AutoCloner

Multiple sequence alignment - TraesCS1D01G408200

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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	TraesCS1D01G408200	chr1D	100.000	3116	0	0	1	3116	470658063	470654948	0.000000e+00	5755.0
1	TraesCS1D01G408200	chr1D	80.964	1245	197	26	886	2111	470648568	470647345	0.000000e+00	950.0
2	TraesCS1D01G408200	chr1D	77.898	1199	202	39	930	2111	470625840	470624688	0.000000e+00	688.0
3	TraesCS1D01G408200	chr1D	74.778	1241	240	51	948	2143	470810411	470811623	1.000000e-134	490.0
4	TraesCS1D01G408200	chr1D	72.574	1185	253	52	979	2119	470798149	470799305	3.880000e-84	322.0
5	TraesCS1D01G408200	chr1D	89.062	192	20	1	163	354	470657240	470657050	1.440000e-58	237.0
6	TraesCS1D01G408200	chr1D	89.062	192	20	1	824	1014	470657901	470657710	1.440000e-58	237.0
7	TraesCS1D01G408200	chr1D	83.750	80	10	3	1951	2029	470804462	470804539	4.310000e-09	73.1
8	TraesCS1D01G408200	chr1A	92.237	3156	156	32	1	3116	564374419	564371313	0.000000e+00	4388.0
9	TraesCS1D01G408200	chr1A	81.350	1244	200	22	886	2111	564345915	564344686	0.000000e+00	983.0
10	TraesCS1D01G408200	chr1A	79.125	1212	205	27	928	2111	564313875	564312684	0.000000e+00	793.0
11	TraesCS1D01G408200	chr1A	79.004	1205	199	36	928	2111	564334719	564333548	0.000000e+00	774.0
12	TraesCS1D01G408200	chr1A	75.827	695	123	36	919	1590	564575973	564576645	8.390000e-81	311.0
13	TraesCS1D01G408200	chr1A	86.735	196	21	2	163	354	564373591	564373397	2.430000e-51	213.0
14	TraesCS1D01G408200	chr1A	82.653	196	19	6	824	1014	564374257	564374072	3.220000e-35	159.0
15	TraesCS1D01G408200	chr1B	93.439	1570	66	16	163	1721	653976326	653974783	0.000000e+00	2294.0
16	TraesCS1D01G408200	chr1B	93.112	842	46	7	2069	2903	653974789	653973953	0.000000e+00	1223.0
17	TraesCS1D01G408200	chr1B	93.703	794	39	2	230	1014	653976927	653976136	0.000000e+00	1179.0
18	TraesCS1D01G408200	chr1B	81.764	1179	186	16	948	2107	653938882	653937714	0.000000e+00	959.0
19	TraesCS1D01G408200	chr1B	77.583	1200	198	42	928	2109	653890635	653889489	0.000000e+00	660.0
20	TraesCS1D01G408200	chr1B	74.659	1247	250	49	948	2158	654240314	654241530	2.790000e-135	492.0
21	TraesCS1D01G408200	chr1B	72.385	1300	289	48	903	2162	654092563	654093832	6.400000e-92	348.0
22	TraesCS1D01G408200	chr1B	91.943	211	9	2	2906	3116	653972352	653972150	3.930000e-74	289.0
23	TraesCS1D01G408200	chr1B	89.062	192	20	1	163	354	653975680	653975490	1.440000e-58	237.0
24	TraesCS1D01G408200	chr1B	83.750	80	10	3	1951	2029	654214092	654214169	4.310000e-09	73.1
25	TraesCS1D01G408200	chr1B	83.750	80	10	3	1951	2029	654220187	654220264	4.310000e-09	73.1
26	TraesCS1D01G408200	chr4A	74.727	550	121	16	960	1501	40437064	40436525	2.420000e-56	230.0
27	TraesCS1D01G408200	chr4A	74.561	456	106	9	960	1409	40413529	40413078	1.140000e-44	191.0

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	TraesCS1D01G408200	chr1D	470654948	470658063	3115	True	2076.333333	5755	92.708000	1	3116	3	chr1D.!!$R3	3115
1	TraesCS1D01G408200	chr1D	470647345	470648568	1223	True	950.000000	950	80.964000	886	2111	1	chr1D.!!$R2	1225
2	TraesCS1D01G408200	chr1D	470624688	470625840	1152	True	688.000000	688	77.898000	930	2111	1	chr1D.!!$R1	1181
3	TraesCS1D01G408200	chr1D	470810411	470811623	1212	False	490.000000	490	74.778000	948	2143	1	chr1D.!!$F3	1195
4	TraesCS1D01G408200	chr1D	470798149	470799305	1156	False	322.000000	322	72.574000	979	2119	1	chr1D.!!$F1	1140
5	TraesCS1D01G408200	chr1A	564371313	564374419	3106	True	1586.666667	4388	87.208333	1	3116	3	chr1A.!!$R4	3115
6	TraesCS1D01G408200	chr1A	564344686	564345915	1229	True	983.000000	983	81.350000	886	2111	1	chr1A.!!$R3	1225
7	TraesCS1D01G408200	chr1A	564312684	564313875	1191	True	793.000000	793	79.125000	928	2111	1	chr1A.!!$R1	1183
8	TraesCS1D01G408200	chr1A	564333548	564334719	1171	True	774.000000	774	79.004000	928	2111	1	chr1A.!!$R2	1183
9	TraesCS1D01G408200	chr1A	564575973	564576645	672	False	311.000000	311	75.827000	919	1590	1	chr1A.!!$F1	671
10	TraesCS1D01G408200	chr1B	653972150	653976927	4777	True	1044.400000	2294	92.251800	163	3116	5	chr1B.!!$R3	2953
11	TraesCS1D01G408200	chr1B	653937714	653938882	1168	True	959.000000	959	81.764000	948	2107	1	chr1B.!!$R2	1159
12	TraesCS1D01G408200	chr1B	653889489	653890635	1146	True	660.000000	660	77.583000	928	2109	1	chr1B.!!$R1	1181
13	TraesCS1D01G408200	chr1B	654240314	654241530	1216	False	492.000000	492	74.659000	948	2158	1	chr1B.!!$F4	1210
14	TraesCS1D01G408200	chr1B	654092563	654093832	1269	False	348.000000	348	72.385000	903	2162	1	chr1B.!!$F1	1259
15	TraesCS1D01G408200	chr4A	40436525	40437064	539	True	230.000000	230	74.727000	960	1501	1	chr4A.!!$R2	541

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
711	725	1.200948	GGTTCAGCCATGACTTTCTGC	59.799	52.381	0.0	0.0	34.35	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2670	3471	0.100682	TATGTCGACGAGAAGCAGGC	59.899	55.0	11.62	0.0	0.0	4.85	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	2.492484	ACTACTAAGTTGGTGGCTCTCG	59.508	50.000	1.52	0.00	29.00	4.04
114	115	2.741122	TACTTGTTTTCCAACACGCG	57.259	45.000	3.53	3.53	42.87	6.01
140	141	3.521947	AAACTAGATACACGTGGAGGC	57.478	47.619	21.57	7.96	0.00	4.70
169	170	4.336713	GCTTAGATCTCATGGTTTTGACCC	59.663	45.833	0.00	0.00	0.00	4.46
200	201	2.930950	TCAGTTAAACTGCAGCTTGGT	58.069	42.857	15.27	0.00	45.54	3.67
231	232	5.818857	AGCAACAGCATTGTTTCAAAGAAAT	59.181	32.000	3.05	0.00	45.01	2.17
476	481	1.447317	AAGTGGTTGGCTTGTCGCTG	61.447	55.000	0.00	0.00	39.13	5.18
477	482	3.286751	TGGTTGGCTTGTCGCTGC	61.287	61.111	0.00	0.00	39.13	5.25
478	483	4.389576	GGTTGGCTTGTCGCTGCG	62.390	66.667	17.25	17.25	39.13	5.18
479	484	3.649986	GTTGGCTTGTCGCTGCGT	61.650	61.111	22.48	0.00	39.13	5.24
480	485	3.345808	TTGGCTTGTCGCTGCGTC	61.346	61.111	22.48	17.17	39.13	5.19
711	725	1.200948	GGTTCAGCCATGACTTTCTGC	59.799	52.381	0.00	0.00	34.35	4.26
778	815	2.683211	AATTGTTGGGTTCAGGCTCT	57.317	45.000	0.00	0.00	0.00	4.09
1149	1850	2.666098	GGACCCACACTACCGCCAT	61.666	63.158	0.00	0.00	0.00	4.40
1218	1925	1.142870	TCTGTTGCCCAGCTTGTTAGT	59.857	47.619	0.00	0.00	41.25	2.24
1271	1978	2.222953	CTTACGTTCTTGCCGCACCG	62.223	60.000	0.00	0.00	0.00	4.94
1323	2030	6.318900	GCAATGGCCTAGTTCTTTGTAAGTAT	59.681	38.462	3.32	0.00	0.00	2.12
1334	2041	9.209175	AGTTCTTTGTAAGTATAAGAGCAACTG	57.791	33.333	0.00	0.00	33.29	3.16
1566	2292	3.018149	GTTCTCGTCTGACCTATCCACT	58.982	50.000	1.55	0.00	0.00	4.00
1666	2398	0.540365	CACAGCAGGGGGTGACATTT	60.540	55.000	0.42	0.00	45.29	2.32
1739	2480	0.394216	TTGCCGGATGTCCATTGGAG	60.394	55.000	5.05	0.00	35.14	3.86
1745	2486	2.103771	CGGATGTCCATTGGAGTCTCAT	59.896	50.000	5.39	5.94	35.14	2.90
1748	2489	3.339253	TGTCCATTGGAGTCTCATGTG	57.661	47.619	5.39	0.00	29.39	3.21
1804	2554	1.304282	GCATTTCCAGGGGAGAGCA	59.696	57.895	0.00	0.00	31.21	4.26
1876	2634	3.047796	TCTTTGAAGCGTCGTGTTAGTC	58.952	45.455	0.00	0.00	0.00	2.59
1930	2694	0.317269	CAATGATGAATGGCCGCGTC	60.317	55.000	4.92	1.54	0.00	5.19
2063	2836	2.037772	AGATCCAGGATGATTGCCGTAC	59.962	50.000	6.70	0.00	39.69	3.67
2065	2838	2.673258	TCCAGGATGATTGCCGTACTA	58.327	47.619	0.00	0.00	39.69	1.82
2066	2839	2.364324	TCCAGGATGATTGCCGTACTAC	59.636	50.000	0.00	0.00	39.69	2.73
2143	2930	1.814394	ACGTGATGCGGTGAGTAGTAA	59.186	47.619	0.00	0.00	46.52	2.24
2179	2966	9.646427	TTGTGTGCAACTTTTATATTTTATCCC	57.354	29.630	0.00	0.00	38.04	3.85
2229	3016	7.648039	TTCTCTCCTTTCTAAGACATAGACC	57.352	40.000	0.00	0.00	40.38	3.85
2246	3033	8.154649	ACATAGACCAGAAACTTGTTACTTTG	57.845	34.615	0.00	0.00	0.00	2.77
2442	3229	0.457166	TTACCGCGTCAGGAATGTCG	60.457	55.000	4.92	0.00	34.73	4.35
2452	3239	3.807622	GTCAGGAATGTCGTCTTTGTTCA	59.192	43.478	0.00	0.00	0.00	3.18
2456	3243	4.152402	AGGAATGTCGTCTTTGTTCATTCG	59.848	41.667	0.00	0.00	42.67	3.34
2491	3279	3.806591	CATGCCTTGCTTTGTGGAG	57.193	52.632	0.00	0.00	0.00	3.86
2510	3298	5.243954	GTGGAGGAAAAGAAGGTAAGCAAAT	59.756	40.000	0.00	0.00	0.00	2.32
2577	3366	5.555966	TGCTTCCACACTTACATTACATGA	58.444	37.500	0.00	0.00	0.00	3.07
2645	3434	7.166851	TCCGTTAATAACCTTATGTGTTGGAA	58.833	34.615	0.00	0.00	0.00	3.53
2669	3470	5.102313	CACTCTTGCCTTTTTCTTTTCGTT	58.898	37.500	0.00	0.00	0.00	3.85
2670	3471	5.004726	CACTCTTGCCTTTTTCTTTTCGTTG	59.995	40.000	0.00	0.00	0.00	4.10
2678	3479	2.774439	TTCTTTTCGTTGCCTGCTTC	57.226	45.000	0.00	0.00	0.00	3.86
2681	3482	0.586319	TTTTCGTTGCCTGCTTCTCG	59.414	50.000	0.00	0.00	0.00	4.04
2685	3486	1.372997	GTTGCCTGCTTCTCGTCGA	60.373	57.895	0.00	0.00	0.00	4.20
2688	3489	1.153745	GCCTGCTTCTCGTCGACAT	60.154	57.895	17.16	0.00	0.00	3.06
2767	3568	2.260869	GCTGGCCTGCGAAAAGTCA	61.261	57.895	19.59	0.00	0.00	3.41
2783	3584	0.537143	GTCACACCATCTTGCACCCA	60.537	55.000	0.00	0.00	0.00	4.51
2910	5309	9.907229	AGAAAATTTCCTACGAAATCTAATCCT	57.093	29.630	1.57	0.00	45.92	3.24
2951	5350	9.921637	CAATCAAAGAGGTCCTAAGAGTATATC	57.078	37.037	0.00	0.00	0.00	1.63
2952	5351	9.890915	AATCAAAGAGGTCCTAAGAGTATATCT	57.109	33.333	0.00	0.00	41.27	1.98
2953	5352	8.698973	TCAAAGAGGTCCTAAGAGTATATCTG	57.301	38.462	0.00	0.00	38.67	2.90
2954	5353	8.282982	TCAAAGAGGTCCTAAGAGTATATCTGT	58.717	37.037	0.00	0.00	38.67	3.41
2955	5354	9.575868	CAAAGAGGTCCTAAGAGTATATCTGTA	57.424	37.037	0.00	0.00	38.67	2.74
3009	5408	5.764131	TGTAATGGCTTTTAACTGAAACGG	58.236	37.500	0.00	0.00	0.00	4.44
3095	5494	9.515226	ACAGCATTAGTAAACCTCATTTCTAAA	57.485	29.630	0.00	0.00	30.54	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	1.117150	TAACCCAGGTCGCTGTATCC	58.883	55.000	0.00	0.00	0.00	2.59
114	115	6.018994	CCTCCACGTGTATCTAGTTTAATTGC	60.019	42.308	15.65	0.00	0.00	3.56
140	141	6.939132	AAACCATGAGATCTAAGCAATCTG	57.061	37.500	0.00	0.00	33.64	2.90
392	397	3.512329	TCGTTTGTGCAGGTCCTATCTAA	59.488	43.478	0.00	0.00	0.00	2.10
476	481	1.082117	ATCGATTGGTTGTCGGACGC	61.082	55.000	3.34	0.00	39.45	5.19
477	482	0.645355	CATCGATTGGTTGTCGGACG	59.355	55.000	0.00	0.00	39.45	4.79
478	483	1.006832	CCATCGATTGGTTGTCGGAC	58.993	55.000	0.00	0.00	40.99	4.79
479	484	3.451793	CCATCGATTGGTTGTCGGA	57.548	52.632	0.00	0.00	40.99	4.55
499	513	0.888619	TCTCTCATGTTCGGCGTTCT	59.111	50.000	6.85	0.00	0.00	3.01
578	592	5.989168	TGTTTGTGTGTCAATTCTCTACGAT	59.011	36.000	0.00	0.00	35.84	3.73
711	725	8.960591	ACAAGTATTTCTTTGGTATGAATCCAG	58.039	33.333	0.00	0.00	36.28	3.86
754	768	3.454082	AGCCTGAACCCAACAATTTTTCA	59.546	39.130	0.00	0.00	0.00	2.69
853	894	1.889170	GCTGCTAGGAAAACCAAGCTT	59.111	47.619	0.00	0.00	35.95	3.74
1149	1850	3.243907	CGGTGGGAATTTTTGGCAGTTTA	60.244	43.478	0.00	0.00	0.00	2.01
1218	1925	4.535526	TTCCTCATCATTTCGTGACAGA	57.464	40.909	0.00	0.00	40.28	3.41
1271	1978	8.558700	AGCAATCCACAAATTTTAAATGTTCAC	58.441	29.630	0.00	0.00	0.00	3.18
1323	2030	5.755409	TTGGAGGAATACAGTTGCTCTTA	57.245	39.130	8.77	0.00	37.12	2.10
1334	2041	4.278419	AGCGGCAAATATTTGGAGGAATAC	59.722	41.667	25.61	9.31	38.57	1.89
1527	2253	5.505173	AGAACACCTCAAGTTTGTTGATG	57.495	39.130	0.00	0.00	33.59	3.07
1566	2292	1.478916	CATGCAGCATCCACAATCCAA	59.521	47.619	4.38	0.00	0.00	3.53
1666	2398	1.427368	ACCCATTGCCTCCAACACTAA	59.573	47.619	0.00	0.00	32.95	2.24
1739	2480	2.287788	CCAAAGCAACCACACATGAGAC	60.288	50.000	0.00	0.00	0.00	3.36
1745	2486	1.550327	TTGACCAAAGCAACCACACA	58.450	45.000	0.00	0.00	0.00	3.72
1748	2489	3.005684	TGATGATTGACCAAAGCAACCAC	59.994	43.478	0.00	0.00	37.79	4.16
1876	2634	2.630158	CCTTCCAAGTGCATCTCTCAG	58.370	52.381	0.00	0.00	0.00	3.35
1930	2694	0.307760	GCAATCCGATAACCAAGCCG	59.692	55.000	0.00	0.00	0.00	5.52
2063	2836	8.288208	CCACATAATAACGGTAGTCAGTAGTAG	58.712	40.741	0.00	0.00	0.00	2.57
2065	2838	6.460676	GCCACATAATAACGGTAGTCAGTAGT	60.461	42.308	0.00	0.00	0.00	2.73
2066	2839	5.919141	GCCACATAATAACGGTAGTCAGTAG	59.081	44.000	0.00	0.00	0.00	2.57
2143	2930	0.461870	TTGCACACAAGAGACGCTGT	60.462	50.000	0.00	0.00	0.00	4.40
2229	3016	5.357032	ACCCTGACAAAGTAACAAGTTTCTG	59.643	40.000	0.00	0.00	0.00	3.02
2395	3182	2.029244	GGTAAGAACATGCATGACGACG	59.971	50.000	32.75	5.75	0.00	5.12
2396	3183	3.000041	TGGTAAGAACATGCATGACGAC	59.000	45.455	32.75	23.18	0.00	4.34
2397	3184	3.261580	CTGGTAAGAACATGCATGACGA	58.738	45.455	32.75	15.58	0.00	4.20
2442	3229	7.689812	CACAAGATATGTCGAATGAACAAAGAC	59.310	37.037	0.00	0.00	41.46	3.01
2452	3239	3.940852	TGCAAGCACAAGATATGTCGAAT	59.059	39.130	0.00	0.00	41.46	3.34
2456	3243	3.369385	GCATGCAAGCACAAGATATGTC	58.631	45.455	14.21	0.00	41.46	3.06
2491	3279	7.970614	CACATCTATTTGCTTACCTTCTTTTCC	59.029	37.037	0.00	0.00	0.00	3.13
2510	3298	6.098838	AGTGAATTCTCCACATAGCACATCTA	59.901	38.462	7.05	0.00	37.01	1.98
2519	3308	4.910195	AGTGCAAGTGAATTCTCCACATA	58.090	39.130	7.05	0.00	37.01	2.29
2577	3366	9.174166	GTTGGACATATATGTAGGAAACAACTT	57.826	33.333	18.28	0.00	42.70	2.66
2599	3388	5.118286	GGAAATAATTGCCCATGAAGTTGG	58.882	41.667	0.00	0.00	36.46	3.77
2645	3434	4.157840	ACGAAAAGAAAAAGGCAAGAGTGT	59.842	37.500	0.00	0.00	0.00	3.55
2648	3437	4.026558	GCAACGAAAAGAAAAAGGCAAGAG	60.027	41.667	0.00	0.00	0.00	2.85
2649	3438	3.862845	GCAACGAAAAGAAAAAGGCAAGA	59.137	39.130	0.00	0.00	0.00	3.02
2650	3439	3.001228	GGCAACGAAAAGAAAAAGGCAAG	59.999	43.478	0.00	0.00	0.00	4.01
2651	3440	2.933260	GGCAACGAAAAGAAAAAGGCAA	59.067	40.909	0.00	0.00	0.00	4.52
2652	3441	2.167487	AGGCAACGAAAAGAAAAAGGCA	59.833	40.909	0.00	0.00	46.39	4.75
2653	3442	2.539688	CAGGCAACGAAAAGAAAAAGGC	59.460	45.455	0.00	0.00	46.39	4.35
2669	3470	1.877576	ATGTCGACGAGAAGCAGGCA	61.878	55.000	11.62	0.00	0.00	4.75
2670	3471	0.100682	TATGTCGACGAGAAGCAGGC	59.899	55.000	11.62	0.00	0.00	4.85
2767	3568	1.228552	GGTGGGTGCAAGATGGTGT	60.229	57.895	0.00	0.00	0.00	4.16
2783	3584	4.468153	TGTTTTTGCCCTAAAGTTCAAGGT	59.532	37.500	4.09	0.00	0.00	3.50
2825	3626	4.631813	CCCACTCGAACCTATTTGAAGAAG	59.368	45.833	0.00	0.00	0.00	2.85
2828	3629	3.684788	CACCCACTCGAACCTATTTGAAG	59.315	47.826	0.00	0.00	0.00	3.02
2910	5309	8.752187	CCTCTTTGATTGAAAGGATATTTTGGA	58.248	33.333	0.00	0.00	41.43	3.53
3009	5408	1.885887	TGCAATTTAGTGGTCACCTGC	59.114	47.619	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.