AutoCloner

Multiple sequence alignment - TraesCS7B01G248300

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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	TraesCS7B01G248300	chr7B	100.000	3547	0	0	1	3547	458613857	458610311	0.000000e+00	6551
1	TraesCS7B01G248300	chr7D	93.661	3581	140	35	1	3540	441983602	441980068	0.000000e+00	5275
2	TraesCS7B01G248300	chr7D	95.480	177	8	0	3371	3547	486068386	486068210	2.080000e-72	283
3	TraesCS7B01G248300	chr7D	95.480	177	7	1	3371	3547	59421710	59421535	7.500000e-72	281
4	TraesCS7B01G248300	chr7D	95.480	177	7	1	3371	3547	553802868	553803043	7.500000e-72	281
5	TraesCS7B01G248300	chr7A	92.651	1660	79	22	1046	2696	492782096	492780471	0.000000e+00	2350
6	TraesCS7B01G248300	chr7A	85.472	826	54	28	122	923	492782932	492782149	0.000000e+00	800
7	TraesCS7B01G248300	chr7A	84.817	764	77	17	2644	3372	191278410	191279169	0.000000e+00	732
8	TraesCS7B01G248300	chr7A	91.228	456	29	2	2917	3372	492780033	492779589	8.420000e-171	610
9	TraesCS7B01G248300	chr7A	80.469	512	47	29	191	656	492819662	492819158	3.390000e-90	342
10	TraesCS7B01G248300	chr7A	88.930	271	26	2	2730	2996	492780257	492779987	7.340000e-87	331
11	TraesCS7B01G248300	chr5D	84.751	682	88	12	2630	3303	461851610	461852283	0.000000e+00	669
12	TraesCS7B01G248300	chr5D	96.045	177	6	1	3371	3547	45695601	45695776	1.610000e-73	287
13	TraesCS7B01G248300	chr3B	85.736	645	53	10	2630	3237	753796027	753795385	0.000000e+00	645
14	TraesCS7B01G248300	chrUn	83.104	728	66	23	2700	3372	22351766	22351041	8.420000e-171	610
15	TraesCS7B01G248300	chrUn	87.387	555	39	9	2712	3237	442311884	442312436	3.030000e-170	608
16	TraesCS7B01G248300	chr2A	81.609	783	95	23	2634	3372	115142340	115143117	1.410000e-168	603
17	TraesCS7B01G248300	chr4D	89.827	462	43	2	2914	3371	356320322	356320783	1.100000e-164	590
18	TraesCS7B01G248300	chr2D	81.511	741	96	18	2670	3372	113511396	113512133	3.970000e-159	571
19	TraesCS7B01G248300	chr3D	95.480	177	8	0	3371	3547	532362175	532361999	2.080000e-72	283
20	TraesCS7B01G248300	chr3D	95.480	177	7	1	3371	3547	363100601	363100776	7.500000e-72	281
21	TraesCS7B01G248300	chr6D	95.480	177	7	1	3371	3547	312976505	312976330	7.500000e-72	281
22	TraesCS7B01G248300	chr6A	95.480	177	7	1	3371	3547	134154737	134154912	7.500000e-72	281
23	TraesCS7B01G248300	chr1D	79.295	227	36	11	2636	2856	411045117	411045338	7.930000e-32	148

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	TraesCS7B01G248300	chr7B	458610311	458613857	3546	True	6551.00	6551	100.00000	1	3547	1	chr7B.!!$R1	3546
1	TraesCS7B01G248300	chr7D	441980068	441983602	3534	True	5275.00	5275	93.66100	1	3540	1	chr7D.!!$R2	3539
2	TraesCS7B01G248300	chr7A	492779589	492782932	3343	True	1022.75	2350	89.57025	122	3372	4	chr7A.!!$R2	3250
3	TraesCS7B01G248300	chr7A	191278410	191279169	759	False	732.00	732	84.81700	2644	3372	1	chr7A.!!$F1	728
4	TraesCS7B01G248300	chr7A	492819158	492819662	504	True	342.00	342	80.46900	191	656	1	chr7A.!!$R1	465
5	TraesCS7B01G248300	chr5D	461851610	461852283	673	False	669.00	669	84.75100	2630	3303	1	chr5D.!!$F2	673
6	TraesCS7B01G248300	chr3B	753795385	753796027	642	True	645.00	645	85.73600	2630	3237	1	chr3B.!!$R1	607
7	TraesCS7B01G248300	chrUn	22351041	22351766	725	True	610.00	610	83.10400	2700	3372	1	chrUn.!!$R1	672
8	TraesCS7B01G248300	chrUn	442311884	442312436	552	False	608.00	608	87.38700	2712	3237	1	chrUn.!!$F1	525
9	TraesCS7B01G248300	chr2A	115142340	115143117	777	False	603.00	603	81.60900	2634	3372	1	chr2A.!!$F1	738
10	TraesCS7B01G248300	chr2D	113511396	113512133	737	False	571.00	571	81.51100	2670	3372	1	chr2D.!!$F1	702

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
176	177	0.694444	ACTAGCATCCCCCGGATTGT	60.694	55.0	0.73	0.0	39.79	2.71	F
1061	1125	0.603569	ATATAGGGACCGAGCTTGCG	59.396	55.0	0.00	0.0	0.00	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1660	1728	0.034670	GCTTCCTGGTGATGAGCCTT	60.035	55.0	0.0	0.0	0.0	4.35	R
2844	3131	0.035439	TCCTGCCCTTTTGATCGTCC	60.035	55.0	0.0	0.0	0.0	4.79	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
28	29	3.138468	GGGGTAGCTCCTGAAATACCAAT	59.862	47.826	0.00	0.00	39.59	3.16
31	32	6.174049	GGGTAGCTCCTGAAATACCAATATC	58.826	44.000	0.00	0.00	39.59	1.63
83	84	7.875554	ACAATACATATGTCAATATACGGTGCA	59.124	33.333	12.68	0.00	0.00	4.57
91	92	2.218953	ATATACGGTGCAAGGTGTCG	57.781	50.000	0.00	0.00	0.00	4.35
169	170	6.879458	CACTTTAATACATACTAGCATCCCCC	59.121	42.308	0.00	0.00	0.00	5.40
176	177	0.694444	ACTAGCATCCCCCGGATTGT	60.694	55.000	0.73	0.00	39.79	2.71
186	187	2.621526	CCCCCGGATTGTAGCATTTTAC	59.378	50.000	0.73	0.00	0.00	2.01
188	189	3.283751	CCCGGATTGTAGCATTTTACCA	58.716	45.455	0.73	0.00	0.00	3.25
225	226	5.644977	AAGGGCATTACTCACTTTTTAGC	57.355	39.130	0.00	0.00	0.00	3.09
278	292	6.817765	TTCCAAATGATAGGTTTGTCACTC	57.182	37.500	0.00	0.00	35.35	3.51
372	392	6.325596	TGAGATAGAAACTGATCACAGAACG	58.674	40.000	0.00	0.00	46.03	3.95
400	421	1.248101	AAACCCCTTGCATGCGTACC	61.248	55.000	14.09	0.00	0.00	3.34
410	431	3.081061	TGCATGCGTACCTTCTCAAAAT	58.919	40.909	14.09	0.00	0.00	1.82
461	492	7.512992	ACATCCATCCTTGAGTTTATCTTAGG	58.487	38.462	0.00	0.00	32.82	2.69
502	550	5.009110	TGAGCATCACGGAAAAATACACAAA	59.991	36.000	0.00	0.00	42.56	2.83
511	559	5.108405	CGGAAAAATACACAAACAGAAAGCG	60.108	40.000	0.00	0.00	0.00	4.68
564	612	4.934356	TCCAAAATGGAAAGCTGTATCCT	58.066	39.130	13.00	0.00	45.00	3.24
566	614	4.463891	CCAAAATGGAAAGCTGTATCCTGT	59.536	41.667	13.00	2.05	40.96	4.00
567	615	5.652014	CCAAAATGGAAAGCTGTATCCTGTA	59.348	40.000	13.00	0.00	40.96	2.74
582	630	4.271696	TCCTGTATGTATGTATGCAGCC	57.728	45.455	0.00	0.00	38.83	4.85
624	679	2.357517	CCCAGACGGCTCACACAC	60.358	66.667	0.00	0.00	0.00	3.82
721	785	2.829914	GCATGCATGGCCGGAGAA	60.830	61.111	27.34	0.00	0.00	2.87
726	790	2.768492	GCATGGCCGGAGAAGCAAG	61.768	63.158	5.05	0.00	0.00	4.01
828	892	8.026607	CGCATCCAGACCTTTTTAAGATTTTAA	58.973	33.333	0.00	0.00	0.00	1.52
829	893	9.875691	GCATCCAGACCTTTTTAAGATTTTAAT	57.124	29.630	0.00	0.00	0.00	1.40
912	976	1.656652	AGCAATGGACAGATACGTGC	58.343	50.000	0.00	0.00	0.00	5.34
923	987	1.202463	AGATACGTGCTGCTAAGGCTG	60.202	52.381	0.00	0.00	39.59	4.85
934	998	0.798776	CTAAGGCTGAAGCAACACGG	59.201	55.000	4.43	0.00	44.36	4.94
973	1037	3.460825	GCATCCCCTGGGTCCTATATAA	58.539	50.000	12.71	0.00	36.47	0.98
1022	1086	0.742281	CTCATCGCAACCCACCTCTG	60.742	60.000	0.00	0.00	0.00	3.35
1031	1095	1.001641	CCCACCTCTGGCTTCCAAG	60.002	63.158	0.00	0.00	36.00	3.61
1036	1100	2.503356	CACCTCTGGCTTCCAAGTCTAT	59.497	50.000	0.00	0.00	30.80	1.98
1037	1101	3.706594	CACCTCTGGCTTCCAAGTCTATA	59.293	47.826	0.00	0.00	30.80	1.31
1038	1102	3.707102	ACCTCTGGCTTCCAAGTCTATAC	59.293	47.826	0.00	0.00	30.80	1.47
1039	1103	3.706594	CCTCTGGCTTCCAAGTCTATACA	59.293	47.826	0.00	0.00	30.80	2.29
1040	1104	4.346418	CCTCTGGCTTCCAAGTCTATACAT	59.654	45.833	0.00	0.00	30.80	2.29
1041	1105	5.540337	CCTCTGGCTTCCAAGTCTATACATA	59.460	44.000	0.00	0.00	30.80	2.29
1042	1106	6.042093	CCTCTGGCTTCCAAGTCTATACATAA	59.958	42.308	0.00	0.00	30.80	1.90
1043	1107	7.256475	CCTCTGGCTTCCAAGTCTATACATAAT	60.256	40.741	0.00	0.00	30.80	1.28
1044	1108	8.721133	TCTGGCTTCCAAGTCTATACATAATA	57.279	34.615	0.00	0.00	30.80	0.98
1061	1125	0.603569	ATATAGGGACCGAGCTTGCG	59.396	55.000	0.00	0.00	0.00	4.85
1069	1133	2.429069	CGAGCTTGCGGTTTTGCC	60.429	61.111	0.00	0.00	0.00	4.52
1083	1147	3.320826	GGTTTTGCCAAGGTAACACATCT	59.679	43.478	8.18	0.00	36.50	2.90
1084	1148	4.521256	GGTTTTGCCAAGGTAACACATCTA	59.479	41.667	8.18	0.00	36.50	1.98
1085	1149	5.335661	GGTTTTGCCAAGGTAACACATCTAG	60.336	44.000	8.18	0.00	36.50	2.43
1097	1161	6.864165	GGTAACACATCTAGTATCTGCTTAGC	59.136	42.308	0.00	0.00	0.00	3.09
1174	1242	2.803479	TGCGTGCATGCAAACACA	59.197	50.000	30.70	15.07	43.02	3.72
1335	1403	4.593864	GGAGATGGAGGCGACGGC	62.594	72.222	14.41	14.41	38.90	5.68
1789	1866	4.728102	CGCTACGTGCCGGTTCCA	62.728	66.667	1.90	0.00	38.78	3.53
1799	1876	1.238625	GCCGGTTCCATTTCCGTTCA	61.239	55.000	1.90	0.00	44.51	3.18
1827	1904	2.653702	GATAGGAGCCGCAGCGAT	59.346	61.111	18.75	3.86	46.67	4.58
1945	2022	6.147821	GTGAAAACTCTGCTGCTGAAACTATA	59.852	38.462	10.47	0.00	0.00	1.31
2008	2085	2.976490	GCCCACTGTCCATCCTGCT	61.976	63.158	0.00	0.00	0.00	4.24
2225	2302	0.980754	TGGTGAGAGTGTGGTGGTGT	60.981	55.000	0.00	0.00	0.00	4.16
2238	2315	0.664166	GTGGTGTCGCAAAGCAATGG	60.664	55.000	0.00	0.00	0.00	3.16
2273	2350	2.618816	GGTGCAGATGGGATGTTTCTGA	60.619	50.000	3.47	0.00	39.36	3.27
2314	2391	1.079127	CCTGATGTTTCCCGACGCT	60.079	57.895	0.00	0.00	0.00	5.07
2802	3064	4.260990	CGCTACCAAAAAGACACATGTTCA	60.261	41.667	0.00	0.00	0.00	3.18
2844	3131	3.785505	GCGATTGAACATAGCCAAAGTCG	60.786	47.826	0.00	0.00	31.68	4.18
2983	3282	3.653009	GCGCAGTTGCAGTGCTCA	61.653	61.111	17.60	0.00	42.22	4.26
3137	3502	0.809385	TTCCTCTTCTTCGCGACGAT	59.191	50.000	16.53	0.00	35.23	3.73
3508	3875	1.346365	GAAGCGTTATGACAGCACGA	58.654	50.000	12.21	0.00	35.93	4.35
3540	3907	2.728922	GTATGTCTTCACGATCCGACC	58.271	52.381	0.00	0.00	0.00	4.79
3541	3908	0.100682	ATGTCTTCACGATCCGACCG	59.899	55.000	0.00	0.00	0.00	4.79
3542	3909	0.956902	TGTCTTCACGATCCGACCGA	60.957	55.000	0.00	0.00	0.00	4.69
3543	3910	0.381089	GTCTTCACGATCCGACCGAT	59.619	55.000	0.00	0.00	0.00	4.18
3544	3911	0.661552	TCTTCACGATCCGACCGATC	59.338	55.000	0.00	0.00	43.58	3.69
3545	3912	0.317938	CTTCACGATCCGACCGATCC	60.318	60.000	0.00	0.00	44.07	3.36
3546	3913	0.750546	TTCACGATCCGACCGATCCT	60.751	55.000	0.00	0.00	44.07	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.711547	GGTATTTCAGGAGCTACCCCAT	59.288	50.000	0.00	0.00	40.05	4.00
62	63	5.700832	CCTTGCACCGTATATTGACATATGT	59.299	40.000	8.43	8.43	0.00	2.29
70	71	2.284150	CGACACCTTGCACCGTATATTG	59.716	50.000	0.00	0.00	0.00	1.90
83	84	0.528470	GAGTCAGCTAGCGACACCTT	59.472	55.000	28.68	15.94	35.77	3.50
160	161	2.056906	GCTACAATCCGGGGGATGCT	62.057	60.000	0.00	0.00	42.27	3.79
169	170	4.955925	TGTGGTAAAATGCTACAATCCG	57.044	40.909	0.00	0.00	0.00	4.18
176	177	9.015367	TGCTAGTATTTTTGTGGTAAAATGCTA	57.985	29.630	14.49	14.49	43.75	3.49
186	187	4.021544	TGCCCTTTGCTAGTATTTTTGTGG	60.022	41.667	0.00	0.00	42.00	4.17
188	189	6.358974	AATGCCCTTTGCTAGTATTTTTGT	57.641	33.333	0.00	0.00	42.00	2.83
251	252	8.650490	AGTGACAAACCTATCATTTGGAATTTT	58.350	29.630	2.84	0.00	40.64	1.82
255	256	6.542821	AGAGTGACAAACCTATCATTTGGAA	58.457	36.000	2.84	0.00	40.64	3.53
278	292	0.890996	AACTTTGGCGCCCTCTCAAG	60.891	55.000	26.77	19.04	0.00	3.02
372	392	0.176449	GCAAGGGGTTTGATCCATGC	59.824	55.000	0.00	0.00	39.21	4.06
400	421	6.317857	GTTTGCTAGCCACTATTTTGAGAAG	58.682	40.000	13.29	0.00	0.00	2.85
461	492	3.949754	TGCTCAAGGATGGATGTTTCATC	59.050	43.478	1.60	1.60	40.02	2.92
464	495	3.949754	TGATGCTCAAGGATGGATGTTTC	59.050	43.478	0.00	0.00	0.00	2.78
502	550	1.548973	CGTTCACTCGCGCTTTCTGT	61.549	55.000	5.56	0.00	0.00	3.41
511	559	1.999051	CATACAGCCGTTCACTCGC	59.001	57.895	0.00	0.00	0.00	5.03
564	612	5.246883	AGAGATGGCTGCATACATACATACA	59.753	40.000	0.50	0.00	0.00	2.29
566	614	6.364568	AAGAGATGGCTGCATACATACATA	57.635	37.500	0.50	0.00	0.00	2.29
567	615	4.904895	AGAGATGGCTGCATACATACAT	57.095	40.909	0.50	0.00	0.00	2.29
582	630	2.278857	CGACGCCGGGAAGAGATG	60.279	66.667	2.18	0.00	0.00	2.90
702	766	3.896133	CTCCGGCCATGCATGCAC	61.896	66.667	25.37	14.61	0.00	4.57
705	769	2.842256	GCTTCTCCGGCCATGCATG	61.842	63.158	20.19	20.19	0.00	4.06
707	771	3.565961	TTGCTTCTCCGGCCATGCA	62.566	57.895	2.24	2.48	0.00	3.96
721	785	1.968540	GCAGCGTTCTTCCCTTGCT	60.969	57.895	0.00	0.00	36.05	3.91
726	790	1.016653	GTCTCTGCAGCGTTCTTCCC	61.017	60.000	9.47	0.00	0.00	3.97
912	976	1.198637	GTGTTGCTTCAGCCTTAGCAG	59.801	52.381	4.69	0.00	46.95	4.24
923	987	1.523758	ATGAACTCCCGTGTTGCTTC	58.476	50.000	0.00	0.00	0.00	3.86
929	993	0.249398	GCCAGTATGAACTCCCGTGT	59.751	55.000	0.00	0.00	39.69	4.49
934	998	1.312815	GCCATGCCAGTATGAACTCC	58.687	55.000	0.00	0.00	39.69	3.85
973	1037	3.322466	CACGAGGAGGGTGGCCTT	61.322	66.667	3.32	0.00	35.44	4.35
1031	1095	7.720515	AGCTCGGTCCCTATATTATGTATAGAC	59.279	40.741	7.98	0.00	30.99	2.59
1036	1100	5.105473	GCAAGCTCGGTCCCTATATTATGTA	60.105	44.000	0.00	0.00	0.00	2.29
1037	1101	4.322801	GCAAGCTCGGTCCCTATATTATGT	60.323	45.833	0.00	0.00	0.00	2.29
1038	1102	4.184629	GCAAGCTCGGTCCCTATATTATG	58.815	47.826	0.00	0.00	0.00	1.90
1039	1103	3.119101	CGCAAGCTCGGTCCCTATATTAT	60.119	47.826	0.00	0.00	0.00	1.28
1040	1104	2.230508	CGCAAGCTCGGTCCCTATATTA	59.769	50.000	0.00	0.00	0.00	0.98
1041	1105	1.000955	CGCAAGCTCGGTCCCTATATT	59.999	52.381	0.00	0.00	0.00	1.28
1042	1106	0.603569	CGCAAGCTCGGTCCCTATAT	59.396	55.000	0.00	0.00	0.00	0.86
1043	1107	1.461091	CCGCAAGCTCGGTCCCTATA	61.461	60.000	5.70	0.00	44.18	1.31
1044	1108	2.797278	CCGCAAGCTCGGTCCCTAT	61.797	63.158	5.70	0.00	44.18	2.57
1061	1125	3.320826	AGATGTGTTACCTTGGCAAAACC	59.679	43.478	9.98	3.81	39.84	3.27
1069	1133	6.810911	AGCAGATACTAGATGTGTTACCTTG	58.189	40.000	0.00	0.00	0.00	3.61
1083	1147	6.381420	AGAAGAACCAAGCTAAGCAGATACTA	59.619	38.462	0.00	0.00	0.00	1.82
1084	1148	5.188751	AGAAGAACCAAGCTAAGCAGATACT	59.811	40.000	0.00	0.00	0.00	2.12
1085	1149	5.423886	AGAAGAACCAAGCTAAGCAGATAC	58.576	41.667	0.00	0.00	0.00	2.24
1174	1242	1.606313	CCCCATCACCCTGCGTTTT	60.606	57.895	0.00	0.00	0.00	2.43
1335	1403	0.457166	TATGCGGTCGTTGAAGTCCG	60.457	55.000	0.00	0.00	43.70	4.79
1660	1728	0.034670	GCTTCCTGGTGATGAGCCTT	60.035	55.000	0.00	0.00	0.00	4.35
1945	2022	2.841988	GGAGGAGGCGGAGATGCT	60.842	66.667	0.00	0.00	34.52	3.79
2008	2085	2.163818	AAGCGCACAAGTAGTAAGCA	57.836	45.000	11.47	0.00	35.19	3.91
2225	2302	1.007502	GCACACCATTGCTTTGCGA	60.008	52.632	0.00	0.00	39.59	5.10
2238	2315	0.890542	TGCACCATCTTCCTGCACAC	60.891	55.000	0.00	0.00	36.00	3.82
2314	2391	1.028905	CCACCAACGGAAAAAGCTCA	58.971	50.000	0.00	0.00	0.00	4.26
2666	2744	0.597377	CAAACGCACAAAGGCCTTCC	60.597	55.000	20.79	6.89	0.00	3.46
2802	3064	1.091771	CGACCTTTGGCATGATCGCT	61.092	55.000	0.00	0.00	0.00	4.93
2844	3131	0.035439	TCCTGCCCTTTTGATCGTCC	60.035	55.000	0.00	0.00	0.00	4.79
2983	3282	2.901840	CACTGCCACGCCAACACT	60.902	61.111	0.00	0.00	0.00	3.55
3137	3502	0.679505	CGACCTTCTCAGGACCAACA	59.320	55.000	0.00	0.00	44.19	3.33
3508	3875	5.971792	CGTGAAGACATACGACTACATCAAT	59.028	40.000	0.00	0.00	42.54	2.57
3523	3890	0.956902	TCGGTCGGATCGTGAAGACA	60.957	55.000	10.85	0.00	35.49	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.