0.00	0.00	0.00	4.08
1826	3921	6.209788	GGTCCTATTCTAGTCATCAAGGTAGG	59.790	46.154	0.00	0.00	0.00	3.18
1962	4088	0.962356	AAGATTGGTGCGAGCTTGGG	60.962	55.000	2.37	0.00	0.00	4.12
2133	4270	8.256611	TCAGATTTCACTAGCTTGTTATTGAC	57.743	34.615	0.00	0.00	0.00	3.18
2220	4357	3.895232	TGATCCAGAGCAAACTAGTCC	57.105	47.619	0.00	0.00	0.00	3.85
2406	4819	1.815003	GTTCCAGAGAAATGTGGCCAG	59.185	52.381	5.11	0.00	32.58	4.85
2588	5001	4.764050	TCTTCAGAACCACCTGTGTTTA	57.236	40.909	0.00	0.00	35.71	2.01
2603	5016	9.535878	CACCTGTGTTTATTTTTAGCCTTAAAA	57.464	29.630	0.00	0.00	37.06	1.52
2604	5017	9.537192	ACCTGTGTTTATTTTTAGCCTTAAAAC	57.463	29.630	0.00	0.00	38.21	2.43
2605	5018	9.758651	CCTGTGTTTATTTTTAGCCTTAAAACT	57.241	29.630	0.00	0.00	38.21	2.66
2625	5038	0.609957	CAATGCCTGAACCCAGCTCA	60.610	55.000	0.00	0.00	39.07	4.26
2671	5085	7.961326	AGCATGTGAAGTATATTTCCCTTTT	57.039	32.000	5.61	0.00	0.00	2.27
2676	5090	9.620259	ATGTGAAGTATATTTCCCTTTTCTCTC	57.380	33.333	5.61	0.00	0.00	3.20
2793	5209	5.484290	ACTGGTGCCTACAGTCTACTAAATT	59.516	40.000	0.00	0.00	45.50	1.82
2817	5235	1.774110	ACACACATTTGCAGTGGGAA	58.226	45.000	13.27	0.00	42.98	3.97
2902	5327	2.802787	ACTGTGACTCTCTTTGTCCG	57.197	50.000	0.00	0.00	33.83	4.79
2969	5396	2.297701	ACCAGCATCAACGTTCAAGTT	58.702	42.857	0.00	0.00	34.15	2.66
3031	5459	0.751643	AGTTCGTTTGGCACTTGGCT	60.752	50.000	4.25	0.00	44.01	4.75
3094	5524	4.454161	ACAAATCATCGTCGGTTTGATCAA	59.546	37.500	16.00	3.38	35.93	2.57
3158	5588	7.451255	AGAACCATCAAACTGTAATGGATTTCA	59.549	33.333	18.28	0.00	42.13	2.69
3220	5650	3.591977	AGTTTTAATGGTGTCTAGGGGCT	59.408	43.478	0.00	0.00	0.00	5.19
3447	8503	7.040478	TGACATTAAACAATAGCAAGAGCAAGT	60.040	33.333	0.00	0.00	45.49	3.16
3449	8505	8.454106	ACATTAAACAATAGCAAGAGCAAGTAG	58.546	33.333	0.00	0.00	45.49	2.57
3512	8568	6.144886	TCACATAACTGTCAAACGTACATGTC	59.855	38.462	0.00	0.00	31.62	3.06
3522	8578	5.228427	TCAAACGTACATGTCGTATCAATCG	59.772	40.000	18.95	7.76	40.69	3.34
3523	8579	3.624900	ACGTACATGTCGTATCAATCGG	58.375	45.455	17.73	0.00	39.78	4.18
3524	8580	3.313249	ACGTACATGTCGTATCAATCGGA	59.687	43.478	17.73	0.00	39.78	4.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.134371	GTGGGGAGTGAGTGAATAGGC	60.134	57.143	0.00	0.00	0.00	3.93
49	51	8.722342	TTTTTCACGAATATGTAAGAACTTGC	57.278	30.769	0.00	0.00	0.00	4.01
99	101	7.654923	TCTTCTGCATATCATCACTTACATGTC	59.345	37.037	0.00	0.00	0.00	3.06
162	164	4.683334	GGCTTGGCAACGACGCAC	62.683	66.667	10.75	0.00	42.51	5.34
163	165	4.927782	AGGCTTGGCAACGACGCA	62.928	61.111	10.75	0.00	42.51	5.24
164	166	3.194272	AAAGGCTTGGCAACGACGC	62.194	57.895	0.00	0.00	42.51	5.19
165	167	1.082104	GAAAGGCTTGGCAACGACG	60.082	57.895	0.00	0.00	42.51	5.12
166	168	0.040067	CAGAAAGGCTTGGCAACGAC	60.040	55.000	0.00	0.00	42.51	4.34
167	169	0.465460	ACAGAAAGGCTTGGCAACGA	60.465	50.000	0.00	0.00	42.51	3.85
168	170	0.318107	CACAGAAAGGCTTGGCAACG	60.318	55.000	0.00	0.00	42.51	4.10
169	171	0.032540	CCACAGAAAGGCTTGGCAAC	59.967	55.000	0.00	0.00	0.00	4.17
170	172	1.114722	CCCACAGAAAGGCTTGGCAA	61.115	55.000	0.00	0.00	0.00	4.52
171	173	1.531365	CCCACAGAAAGGCTTGGCA	60.531	57.895	0.00	0.00	0.00	4.92
172	174	2.935740	GCCCACAGAAAGGCTTGGC	61.936	63.158	0.00	4.15	46.14	4.52
173	175	3.369921	GCCCACAGAAAGGCTTGG	58.630	61.111	0.00	0.00	46.14	3.61
178	180	1.002087	AGTCGTTAGCCCACAGAAAGG	59.998	52.381	0.00	0.00	0.00	3.11
179	181	2.457366	AGTCGTTAGCCCACAGAAAG	57.543	50.000	0.00	0.00	0.00	2.62
180	182	2.762745	GAAGTCGTTAGCCCACAGAAA	58.237	47.619	0.00	0.00	0.00	2.52
223	225	5.806654	ATTTTTGCAAACCTCATACCAGT	57.193	34.783	12.39	0.00	0.00	4.00
243	245	1.103398	GCCCGCTGGTGATAGCAATT	61.103	55.000	0.00	0.00	43.87	2.32
245	247	2.124736	GCCCGCTGGTGATAGCAA	60.125	61.111	0.00	0.00	43.87	3.91
247	249	2.280457	GAGCCCGCTGGTGATAGC	60.280	66.667	0.00	0.00	40.29	2.97
408	410	0.542702	AAGTTGGGGTGCCAAGATGG	60.543	55.000	0.00	0.00	41.55	3.51
445	447	1.490574	ACCTAGGCAGGAGTGTGATC	58.509	55.000	9.30	0.00	45.91	2.92
485	487	0.041238	TCTTCGTGGTCCCCTCTGAT	59.959	55.000	0.00	0.00	0.00	2.90
489	491	1.292541	GTGTCTTCGTGGTCCCCTC	59.707	63.158	0.00	0.00	0.00	4.30
491	493	2.346365	GGTGTCTTCGTGGTCCCC	59.654	66.667	0.00	0.00	0.00	4.81
517	519	8.819974	GCTATGCATATTACAATTTTGTTTGCT	58.180	29.630	6.92	1.55	42.35	3.91
518	520	8.602328	TGCTATGCATATTACAATTTTGTTTGC	58.398	29.630	6.92	1.91	36.75	3.68
562	564	8.612145	ACTGGGTATTTAACTTAACTGGATCTT	58.388	33.333	0.00	0.00	0.00	2.40
570	572	6.178324	AGGAGCACTGGGTATTTAACTTAAC	58.822	40.000	0.00	0.00	0.00	2.01
571	573	6.382919	AGGAGCACTGGGTATTTAACTTAA	57.617	37.500	0.00	0.00	0.00	1.85
572	574	7.499200	TTAGGAGCACTGGGTATTTAACTTA	57.501	36.000	0.00	0.00	0.00	2.24
573	575	4.929146	AGGAGCACTGGGTATTTAACTT	57.071	40.909	0.00	0.00	0.00	2.66
574	576	6.157994	TGATTAGGAGCACTGGGTATTTAACT	59.842	38.462	0.00	0.00	0.00	2.24
575	577	6.354130	TGATTAGGAGCACTGGGTATTTAAC	58.646	40.000	0.00	0.00	0.00	2.01
589	591	7.721402	TGAGAGTTCTCTATTTGATTAGGAGC	58.279	38.462	10.27	0.00	43.25	4.70
626	628	2.618045	CGTAGGCCCATTCACCTCTTTT	60.618	50.000	0.00	0.00	37.50	2.27
647	649	6.858993	GTCGATCTCCTCTACATGTTCATAAC	59.141	42.308	2.30	0.00	0.00	1.89
839	2898	6.038936	CGTCCACTCTTTTCCCTTTTCTTTTA	59.961	38.462	0.00	0.00	0.00	1.52
874	2933	2.740055	GGATATGCGCGGCTGGAG	60.740	66.667	8.83	0.00	0.00	3.86
983	3043	1.418334	CATCGTCCCTGGGAAGAGAT	58.582	55.000	30.31	24.01	42.78	2.75
1788	3883	0.535335	TAGGACCGACAGCATTGACC	59.465	55.000	0.00	0.00	0.00	4.02
1826	3921	2.097629	GCAGAAAGAAAGGCGGTAATCC	59.902	50.000	0.00	0.00	0.00	3.01
1893	3988	0.753262	AAGCTCAGTTCAGACACCGT	59.247	50.000	0.00	0.00	0.00	4.83
1933	4059	1.453155	CACCAATCTTCAGGAACGGG	58.547	55.000	0.00	0.00	0.00	5.28
1962	4088	2.847441	ACGAGAAACCTTTCCCTGTTC	58.153	47.619	0.00	0.00	37.92	3.18
2220	4357	7.993183	AGAAAGGTACATACATAATTGTGGGAG	59.007	37.037	7.15	0.00	36.53	4.30
2406	4819	2.952978	TCCCTCGTGAAGAGCTTATCTC	59.047	50.000	0.00	0.00	45.54	2.75
2588	5001	7.603784	CAGGCATTGAGTTTTAAGGCTAAAAAT	59.396	33.333	0.00	0.00	38.43	1.82
2603	5016	0.610232	GCTGGGTTCAGGCATTGAGT	60.610	55.000	0.00	0.00	41.19	3.41
2604	5017	0.323178	AGCTGGGTTCAGGCATTGAG	60.323	55.000	0.00	0.00	41.19	3.02
2605	5018	0.322816	GAGCTGGGTTCAGGCATTGA	60.323	55.000	0.00	0.00	41.19	2.57
2606	5019	0.609957	TGAGCTGGGTTCAGGCATTG	60.610	55.000	0.00	0.00	41.19	2.82
2793	5209	3.818210	CCCACTGCAAATGTGTGTACTTA	59.182	43.478	4.13	0.00	33.92	2.24
2805	5223	3.096092	ACAAGAAAGTTCCCACTGCAAA	58.904	40.909	0.00	0.00	31.60	3.68
2817	5235	4.348168	ACATGTACTGGGAGACAAGAAAGT	59.652	41.667	0.00	0.00	0.00	2.66
2902	5327	5.529800	ACCACAAGTTGTGTATGACTTAACC	59.470	40.000	29.28	0.00	46.45	2.85
2969	5396	1.837439	AGGGATAGCACGAATTGGTCA	59.163	47.619	0.00	0.00	37.13	4.02
3031	5459	6.183361	TGCCCATCAGGATTCATACTAAATCA	60.183	38.462	0.00	0.00	38.24	2.57
3094	5524	7.604164	CAGTCCAGCCGTTATAATATTCAGATT	59.396	37.037	0.00	0.00	0.00	2.40
3110	5540	1.669115	CCACAAGACAGTCCAGCCG	60.669	63.158	0.00	0.00	0.00	5.52
3447	8503	4.095782	GTGGTTTCTGTCACAAGTTTGCTA	59.904	41.667	0.00	0.00	34.32	3.49
3449	8505	3.179048	GTGGTTTCTGTCACAAGTTTGC	58.821	45.455	0.00	0.00	34.32	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.