AutoCloner

Multiple sequence alignment - TraesCS2D01G294300

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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	TraesCS2D01G294300	chr2D	100.000	2694	0	0	1	2694	376619801	376622494	0.000000e+00	4975
1	TraesCS2D01G294300	chr2D	74.290	599	107	32	1932	2521	83048110	83048670	2.720000e-50	209
2	TraesCS2D01G294300	chr2D	75.248	404	77	14	2130	2521	596576076	596575684	1.280000e-38	171
3	TraesCS2D01G294300	chr2B	93.552	1706	76	11	695	2371	448079843	448081543	0.000000e+00	2510
4	TraesCS2D01G294300	chr2B	88.950	362	36	2	309	666	448076868	448077229	6.840000e-121	444
5	TraesCS2D01G294300	chr2B	89.041	292	26	4	1	287	448073970	448074260	9.170000e-95	357
6	TraesCS2D01G294300	chr2B	92.308	91	5	2	2604	2694	448081627	448081715	7.830000e-26	128
7	TraesCS2D01G294300	chr2A	89.994	1599	99	26	644	2208	510301325	510302896	0.000000e+00	2010
8	TraesCS2D01G294300	chr2A	83.801	463	54	14	2236	2694	510302892	510303337	1.150000e-113	420
9	TraesCS2D01G294300	chr2A	75.042	601	116	21	1932	2515	777533208	777533791	5.760000e-62	248
10	TraesCS2D01G294300	chr5B	77.165	635	83	28	38	646	557276318	557275720	2.010000e-81	313
11	TraesCS2D01G294300	chr5B	75.080	626	123	18	1932	2539	294124960	294125570	7.400000e-66	261
12	TraesCS2D01G294300	chr5B	74.950	499	104	16	1932	2425	697983250	697982768	2.720000e-50	209
13	TraesCS2D01G294300	chr1D	76.000	600	114	19	1932	2515	389330474	389331059	1.580000e-72	283
14	TraesCS2D01G294300	chr1B	75.908	606	115	21	1932	2521	47628533	47627943	5.680000e-72	281
15	TraesCS2D01G294300	chr1B	75.285	526	110	15	1932	2452	269218262	269218772	1.610000e-57	233
16	TraesCS2D01G294300	chr6A	75.394	634	115	28	1952	2567	116861135	116861745	4.420000e-68	268
17	TraesCS2D01G294300	chrUn	75.365	617	115	22	1942	2539	46070234	46069636	2.060000e-66	263
18	TraesCS2D01G294300	chr5A	75.084	598	115	23	1932	2521	669121190	669120619	5.760000e-62	248
19	TraesCS2D01G294300	chr6D	75.615	488	96	17	1932	2413	315652523	315652993	1.260000e-53	220
20	TraesCS2D01G294300	chr3D	75.403	496	101	15	1932	2422	533718409	533718888	1.260000e-53	220
21	TraesCS2D01G294300	chr3D	79.845	258	48	4	1932	2187	389256355	389256610	4.580000e-43	185
22	TraesCS2D01G294300	chr3A	75.101	494	106	12	1932	2422	158355397	158355876	5.840000e-52	215
23	TraesCS2D01G294300	chr6B	77.385	283	58	6	1932	2211	153401369	153401090	2.150000e-36	163

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	TraesCS2D01G294300	chr2D	376619801	376622494	2693	False	4975.00	4975	100.00000	1	2694	1	chr2D.!!$F2	2693
1	TraesCS2D01G294300	chr2D	83048110	83048670	560	False	209.00	209	74.29000	1932	2521	1	chr2D.!!$F1	589
2	TraesCS2D01G294300	chr2B	448073970	448081715	7745	False	859.75	2510	90.96275	1	2694	4	chr2B.!!$F1	2693
3	TraesCS2D01G294300	chr2A	510301325	510303337	2012	False	1215.00	2010	86.89750	644	2694	2	chr2A.!!$F2	2050
4	TraesCS2D01G294300	chr2A	777533208	777533791	583	False	248.00	248	75.04200	1932	2515	1	chr2A.!!$F1	583
5	TraesCS2D01G294300	chr5B	557275720	557276318	598	True	313.00	313	77.16500	38	646	1	chr5B.!!$R1	608
6	TraesCS2D01G294300	chr5B	294124960	294125570	610	False	261.00	261	75.08000	1932	2539	1	chr5B.!!$F1	607
7	TraesCS2D01G294300	chr1D	389330474	389331059	585	False	283.00	283	76.00000	1932	2515	1	chr1D.!!$F1	583
8	TraesCS2D01G294300	chr1B	47627943	47628533	590	True	281.00	281	75.90800	1932	2521	1	chr1B.!!$R1	589
9	TraesCS2D01G294300	chr1B	269218262	269218772	510	False	233.00	233	75.28500	1932	2452	1	chr1B.!!$F1	520
10	TraesCS2D01G294300	chr6A	116861135	116861745	610	False	268.00	268	75.39400	1952	2567	1	chr6A.!!$F1	615
11	TraesCS2D01G294300	chrUn	46069636	46070234	598	True	263.00	263	75.36500	1942	2539	1	chrUn.!!$R1	597
12	TraesCS2D01G294300	chr5A	669120619	669121190	571	True	248.00	248	75.08400	1932	2521	1	chr5A.!!$R1	589

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
308	335	0.6207	ACTTCCATCGGGGCTACCTT	60.621	55.0	0.0	0.0	36.97	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1921	7193	1.658994	TCCGCAAAAAGTATAGGCCG	58.341	50.0	0.0	0.0	0.0	6.13	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
30	31	7.706179	CCCCTTTGCAACAAATATAGTGTTATG	59.294	37.037	0.00	0.00	37.09	1.90
31	32	8.250332	CCCTTTGCAACAAATATAGTGTTATGT	58.750	33.333	0.00	0.00	37.09	2.29
43	44	2.000447	GTGTTATGTTCGGTCCTCTGC	59.000	52.381	0.00	0.00	0.00	4.26
45	46	2.236146	TGTTATGTTCGGTCCTCTGCAT	59.764	45.455	0.00	0.00	0.00	3.96
72	73	2.694628	AGGCTTGTTGCAATCACTCAAA	59.305	40.909	0.59	0.00	45.15	2.69
98	108	6.521151	AATTCTTTCTGAAACATGGCCTAG	57.479	37.500	3.32	0.00	38.29	3.02
166	178	2.029844	GTCACAGTTGAGAGCCGCC	61.030	63.158	0.00	0.00	30.10	6.13
244	266	4.883354	GAGCCATGGGAAGCCGGG	62.883	72.222	15.13	0.00	0.00	5.73
283	305	1.472552	CCATGGCGGACATAGTCGAAA	60.473	52.381	0.00	0.00	37.84	3.46
308	335	0.620700	ACTTCCATCGGGGCTACCTT	60.621	55.000	0.00	0.00	36.97	3.50
336	2944	1.037030	CCCCATGCTATGCAACGGTT	61.037	55.000	0.00	0.00	43.62	4.44
405	3013	2.401766	GGGCGTGAGGTGCATTGAG	61.402	63.158	0.00	0.00	0.00	3.02
418	3026	2.827322	TGCATTGAGGATGTGAAAAGGG	59.173	45.455	0.00	0.00	38.07	3.95
447	3055	0.899717	ATGTGTGGATGGTTGGTGGC	60.900	55.000	0.00	0.00	0.00	5.01
480	3088	6.042437	TCTGCATTGAGGATGTGTCTATACAT	59.958	38.462	0.00	0.00	43.61	2.29
497	3105	2.985896	ACATCATGGACCGTAACAAGG	58.014	47.619	0.00	0.00	0.00	3.61
500	3108	2.193127	TCATGGACCGTAACAAGGGAT	58.807	47.619	0.00	0.00	0.00	3.85
574	3195	0.676466	TTGCCTGCCGTTCGATCAAT	60.676	50.000	0.00	0.00	0.00	2.57
592	3214	0.991920	ATCTTGGATTGGACGGGTGT	59.008	50.000	0.00	0.00	0.00	4.16
672	3297	8.810652	TTGCTAAAGCGAAAGATAAATTTGTT	57.189	26.923	0.00	0.00	45.83	2.83
686	3311	8.184192	AGATAAATTTGTTATTTCAGCACCTCG	58.816	33.333	0.00	0.00	0.00	4.63
849	6058	4.096003	ACATCAGGAACGGCCCCG	62.096	66.667	4.96	4.96	46.03	5.73
884	6093	2.664851	CGTTTGCTCTCGCCACCA	60.665	61.111	0.00	0.00	34.43	4.17
998	6207	1.630244	CGCAGCACACCAGCTTAGAC	61.630	60.000	0.00	0.00	43.70	2.59
1130	6342	3.749665	TTTTTCTGGCACCCATTTGAG	57.250	42.857	0.00	0.00	30.82	3.02
1242	6489	2.159043	AGGATCACCTGCATGACGTAAG	60.159	50.000	0.00	0.00	45.92	2.34
1481	6728	3.003173	CTCGCCCACTTCCCCTCA	61.003	66.667	0.00	0.00	0.00	3.86
1510	6757	0.034059	CTCCAGTCGCAGTTCTGGTT	59.966	55.000	10.37	0.00	45.05	3.67
1533	6780	2.486592	GGATAAACCCAAACCACTCGTG	59.513	50.000	0.00	0.00	0.00	4.35
1581	6853	5.245977	ACTTGGGGTTTGATTCTGGTTAATG	59.754	40.000	0.00	0.00	0.00	1.90
1710	6982	9.871238	CCAGAAGTAGTGAATTAACTAGCTTTA	57.129	33.333	2.61	0.00	33.35	1.85
1725	6997	7.739954	AACTAGCTTTAGTTCATGCATGTGCA	61.740	38.462	25.43	10.44	44.79	4.57
1740	7012	0.108138	GTGCATCGTCCTTAGGCTGT	60.108	55.000	0.00	0.00	0.00	4.40
1887	7159	5.164061	GCACAAAACTGAGTTCAACAACAAG	60.164	40.000	0.00	0.00	34.60	3.16
1888	7160	5.920273	CACAAAACTGAGTTCAACAACAAGT	59.080	36.000	0.00	0.00	34.68	3.16
1900	7172	8.355913	AGTTCAACAACAAGTACTACTACTACC	58.644	37.037	0.00	0.00	34.60	3.18
1901	7173	6.902341	TCAACAACAAGTACTACTACTACCG	58.098	40.000	0.00	0.00	32.46	4.02
1908	7180	6.071728	ACAAGTACTACTACTACCGCAACAAT	60.072	38.462	0.00	0.00	32.46	2.71
1921	7193	3.672867	CCGCAACAATAATTTGTCACCAC	59.327	43.478	0.00	0.00	45.30	4.16
2063	7339	1.222115	GGAGCGAGTCAAAAGTGCGT	61.222	55.000	0.00	0.00	0.00	5.24
2105	7381	3.194116	TCATCAGAATTGGGCAAGCTTTC	59.806	43.478	0.00	0.00	0.00	2.62
2149	7425	3.482436	TGTCGTGCTAAAATCCCAAAGT	58.518	40.909	0.00	0.00	0.00	2.66
2195	7471	3.375299	GCCAACAATGAAGAGAAGCGTAT	59.625	43.478	0.00	0.00	0.00	3.06
2214	7490	5.587844	GCGTATATCGGAAGGATCTAACCTA	59.412	44.000	0.00	0.00	38.49	3.08
2250	7536	5.178797	CGTAGACTGGATCCAAACAAATCT	58.821	41.667	17.00	13.22	0.00	2.40
2525	7814	3.437198	CCCTAAGGCCACTAGAGATGAGA	60.437	52.174	5.01	0.00	0.00	3.27
2528	7817	3.326946	AGGCCACTAGAGATGAGACAT	57.673	47.619	5.01	0.00	0.00	3.06
2535	7824	4.457257	CACTAGAGATGAGACATATCGGCA	59.543	45.833	0.00	0.00	0.00	5.69
2542	7831	1.887242	GACATATCGGCAGCGGCAA	60.887	57.895	11.88	0.00	43.71	4.52
2578	7867	1.689984	GTAACCCTCGTCCTAGGAGG	58.310	60.000	23.00	23.00	46.84	4.30
2589	7878	1.902508	TCCTAGGAGGAGTTGCTTGTG	59.097	52.381	7.62	0.00	40.06	3.33
2590	7879	1.065854	CCTAGGAGGAGTTGCTTGTGG	60.066	57.143	1.05	0.00	37.67	4.17
2591	7880	0.984230	TAGGAGGAGTTGCTTGTGGG	59.016	55.000	0.00	0.00	0.00	4.61
2595	7884	1.603739	GGAGTTGCTTGTGGGGGAC	60.604	63.158	0.00	0.00	0.00	4.46
2599	7888	1.527380	TTGCTTGTGGGGGACGAAC	60.527	57.895	0.00	0.00	0.00	3.95
2670	7960	7.875327	AGCCACAACTCTAAACTTTTTCTTA	57.125	32.000	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	5.221185	GCAGAGGACCGAACATAACACTATA	60.221	44.000	0.00	0.00	0.00	1.31
30	31	2.094182	TCTTGTATGCAGAGGACCGAAC	60.094	50.000	0.00	0.00	0.00	3.95
31	32	2.166459	CTCTTGTATGCAGAGGACCGAA	59.834	50.000	0.00	0.00	0.00	4.30
43	44	3.921119	TTGCAACAAGCCTCTTGTATG	57.079	42.857	11.99	12.52	44.83	2.39
45	46	3.253188	GTGATTGCAACAAGCCTCTTGTA	59.747	43.478	11.99	0.00	44.83	2.41
72	73	6.594744	AGGCCATGTTTCAGAAAGAATTTTT	58.405	32.000	5.01	0.00	39.27	1.94
98	108	6.391537	TCTGTTTGGTTTTGTTTCTACAACC	58.608	36.000	0.00	0.00	43.66	3.77
145	155	0.318699	CGGCTCTCAACTGTGACGAA	60.319	55.000	0.00	0.00	0.00	3.85
147	157	2.375766	GCGGCTCTCAACTGTGACG	61.376	63.158	0.00	0.00	0.00	4.35
148	158	2.029844	GGCGGCTCTCAACTGTGAC	61.030	63.158	0.00	0.00	0.00	3.67
151	161	3.303135	TCGGCGGCTCTCAACTGT	61.303	61.111	7.21	0.00	0.00	3.55
154	164	1.226717	CTAGTCGGCGGCTCTCAAC	60.227	63.158	21.03	0.00	0.00	3.18
166	178	1.010574	CTCTTCGCCGCTCTAGTCG	60.011	63.158	0.00	0.00	0.00	4.18
236	258	2.124942	CCAAGCTCTCCCGGCTTC	60.125	66.667	0.00	0.00	46.59	3.86
244	266	1.153005	CCATGGAGGCCAAGCTCTC	60.153	63.158	5.56	0.00	36.95	3.20
272	294	4.523173	TGGAAGTCTGAGTTTCGACTATGT	59.477	41.667	0.00	0.00	39.44	2.29
283	305	1.617947	GCCCCGATGGAAGTCTGAGT	61.618	60.000	0.00	0.00	35.39	3.41
332	2940	3.915437	AAATCAAACCTGCTACAACCG	57.085	42.857	0.00	0.00	0.00	4.44
336	2944	4.919774	TCCCTAAATCAAACCTGCTACA	57.080	40.909	0.00	0.00	0.00	2.74
405	3013	6.248569	TCTATCCTTACCCTTTTCACATCC	57.751	41.667	0.00	0.00	0.00	3.51
418	3026	5.552870	ACCATCCACACATCTATCCTTAC	57.447	43.478	0.00	0.00	0.00	2.34
447	3055	2.892374	TCCTCAATGCAGACACGTATG	58.108	47.619	0.00	0.00	0.00	2.39
480	3088	1.646912	TCCCTTGTTACGGTCCATGA	58.353	50.000	0.00	0.00	0.00	3.07
497	3105	0.523072	ACATGAAGCGCAACACATCC	59.477	50.000	11.47	0.00	0.00	3.51
500	3108	2.967459	CTTACATGAAGCGCAACACA	57.033	45.000	11.47	4.07	0.00	3.72
574	3195	0.036164	CACACCCGTCCAATCCAAGA	59.964	55.000	0.00	0.00	0.00	3.02
592	3214	4.063967	ACGCATCGGCCGTCTTCA	62.064	61.111	27.15	5.24	36.38	3.02
612	3234	2.353704	CGCTCAACCACTGGATTACTCA	60.354	50.000	0.71	0.00	0.00	3.41
686	3311	1.079503	CTTCGCCTGTTTCCTGTAGC	58.920	55.000	0.00	0.00	0.00	3.58
691	3316	1.003233	GGAGCTTCGCCTGTTTCCT	60.003	57.895	0.00	0.00	0.00	3.36
718	5927	7.792364	ATATCGATGGTGACCTTTATCCTAA	57.208	36.000	8.54	0.00	0.00	2.69
849	6058	0.462759	CGAGAGGGGGAGATTGTTGC	60.463	60.000	0.00	0.00	0.00	4.17
884	6093	4.796231	GCACGGATGGAGACGCGT	62.796	66.667	13.85	13.85	0.00	6.01
1119	6331	4.023279	TCAACGTCAAATCTCAAATGGGTG	60.023	41.667	0.00	0.00	0.00	4.61
1124	6336	6.638063	CACAACATCAACGTCAAATCTCAAAT	59.362	34.615	0.00	0.00	0.00	2.32
1125	6337	5.970612	CACAACATCAACGTCAAATCTCAAA	59.029	36.000	0.00	0.00	0.00	2.69
1126	6338	5.065859	ACACAACATCAACGTCAAATCTCAA	59.934	36.000	0.00	0.00	0.00	3.02
1127	6339	4.574421	ACACAACATCAACGTCAAATCTCA	59.426	37.500	0.00	0.00	0.00	3.27
1128	6340	5.095691	ACACAACATCAACGTCAAATCTC	57.904	39.130	0.00	0.00	0.00	2.75
1129	6341	5.179368	CCTACACAACATCAACGTCAAATCT	59.821	40.000	0.00	0.00	0.00	2.40
1130	6342	5.382303	CCTACACAACATCAACGTCAAATC	58.618	41.667	0.00	0.00	0.00	2.17
1242	6489	6.639686	TGTATGTGTAAAACAGAGTCGTCTTC	59.360	38.462	0.00	0.00	43.64	2.87
1510	6757	3.583966	ACGAGTGGTTTGGGTTTATCCTA	59.416	43.478	0.00	0.00	36.25	2.94
1581	6853	2.095567	CACAGCCTGCAGTGTCAATTAC	60.096	50.000	13.81	0.00	0.00	1.89
1725	6997	2.093447	CCTTGAACAGCCTAAGGACGAT	60.093	50.000	0.00	0.00	42.82	3.73
1740	7012	1.968017	CGCAGAAGCAGCCCTTGAA	60.968	57.895	0.00	0.00	42.27	2.69
1887	7159	8.862550	AATTATTGTTGCGGTAGTAGTAGTAC	57.137	34.615	6.61	6.61	0.00	2.73
1888	7160	9.304731	CAAATTATTGTTGCGGTAGTAGTAGTA	57.695	33.333	0.00	0.00	0.00	1.82
1908	7180	3.637911	ATAGGCCGTGGTGACAAATTA	57.362	42.857	0.00	0.00	46.06	1.40
1921	7193	1.658994	TCCGCAAAAAGTATAGGCCG	58.341	50.000	0.00	0.00	0.00	6.13
1965	7238	4.019771	TGTGTCCTTTGTACTGCCATGATA	60.020	41.667	0.00	0.00	0.00	2.15
2063	7339	2.498941	GGAGGGGCGATGATGACGA	61.499	63.158	0.00	0.00	0.00	4.20
2105	7381	4.315803	ACTTCCTGGTCGTTTATGACAAG	58.684	43.478	4.63	2.43	40.72	3.16
2149	7425	2.839975	TGTTGTTCTGATGCGTTGGTA	58.160	42.857	0.00	0.00	0.00	3.25
2195	7471	8.945195	TGTTAATAGGTTAGATCCTTCCGATA	57.055	34.615	0.00	0.00	38.86	2.92
2214	7490	6.971726	TCCAGTCTACGTCCATATGTTAAT	57.028	37.500	1.24	0.00	0.00	1.40
2250	7536	6.452494	TTTGGTCGGTGTTTTTCTTCAATA	57.548	33.333	0.00	0.00	0.00	1.90
2445	7734	3.329093	GGAGGGCTCCTGCTTCAT	58.671	61.111	5.65	0.00	46.16	2.57
2483	7772	4.127744	ATGGATGCGGGGTGTGGG	62.128	66.667	0.00	0.00	0.00	4.61
2484	7773	2.829914	CATGGATGCGGGGTGTGG	60.830	66.667	0.00	0.00	0.00	4.17
2485	7774	2.829914	CCATGGATGCGGGGTGTG	60.830	66.667	5.56	0.00	0.00	3.82
2486	7775	4.820744	GCCATGGATGCGGGGTGT	62.821	66.667	18.40	0.00	0.00	4.16
2525	7814	2.180204	GTTGCCGCTGCCGATATGT	61.180	57.895	0.00	0.00	36.33	2.29
2545	7834	3.777910	TTACCCTCCTTCCGCGGC	61.778	66.667	23.51	0.00	0.00	6.53
2546	7835	2.186125	GTTACCCTCCTTCCGCGG	59.814	66.667	22.12	22.12	0.00	6.46
2547	7836	2.186125	GGTTACCCTCCTTCCGCG	59.814	66.667	0.00	0.00	0.00	6.46
2578	7867	1.966451	CGTCCCCCACAAGCAACTC	60.966	63.158	0.00	0.00	0.00	3.01
2589	7878	2.435410	ATTTCGCGTTCGTCCCCC	60.435	61.111	5.77	0.00	36.96	5.40
2590	7879	2.782615	CATTTCGCGTTCGTCCCC	59.217	61.111	5.77	0.00	36.96	4.81
2591	7880	2.097728	GCATTTCGCGTTCGTCCC	59.902	61.111	5.77	0.00	36.96	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.