AutoCloner

Multiple sequence alignment - TraesCS1D01G080400

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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	TraesCS1D01G080400	chr1D	100.000	3121	0	0	1	3121	62888848	62891968	0.000000e+00	5764
1	TraesCS1D01G080400	chr1D	85.009	1114	146	17	1023	2128	63357075	63358175	0.000000e+00	1112
2	TraesCS1D01G080400	chr1D	83.743	1138	152	20	1022	2128	62935760	62936895	0.000000e+00	1046
3	TraesCS1D01G080400	chr1D	79.028	391	47	17	6	389	62871770	62872132	5.200000e-58	235
4	TraesCS1D01G080400	chr1B	92.564	2636	133	23	144	2732	100421427	100424046	0.000000e+00	3723
5	TraesCS1D01G080400	chr1B	84.182	1119	156	16	1022	2128	100631049	100632158	0.000000e+00	1066
6	TraesCS1D01G080400	chr1B	83.617	1117	160	19	1023	2128	101142998	101144102	0.000000e+00	1027
7	TraesCS1D01G080400	chr1B	95.477	398	18	0	2724	3121	100424229	100424626	1.220000e-178	636
8	TraesCS1D01G080400	chr1B	97.163	141	3	1	1	140	100421124	100421264	1.450000e-58	237
9	TraesCS1D01G080400	chr1B	79.518	332	44	14	63	390	100418683	100418994	6.780000e-52	215
10	TraesCS1D01G080400	chr1B	97.674	43	1	0	1205	1247	556064131	556064089	1.200000e-09	75
11	TraesCS1D01G080400	chr1B	88.710	62	5	2	1187	1247	556966465	556966525	1.200000e-09	75
12	TraesCS1D01G080400	chr1A	91.296	2160	145	23	6	2130	61008048	61010199	0.000000e+00	2907
13	TraesCS1D01G080400	chr1A	83.049	1115	169	13	1022	2128	61341184	61342286	0.000000e+00	994
14	TraesCS1D01G080400	chr1A	85.714	798	110	4	1326	2121	62254235	62253440	0.000000e+00	839
15	TraesCS1D01G080400	chr1A	84.368	838	125	4	1295	2128	61284467	61285302	0.000000e+00	817
16	TraesCS1D01G080400	chr1A	86.026	229	29	1	1023	1248	62254694	62254466	3.110000e-60	243
17	TraesCS1D01G080400	chr1A	92.568	148	11	0	2822	2969	61012647	61012794	2.440000e-51	213
18	TraesCS1D01G080400	chr1A	83.920	199	23	7	2224	2417	61011302	61011496	6.880000e-42	182
19	TraesCS1D01G080400	chr1A	79.182	269	31	13	6	271	61002341	61002587	2.490000e-36	163
20	TraesCS1D01G080400	chr4B	88.710	62	5	2	1187	1247	633399105	633399165	1.200000e-09	75
21	TraesCS1D01G080400	chr4B	88.710	62	5	2	1187	1247	633466237	633466297	1.200000e-09	75

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	TraesCS1D01G080400	chr1D	62888848	62891968	3120	False	5764.000000	5764	100.000000	1	3121	1	chr1D.!!$F2	3120
1	TraesCS1D01G080400	chr1D	63357075	63358175	1100	False	1112.000000	1112	85.009000	1023	2128	1	chr1D.!!$F4	1105
2	TraesCS1D01G080400	chr1D	62935760	62936895	1135	False	1046.000000	1046	83.743000	1022	2128	1	chr1D.!!$F3	1106
3	TraesCS1D01G080400	chr1B	100418683	100424626	5943	False	1202.750000	3723	91.180500	1	3121	4	chr1B.!!$F4	3120
4	TraesCS1D01G080400	chr1B	100631049	100632158	1109	False	1066.000000	1066	84.182000	1022	2128	1	chr1B.!!$F1	1106
5	TraesCS1D01G080400	chr1B	101142998	101144102	1104	False	1027.000000	1027	83.617000	1023	2128	1	chr1B.!!$F2	1105
6	TraesCS1D01G080400	chr1A	61008048	61012794	4746	False	1100.666667	2907	89.261333	6	2969	3	chr1A.!!$F4	2963
7	TraesCS1D01G080400	chr1A	61341184	61342286	1102	False	994.000000	994	83.049000	1022	2128	1	chr1A.!!$F3	1106
8	TraesCS1D01G080400	chr1A	61284467	61285302	835	False	817.000000	817	84.368000	1295	2128	1	chr1A.!!$F2	833
9	TraesCS1D01G080400	chr1A	62253440	62254694	1254	True	541.000000	839	85.870000	1023	2121	2	chr1A.!!$R1	1098

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
570	3181	0.309922	CTCCACCATGCATGATTCGC	59.690	55.0	28.31	0.0	0.00	4.70	F
975	3607	0.597568	CGAGCACCTGCCATCAAAAA	59.402	50.0	0.00	0.0	43.38	1.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1400	4192	0.536460	CACGTAGGCTGGGGTTGTTT	60.536	55.000	0.0	0.0	0.00	2.83	R
2179	4973	1.203052	CTGCCAGTCCATCGCAAAAAT	59.797	47.619	0.0	0.0	30.85	1.82	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
60	2503	4.329545	ACGTTGGTGCATCCGGCT	62.330	61.111	0.00	0.00	45.15	5.52
140	2583	8.309656	TGGAGAATAGTACATGCATCTATCAAG	58.690	37.037	0.00	0.00	0.00	3.02
196	2798	5.955961	ATTTTGGCATGCCTAAAAGGTAT	57.044	34.783	37.77	24.30	41.64	2.73
197	2799	5.753721	TTTTGGCATGCCTAAAAGGTATT	57.246	34.783	34.38	0.00	38.73	1.89
198	2800	4.734398	TTGGCATGCCTAAAAGGTATTG	57.266	40.909	35.53	0.00	38.73	1.90
199	2801	3.707316	TGGCATGCCTAAAAGGTATTGT	58.293	40.909	35.53	0.00	38.73	2.71
200	2802	4.861196	TGGCATGCCTAAAAGGTATTGTA	58.139	39.130	35.53	8.95	38.73	2.41
201	2803	5.454062	TGGCATGCCTAAAAGGTATTGTAT	58.546	37.500	35.53	0.00	38.73	2.29
234	2843	8.174733	AGCAAGTCTTAAAGCATTGCATATAT	57.825	30.769	11.91	0.00	46.66	0.86
328	2937	4.897670	TCTCATAATCTGACTCATCTGCCA	59.102	41.667	0.00	0.00	0.00	4.92
330	2939	5.363101	TCATAATCTGACTCATCTGCCAAC	58.637	41.667	0.00	0.00	0.00	3.77
356	2965	3.537580	TCCACAAGTAACCTTCACACAC	58.462	45.455	0.00	0.00	0.00	3.82
400	3010	2.774007	CGACTGTTTCGCCAATGATTC	58.226	47.619	0.00	0.00	41.87	2.52
441	3051	4.470602	TGGTCGGATAGATAGTGACACAT	58.529	43.478	8.59	0.00	0.00	3.21
528	3138	2.293677	CTCGCTATGGAGTACGGACAAT	59.706	50.000	0.00	0.00	0.00	2.71
529	3139	2.292569	TCGCTATGGAGTACGGACAATC	59.707	50.000	0.00	0.00	0.00	2.67
570	3181	0.309922	CTCCACCATGCATGATTCGC	59.690	55.000	28.31	0.00	0.00	4.70
583	3194	1.217001	GATTCGCGCATCATACACCA	58.783	50.000	13.97	0.00	0.00	4.17
590	3201	2.095567	GCGCATCATACACCATCCATTC	60.096	50.000	0.30	0.00	0.00	2.67
692	3310	1.071814	ACGCTTACGAAAAGGCCCA	59.928	52.632	0.00	0.00	43.93	5.36
834	3458	5.595952	TGCATGCATATATAAACACCAACCA	59.404	36.000	18.46	0.00	0.00	3.67
839	3463	8.988546	TGCATATATAAACACCAACCAGTATT	57.011	30.769	0.00	0.00	0.00	1.89
974	3606	1.865788	GCGAGCACCTGCCATCAAAA	61.866	55.000	0.00	0.00	43.38	2.44
975	3607	0.597568	CGAGCACCTGCCATCAAAAA	59.402	50.000	0.00	0.00	43.38	1.94
998	3630	1.339727	GGCCATTAGTGAACCTTCGGT	60.340	52.381	0.00	0.00	37.65	4.69
1745	4539	1.437573	CTCCTTCACGCAGCGGATA	59.562	57.895	21.15	0.12	0.00	2.59
1850	4644	1.276138	TCCACAGACAACATGAGCGAT	59.724	47.619	0.00	0.00	0.00	4.58
2144	4938	8.137745	AGACCATCACCACAAATTTATTCATT	57.862	30.769	0.00	0.00	0.00	2.57
2147	4941	8.373981	ACCATCACCACAAATTTATTCATTTGA	58.626	29.630	12.05	0.00	43.99	2.69
2161	4955	6.710597	ATTCATTTGATTGATGGGAGACTG	57.289	37.500	0.00	0.00	0.00	3.51
2171	4965	3.266772	TGATGGGAGACTGGCAGTTAATT	59.733	43.478	22.98	8.06	0.00	1.40
2174	4968	5.249780	TGGGAGACTGGCAGTTAATTTTA	57.750	39.130	22.98	2.89	0.00	1.52
2177	4971	7.406916	TGGGAGACTGGCAGTTAATTTTATTA	58.593	34.615	22.98	0.00	0.00	0.98
2179	4973	9.569122	GGGAGACTGGCAGTTAATTTTATTATA	57.431	33.333	22.98	0.00	0.00	0.98
2311	6143	7.870954	ACACGAGTGTATAATTCAGAAGAACAA	59.129	33.333	7.14	0.00	42.90	2.83
2400	6237	5.726688	GCACGAGCGAGCAATATTTAAGAAA	60.727	40.000	7.40	0.00	0.00	2.52
2473	6960	0.816825	CCAAGATGGCATCCGGAGTG	60.817	60.000	23.33	13.25	0.00	3.51
2533	7064	0.321653	AAACGCTAGTTGGGCCTGAG	60.322	55.000	4.53	0.00	41.05	3.35
2537	7068	1.808133	CGCTAGTTGGGCCTGAGATTC	60.808	57.143	4.53	0.00	0.00	2.52
2652	7189	4.051922	GTGTATCTAGACCCATTTCAGCG	58.948	47.826	0.00	0.00	0.00	5.18
2987	7872	1.275856	CAGATCAGAGCATAGAGGGCC	59.724	57.143	0.00	0.00	0.00	5.80
2994	7879	2.310052	AGAGCATAGAGGGCCAAAAAGT	59.690	45.455	6.18	0.00	0.00	2.66
3059	7944	7.836479	TTCAACCAATATGAATGATGCCATA	57.164	32.000	0.00	0.00	32.10	2.74
3066	7951	7.982224	CAATATGAATGATGCCATAGTGGTAG	58.018	38.462	0.00	0.00	40.46	3.18
3081	7966	2.416547	GTGGTAGAAGTAGTGACGCGTA	59.583	50.000	13.97	0.00	0.00	4.42
3097	7982	2.412716	CGCGTAAGTGCAATGTGTGATT	60.413	45.455	0.00	0.00	43.07	2.57
3106	7991	2.030363	GCAATGTGTGATTTTCGGTCCA	60.030	45.455	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.998106	GAATTATGTACATCACCCTACATAACT	57.002	33.333	12.68	2.88	43.57	2.24
1	2	9.998106	AGAATTATGTACATCACCCTACATAAC	57.002	33.333	12.68	2.88	43.57	1.89
3	4	9.996554	CAAGAATTATGTACATCACCCTACATA	57.003	33.333	12.68	0.00	35.60	2.29
4	5	7.939039	CCAAGAATTATGTACATCACCCTACAT	59.061	37.037	12.68	0.00	37.37	2.29
60	2503	7.354257	GGTTTACACTTTGCTAATTCGTTGTA	58.646	34.615	0.00	0.00	0.00	2.41
109	2552	4.780815	TGCATGTACTATTCTCCAAAGGG	58.219	43.478	0.00	0.00	0.00	3.95
177	2779	4.093011	ACAATACCTTTTAGGCATGCCAA	58.907	39.130	37.18	25.09	39.63	4.52
178	2780	3.707316	ACAATACCTTTTAGGCATGCCA	58.293	40.909	37.18	20.88	39.63	4.92
179	2781	7.519032	TTATACAATACCTTTTAGGCATGCC	57.481	36.000	30.12	30.12	39.63	4.40
196	2798	9.872757	CTTTAAGACTTGCTTTCGTTTATACAA	57.127	29.630	0.00	0.00	38.05	2.41
197	2799	8.013378	GCTTTAAGACTTGCTTTCGTTTATACA	58.987	33.333	0.00	0.00	38.05	2.29
198	2800	8.013378	TGCTTTAAGACTTGCTTTCGTTTATAC	58.987	33.333	0.00	0.00	38.05	1.47
199	2801	8.090250	TGCTTTAAGACTTGCTTTCGTTTATA	57.910	30.769	0.00	0.00	38.05	0.98
200	2802	6.966021	TGCTTTAAGACTTGCTTTCGTTTAT	58.034	32.000	0.00	0.00	38.05	1.40
201	2803	6.366315	TGCTTTAAGACTTGCTTTCGTTTA	57.634	33.333	0.00	0.00	38.05	2.01
234	2843	6.322969	AGTCGTGTGGGTTTGTATGATCTATA	59.677	38.462	0.00	0.00	0.00	1.31
237	2846	3.260884	AGTCGTGTGGGTTTGTATGATCT	59.739	43.478	0.00	0.00	0.00	2.75
238	2847	3.596214	AGTCGTGTGGGTTTGTATGATC	58.404	45.455	0.00	0.00	0.00	2.92
239	2848	3.260884	AGAGTCGTGTGGGTTTGTATGAT	59.739	43.478	0.00	0.00	0.00	2.45
240	2849	2.631062	AGAGTCGTGTGGGTTTGTATGA	59.369	45.455	0.00	0.00	0.00	2.15
328	2937	7.012989	GTGTGAAGGTTACTTGTGGAAATAGTT	59.987	37.037	0.00	0.00	36.97	2.24
330	2939	6.485313	TGTGTGAAGGTTACTTGTGGAAATAG	59.515	38.462	0.00	0.00	36.97	1.73
356	2965	6.183360	CGTATTAACAGCTAACAGAAAAGGGG	60.183	42.308	0.00	0.00	0.00	4.79
441	3051	2.435234	GGTGGCCGACATTACGCA	60.435	61.111	0.00	0.00	0.00	5.24
528	3138	4.553938	GCAAATCAACGTCTTTTCTTCCGA	60.554	41.667	0.00	0.00	0.00	4.55
529	3139	3.664025	GCAAATCAACGTCTTTTCTTCCG	59.336	43.478	0.00	0.00	0.00	4.30
570	3181	2.158254	CGAATGGATGGTGTATGATGCG	59.842	50.000	0.00	0.00	0.00	4.73
590	3201	3.250323	CACGCATCTCGAGGCACG	61.250	66.667	13.56	15.43	41.67	5.34
692	3310	8.232913	TCTTTTCACCTAACAGCAAATAAACT	57.767	30.769	0.00	0.00	0.00	2.66
808	3431	5.703978	TGGTGTTTATATATGCATGCACC	57.296	39.130	25.37	15.75	43.70	5.01
834	3458	5.513233	AGTTGATGGCCAAATGAGAATACT	58.487	37.500	10.96	0.37	36.36	2.12
839	3463	3.438216	TGAGTTGATGGCCAAATGAGA	57.562	42.857	10.96	0.00	36.36	3.27
974	3606	0.696501	AGGTTCACTAATGGCCGGTT	59.303	50.000	1.90	0.00	0.00	4.44
975	3607	0.696501	AAGGTTCACTAATGGCCGGT	59.303	50.000	1.90	0.00	0.00	5.28
998	3630	1.141665	CATGGCGACGACCTCATGA	59.858	57.895	0.00	0.00	39.27	3.07
1400	4192	0.536460	CACGTAGGCTGGGGTTGTTT	60.536	55.000	0.00	0.00	0.00	2.83
1745	4539	1.006102	CTCGCCGGAGAAGTTGTGT	60.006	57.895	9.83	0.00	43.27	3.72
1775	4569	1.183030	ACTTGTCGATGGACGGGTCA	61.183	55.000	3.26	0.00	46.49	4.02
2069	4863	1.373059	GATCTCCCCTTCATCGCCC	59.627	63.158	0.00	0.00	0.00	6.13
2144	4938	1.634973	TGCCAGTCTCCCATCAATCAA	59.365	47.619	0.00	0.00	0.00	2.57
2147	4941	1.293062	ACTGCCAGTCTCCCATCAAT	58.707	50.000	0.00	0.00	0.00	2.57
2171	4965	7.865385	GCCAGTCCATCGCAAAAATATAATAAA	59.135	33.333	0.00	0.00	0.00	1.40
2174	4968	5.301551	TGCCAGTCCATCGCAAAAATATAAT	59.698	36.000	0.00	0.00	0.00	1.28
2177	4971	3.023119	TGCCAGTCCATCGCAAAAATAT	58.977	40.909	0.00	0.00	0.00	1.28
2179	4973	1.203052	CTGCCAGTCCATCGCAAAAAT	59.797	47.619	0.00	0.00	30.85	1.82
2311	6143	9.632638	AGCAAGAAATAGTATCCATGTACATTT	57.367	29.630	5.37	0.00	0.00	2.32
2425	6262	2.158579	TGGTAGGGGTTTCCAAACAGAC	60.159	50.000	4.63	0.00	40.63	3.51
2473	6960	3.510531	AAGGAGAAACTTTGTCCCCTC	57.489	47.619	12.96	0.00	43.81	4.30
2533	7064	4.083484	CCTTGGTAAACACACCTTCGAATC	60.083	45.833	0.00	0.00	39.50	2.52
2537	7068	1.877443	CCCTTGGTAAACACACCTTCG	59.123	52.381	0.00	0.00	39.50	3.79
2617	7149	7.435305	GGTCTAGATACACTAATTTCAGGGAC	58.565	42.308	0.00	0.00	0.00	4.46
2629	7161	4.202161	CGCTGAAATGGGTCTAGATACACT	60.202	45.833	0.00	0.00	0.00	3.55
2685	7222	7.556275	TGCTTATTTATTACTCCCTCTGTTTGG	59.444	37.037	0.00	0.00	0.00	3.28
2715	7252	1.583404	GCGCAACACTTTTGTTCACAG	59.417	47.619	0.30	0.00	44.57	3.66
2717	7254	1.623359	TGCGCAACACTTTTGTTCAC	58.377	45.000	8.16	0.00	44.57	3.18
2978	7863	2.919602	TGGAGACTTTTTGGCCCTCTAT	59.080	45.455	0.00	0.00	0.00	1.98
2987	7872	4.202010	ACGTGAATGGTTGGAGACTTTTTG	60.202	41.667	0.00	0.00	0.00	2.44
2994	7879	2.875933	GTTGAACGTGAATGGTTGGAGA	59.124	45.455	0.00	0.00	0.00	3.71
3055	7940	4.497674	GCGTCACTACTTCTACCACTATGG	60.498	50.000	0.00	0.00	45.02	2.74
3059	7944	1.467734	CGCGTCACTACTTCTACCACT	59.532	52.381	0.00	0.00	0.00	4.00
3066	7951	1.647702	GCACTTACGCGTCACTACTTC	59.352	52.381	18.63	0.00	0.00	3.01
3081	7966	3.068024	ACCGAAAATCACACATTGCACTT	59.932	39.130	0.00	0.00	0.00	3.16
3090	7975	2.616842	ACAACTGGACCGAAAATCACAC	59.383	45.455	0.00	0.00	0.00	3.82
3097	7982	1.673920	GCAAGAACAACTGGACCGAAA	59.326	47.619	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.