AutoCloner

Multiple sequence alignment - TraesCS1B01G060300

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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	TraesCS1B01G060300	chr1B	100.000	2939	0	0	1	2939	43640795	43637857	0.000000e+00	5428
1	TraesCS1B01G060300	chr1B	99.304	862	6	0	2078	2939	540391238	540392099	0.000000e+00	1559
2	TraesCS1B01G060300	chr1D	89.417	2145	95	48	527	2612	27851345	27853416	0.000000e+00	2582
3	TraesCS1B01G060300	chr1D	86.523	512	15	17	2	503	27850811	27851278	5.620000e-142	514
4	TraesCS1B01G060300	chr1A	86.268	2425	125	81	533	2845	28717948	28715620	0.000000e+00	2442
5	TraesCS1B01G060300	chr1A	83.571	280	16	14	193	468	28718584	28718331	4.900000e-58	235
6	TraesCS1B01G060300	chr1A	92.754	138	4	2	2	133	28718745	28718608	8.310000e-46	195
7	TraesCS1B01G060300	chr3A	99.536	862	4	0	2078	2939	307493541	307492680	0.000000e+00	1570
8	TraesCS1B01G060300	chr3B	99.420	862	4	1	2078	2939	736041452	736042312	0.000000e+00	1563
9	TraesCS1B01G060300	chr6B	99.306	864	4	1	2078	2939	27522188	27521325	0.000000e+00	1561
10	TraesCS1B01G060300	chr6B	99.188	862	7	0	2078	2939	653268146	653269007	0.000000e+00	1554
11	TraesCS1B01G060300	chr7B	99.304	862	6	0	2078	2939	249980521	249981382	0.000000e+00	1559
12	TraesCS1B01G060300	chr7A	99.304	862	6	0	2078	2939	41354647	41355508	0.000000e+00	1559
13	TraesCS1B01G060300	chr5B	99.304	862	6	0	2078	2939	508916369	508917230	0.000000e+00	1559

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	TraesCS1B01G060300	chr1B	43637857	43640795	2938	True	5428.000000	5428	100.000	1	2939	1	chr1B.!!$R1	2938
1	TraesCS1B01G060300	chr1B	540391238	540392099	861	False	1559.000000	1559	99.304	2078	2939	1	chr1B.!!$F1	861
2	TraesCS1B01G060300	chr1D	27850811	27853416	2605	False	1548.000000	2582	87.970	2	2612	2	chr1D.!!$F1	2610
3	TraesCS1B01G060300	chr1A	28715620	28718745	3125	True	957.333333	2442	87.531	2	2845	3	chr1A.!!$R1	2843
4	TraesCS1B01G060300	chr3A	307492680	307493541	861	True	1570.000000	1570	99.536	2078	2939	1	chr3A.!!$R1	861
5	TraesCS1B01G060300	chr3B	736041452	736042312	860	False	1563.000000	1563	99.420	2078	2939	1	chr3B.!!$F1	861
6	TraesCS1B01G060300	chr6B	27521325	27522188	863	True	1561.000000	1561	99.306	2078	2939	1	chr6B.!!$R1	861
7	TraesCS1B01G060300	chr6B	653268146	653269007	861	False	1554.000000	1554	99.188	2078	2939	1	chr6B.!!$F1	861
8	TraesCS1B01G060300	chr7B	249980521	249981382	861	False	1559.000000	1559	99.304	2078	2939	1	chr7B.!!$F1	861
9	TraesCS1B01G060300	chr7A	41354647	41355508	861	False	1559.000000	1559	99.304	2078	2939	1	chr7A.!!$F1	861
10	TraesCS1B01G060300	chr5B	508916369	508917230	861	False	1559.000000	1559	99.304	2078	2939	1	chr5B.!!$F1	861

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
876	1275	0.458716	GTGCTGCGTTCCTCCTCTAC	60.459	60.0	0.0	0.0	0.0	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2857	3364	3.769844	TCCAACTGTTCCAGGTATCTCTC	59.23	47.826	0.0	0.0	35.51	3.2	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
156	166	2.505006	CTGCTGCTGCTAGAGGGG	59.495	66.667	17.00	0.00	40.48	4.79
262	277	1.263217	CGTGCCGTCTTAAAAACTGCT	59.737	47.619	5.90	0.00	0.00	4.24
336	353	3.394836	GGCGTCCTCCCTCTGCTT	61.395	66.667	0.00	0.00	0.00	3.91
337	354	2.125350	GCGTCCTCCCTCTGCTTG	60.125	66.667	0.00	0.00	0.00	4.01
338	355	2.125350	CGTCCTCCCTCTGCTTGC	60.125	66.667	0.00	0.00	0.00	4.01
339	356	2.270527	GTCCTCCCTCTGCTTGCC	59.729	66.667	0.00	0.00	0.00	4.52
340	357	3.393970	TCCTCCCTCTGCTTGCCG	61.394	66.667	0.00	0.00	0.00	5.69
380	400	4.021104	CCTATCATACCGTCACATCATGGT	60.021	45.833	0.00	0.00	39.21	3.55
415	435	2.290134	CGGAGCAGATGGATGGATCATT	60.290	50.000	0.00	0.00	0.00	2.57
434	454	6.339587	TCATTGGAAACATTTCTTGGTACC	57.660	37.500	4.43	4.43	42.32	3.34
504	574	1.374190	CACTGCTTCCACTGCCTCT	59.626	57.895	0.00	0.00	0.00	3.69
515	585	1.552337	CACTGCCTCTGGACTGTACAT	59.448	52.381	0.00	0.00	0.00	2.29
518	588	3.449018	ACTGCCTCTGGACTGTACATTAG	59.551	47.826	0.00	0.00	0.00	1.73
520	590	2.103263	GCCTCTGGACTGTACATTAGGG	59.897	54.545	18.31	9.05	0.00	3.53
525	595	4.028131	CTGGACTGTACATTAGGGGTACA	58.972	47.826	0.00	5.41	46.37	2.90
532	602	5.920903	TGTACATTAGGGGTACATACAAGC	58.079	41.667	0.00	0.00	44.39	4.01
533	603	5.664006	TGTACATTAGGGGTACATACAAGCT	59.336	40.000	0.00	0.00	44.39	3.74
587	959	3.350219	AAATAGCTACACCACACCCTG	57.650	47.619	0.00	0.00	0.00	4.45
595	967	0.674895	CACCACACCCTGCTAGCTTC	60.675	60.000	17.23	0.00	0.00	3.86
600	972	0.528684	CACCCTGCTAGCTTCGCTAC	60.529	60.000	17.23	0.00	40.44	3.58
630	1005	7.278875	AGGATATTTTAGGAAGTTGCTCAGAG	58.721	38.462	0.00	0.00	0.00	3.35
643	1018	2.626266	TGCTCAGAGGTCTACGAAAACA	59.374	45.455	0.00	0.00	0.00	2.83
656	1031	9.148104	GGTCTACGAAAACAAAGTTCAGTATAT	57.852	33.333	0.00	0.00	0.00	0.86
695	1070	7.902917	GCACAAAGTTGAAAGGACAAAAATAAC	59.097	33.333	0.00	0.00	0.00	1.89
696	1071	8.930760	CACAAAGTTGAAAGGACAAAAATAACA	58.069	29.630	0.00	0.00	0.00	2.41
717	1092	1.140589	CCAAGCAGAGCGAGACGAT	59.859	57.895	0.00	0.00	0.00	3.73
719	1094	1.140589	AAGCAGAGCGAGACGATGG	59.859	57.895	0.00	0.00	0.00	3.51
728	1103	1.098129	CGAGACGATGGAGGCAGAGA	61.098	60.000	0.00	0.00	0.00	3.10
874	1273	2.659610	GTGCTGCGTTCCTCCTCT	59.340	61.111	0.00	0.00	0.00	3.69
875	1274	1.605058	GGTGCTGCGTTCCTCCTCTA	61.605	60.000	0.00	0.00	0.00	2.43
876	1275	0.458716	GTGCTGCGTTCCTCCTCTAC	60.459	60.000	0.00	0.00	0.00	2.59
877	1276	1.142097	GCTGCGTTCCTCCTCTACC	59.858	63.158	0.00	0.00	0.00	3.18
878	1277	1.324005	GCTGCGTTCCTCCTCTACCT	61.324	60.000	0.00	0.00	0.00	3.08
879	1278	2.022754	GCTGCGTTCCTCCTCTACCTA	61.023	57.143	0.00	0.00	0.00	3.08
975	1392	4.675303	CTCTCCCCACCCCACCCA	62.675	72.222	0.00	0.00	0.00	4.51
1057	1485	0.031314	CATCGACATGGACCTCTCCG	59.969	60.000	0.00	0.00	39.88	4.63
1104	1532	2.095252	GTTCGAGTTCCAGAGCGCC	61.095	63.158	2.29	0.00	0.00	6.53
1313	1744	2.580867	GCCTAGTGTGAGCGCGAG	60.581	66.667	12.10	0.00	0.00	5.03
1873	2328	3.917760	GGATCTCCACCTCCGCCG	61.918	72.222	0.00	0.00	35.64	6.46
1874	2329	3.148279	GATCTCCACCTCCGCCGT	61.148	66.667	0.00	0.00	0.00	5.68
1875	2330	3.432051	GATCTCCACCTCCGCCGTG	62.432	68.421	0.00	0.00	0.00	4.94
1940	2402	0.534652	GAGATGTGCAGGGGATGAGC	60.535	60.000	0.00	0.00	0.00	4.26
1943	2405	1.992519	ATGTGCAGGGGATGAGCCTC	61.993	60.000	0.00	0.00	37.44	4.70
1945	2407	3.157252	GCAGGGGATGAGCCTCGA	61.157	66.667	0.00	0.00	44.30	4.04
1958	2420	6.128007	GGATGAGCCTCGAATGTTTTCTTTTA	60.128	38.462	0.00	0.00	0.00	1.52
1959	2421	6.817765	TGAGCCTCGAATGTTTTCTTTTAT	57.182	33.333	0.00	0.00	0.00	1.40
1960	2422	7.214467	TGAGCCTCGAATGTTTTCTTTTATT	57.786	32.000	0.00	0.00	0.00	1.40
1989	2454	4.956075	TCCCTTCTTTCTTTCTGCTTTTGT	59.044	37.500	0.00	0.00	0.00	2.83
1990	2455	5.045872	CCCTTCTTTCTTTCTGCTTTTGTG	58.954	41.667	0.00	0.00	0.00	3.33
2033	2498	4.018490	TGAGCAATGTGCCTGTGAATTAT	58.982	39.130	0.00	0.00	46.52	1.28
2066	2531	9.189723	GGAATCAAGAACTTCTCTTTGATTTTG	57.810	33.333	14.37	0.00	41.97	2.44
2067	2532	8.585189	AATCAAGAACTTCTCTTTGATTTTGC	57.415	30.769	9.85	0.00	41.97	3.68
2069	2534	6.322201	TCAAGAACTTCTCTTTGATTTTGCCT	59.678	34.615	0.00	0.00	41.97	4.75
2072	2537	8.237811	AGAACTTCTCTTTGATTTTGCCTTTA	57.762	30.769	0.00	0.00	0.00	1.85
2073	2538	8.864087	AGAACTTCTCTTTGATTTTGCCTTTAT	58.136	29.630	0.00	0.00	0.00	1.40
2144	2616	5.314529	TGTTCTACTACTAGCTGTGTGACT	58.685	41.667	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.483916	AGCTTTTTAATGCGGTAAGTAATTTTT	57.516	25.926	0.00	0.00	34.59	1.94
56	60	0.322456	TGGGCCTTCATTGTTCTCGG	60.322	55.000	4.53	0.00	0.00	4.63
140	150	3.085947	CCCCCTCTAGCAGCAGCA	61.086	66.667	3.17	0.00	45.49	4.41
156	166	2.230750	ACGTACTACACAAAGCTCTCCC	59.769	50.000	0.00	0.00	0.00	4.30
158	168	5.294050	ACTACGTACTACACAAAGCTCTC	57.706	43.478	0.00	0.00	0.00	3.20
159	169	5.936956	AGTACTACGTACTACACAAAGCTCT	59.063	40.000	12.88	0.00	45.99	4.09
160	170	6.175712	AGTACTACGTACTACACAAAGCTC	57.824	41.667	12.88	0.00	45.99	4.09
161	171	7.099764	TCTAGTACTACGTACTACACAAAGCT	58.900	38.462	12.88	0.00	45.99	3.74
162	172	7.295952	TCTAGTACTACGTACTACACAAAGC	57.704	40.000	12.88	0.00	45.99	3.51
166	176	9.489084	TTCTTTTCTAGTACTACGTACTACACA	57.511	33.333	12.88	2.49	45.99	3.72
182	192	4.152580	GGACGGTGAGCTTTTCTTTTCTAG	59.847	45.833	0.00	0.00	0.00	2.43
183	193	4.062991	GGACGGTGAGCTTTTCTTTTCTA	58.937	43.478	0.00	0.00	0.00	2.10
184	194	2.879026	GGACGGTGAGCTTTTCTTTTCT	59.121	45.455	0.00	0.00	0.00	2.52
262	277	0.250295	CAAAAGACGGCCAGGACTGA	60.250	55.000	2.24	0.00	0.00	3.41
292	307	1.949525	GCGTCCGGTGATAGGTAGTAA	59.050	52.381	0.00	0.00	0.00	2.24
293	308	1.141657	AGCGTCCGGTGATAGGTAGTA	59.858	52.381	0.00	0.00	0.00	1.82
294	309	0.106819	AGCGTCCGGTGATAGGTAGT	60.107	55.000	0.00	0.00	0.00	2.73
295	310	1.534595	GTAGCGTCCGGTGATAGGTAG	59.465	57.143	0.00	0.00	0.00	3.18
320	337	2.125350	CAAGCAGAGGGAGGACGC	60.125	66.667	0.00	0.00	0.00	5.19
322	339	2.270527	GGCAAGCAGAGGGAGGAC	59.729	66.667	0.00	0.00	0.00	3.85
404	424	6.475596	AGAAATGTTTCCAATGATCCATCC	57.524	37.500	2.04	0.00	37.92	3.51
434	454	1.473258	TCCAATTCAATTCGGCCAGG	58.527	50.000	2.24	0.00	0.00	4.45
504	574	4.063851	TGTACCCCTAATGTACAGTCCA	57.936	45.455	0.00	0.00	42.58	4.02
595	967	5.297547	TCCTAAAATATCCTTGCAGTAGCG	58.702	41.667	0.00	0.00	46.23	4.26
600	972	6.096001	AGCAACTTCCTAAAATATCCTTGCAG	59.904	38.462	0.00	0.00	35.11	4.41
630	1005	5.729974	ACTGAACTTTGTTTTCGTAGACC	57.270	39.130	0.00	0.00	34.32	3.85
658	1033	9.431887	CCTTTCAACTTTGTGCTTATACTAGTA	57.568	33.333	4.77	4.77	0.00	1.82
659	1034	8.154856	TCCTTTCAACTTTGTGCTTATACTAGT	58.845	33.333	0.00	0.00	0.00	2.57
660	1035	8.443937	GTCCTTTCAACTTTGTGCTTATACTAG	58.556	37.037	0.00	0.00	0.00	2.57
661	1036	7.934665	TGTCCTTTCAACTTTGTGCTTATACTA	59.065	33.333	0.00	0.00	0.00	1.82
662	1037	6.770785	TGTCCTTTCAACTTTGTGCTTATACT	59.229	34.615	0.00	0.00	0.00	2.12
663	1038	6.966021	TGTCCTTTCAACTTTGTGCTTATAC	58.034	36.000	0.00	0.00	0.00	1.47
664	1039	7.575414	TTGTCCTTTCAACTTTGTGCTTATA	57.425	32.000	0.00	0.00	0.00	0.98
665	1040	6.463995	TTGTCCTTTCAACTTTGTGCTTAT	57.536	33.333	0.00	0.00	0.00	1.73
695	1070	1.375140	TCTCGCTCTGCTTGGCTTG	60.375	57.895	0.00	0.00	0.00	4.01
696	1071	1.375268	GTCTCGCTCTGCTTGGCTT	60.375	57.895	0.00	0.00	0.00	4.35
717	1092	1.361204	TGGAAATGTCTCTGCCTCCA	58.639	50.000	0.00	0.00	0.00	3.86
719	1094	5.184671	AGAAAATTGGAAATGTCTCTGCCTC	59.815	40.000	0.00	0.00	0.00	4.70
874	1273	3.206412	TCGGGGTTGGTTAGGTATAGGTA	59.794	47.826	0.00	0.00	0.00	3.08
875	1274	2.023113	TCGGGGTTGGTTAGGTATAGGT	60.023	50.000	0.00	0.00	0.00	3.08
876	1275	2.366590	GTCGGGGTTGGTTAGGTATAGG	59.633	54.545	0.00	0.00	0.00	2.57
877	1276	2.035066	CGTCGGGGTTGGTTAGGTATAG	59.965	54.545	0.00	0.00	0.00	1.31
878	1277	2.031120	CGTCGGGGTTGGTTAGGTATA	58.969	52.381	0.00	0.00	0.00	1.47
879	1278	0.826062	CGTCGGGGTTGGTTAGGTAT	59.174	55.000	0.00	0.00	0.00	2.73
975	1392	1.247567	CACCGGAATCTGCAACCTTT	58.752	50.000	9.46	0.00	0.00	3.11
1057	1485	3.521796	GCATTTGGGCGAGGAGGC	61.522	66.667	0.00	0.00	45.91	4.70
1134	1565	3.107975	TAGGCCGCCTCCTCCCTA	61.108	66.667	17.40	0.00	37.66	3.53
1352	1783	3.718210	GAGTACCTCTTGGCGCCCG	62.718	68.421	26.77	15.72	36.63	6.13
1620	2072	4.176851	GAGGACGAGGCGGACGAC	62.177	72.222	8.47	0.00	34.70	4.34
1960	2422	5.893824	AGCAGAAAGAAAGAAGGGAGAAAAA	59.106	36.000	0.00	0.00	0.00	1.94
2033	2498	6.595682	AGAGAAGTTCTTGATTCCTCACAAA	58.404	36.000	6.88	0.00	29.61	2.83
2066	2531	5.591877	AGAGATGAACATGGACAATAAAGGC	59.408	40.000	0.00	0.00	0.00	4.35
2067	2532	7.555554	AGAAGAGATGAACATGGACAATAAAGG	59.444	37.037	0.00	0.00	0.00	3.11
2069	2534	8.868522	AAGAAGAGATGAACATGGACAATAAA	57.131	30.769	0.00	0.00	0.00	1.40
2072	2537	6.479006	TGAAGAAGAGATGAACATGGACAAT	58.521	36.000	0.00	0.00	0.00	2.71
2073	2538	5.868454	TGAAGAAGAGATGAACATGGACAA	58.132	37.500	0.00	0.00	0.00	3.18
2144	2616	6.009589	TGGTGGAAGCATTCTTGATCTTTTA	58.990	36.000	0.00	0.00	46.56	1.52
2857	3364	3.769844	TCCAACTGTTCCAGGTATCTCTC	59.230	47.826	0.00	0.00	35.51	3.20
2910	3417	1.599542	GTGGCTTTGTCAGTGACTCAC	59.400	52.381	23.29	17.49	33.15	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.