AutoCloner

Multiple sequence alignment - TraesCS5A01G471300

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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	TraesCS5A01G471300	chr5A	100.000	3254	0	0	1	3254	647968228	647964975	0.000000e+00	6010
1	TraesCS5A01G471300	chr5A	87.888	1288	137	13	995	2280	648228523	648227253	0.000000e+00	1496
2	TraesCS5A01G471300	chr5A	98.571	630	6	1	2628	3254	137317878	137318507	0.000000e+00	1110
3	TraesCS5A01G471300	chr5A	98.571	630	6	1	2628	3254	624424558	624425187	0.000000e+00	1110
4	TraesCS5A01G471300	chr5A	97.508	642	12	2	2617	3254	624417578	624418219	0.000000e+00	1094
5	TraesCS5A01G471300	chr5A	89.899	693	63	5	4	696	648177121	648176436	0.000000e+00	885
6	TraesCS5A01G471300	chr5A	80.572	664	120	5	33	688	471401925	471402587	1.350000e-138	503
7	TraesCS5A01G471300	chr5A	94.545	165	4	3	690	852	648176395	648176234	1.940000e-62	250
8	TraesCS5A01G471300	chr5A	96.610	59	2	0	794	852	648361973	648361915	7.430000e-17	99
9	TraesCS5A01G471300	chrUn	92.877	1769	105	10	874	2628	294625045	294623284	0.000000e+00	2549
10	TraesCS5A01G471300	chrUn	81.259	667	115	9	33	691	98340871	98340207	6.180000e-147	531
11	TraesCS5A01G471300	chrUn	88.387	155	9	3	690	839	67121724	67121574	9.280000e-41	178
12	TraesCS5A01G471300	chrUn	88.387	155	9	3	690	839	414348000	414347850	9.280000e-41	178
13	TraesCS5A01G471300	chr5D	91.397	1639	117	10	990	2628	520301969	520300355	0.000000e+00	2224
14	TraesCS5A01G471300	chr5D	80.719	612	117	1	29	640	434572674	434572064	2.940000e-130	475
15	TraesCS5A01G471300	chr5B	89.992	1309	114	10	970	2277	655278870	655280162	0.000000e+00	1676
16	TraesCS5A01G471300	chr5B	90.015	1292	111	10	990	2280	655391580	655392854	0.000000e+00	1655
17	TraesCS5A01G471300	chr5B	89.380	1290	110	12	990	2279	655322177	655323439	0.000000e+00	1598
18	TraesCS5A01G471300	chr5B	86.408	206	20	4	2283	2487	655323481	655323679	5.470000e-53	219
19	TraesCS5A01G471300	chr5B	87.117	163	10	4	692	849	655391166	655391322	1.200000e-39	174
20	TraesCS5A01G471300	chr5B	87.407	135	9	3	2494	2628	655323729	655323855	7.270000e-32	148
21	TraesCS5A01G471300	chr1A	98.571	630	6	1	2628	3254	572176577	572177206	0.000000e+00	1110
22	TraesCS5A01G471300	chr6A	97.972	641	9	2	2618	3254	499382319	499381679	0.000000e+00	1109
23	TraesCS5A01G471300	chr6A	98.413	630	7	1	2628	3254	7554407	7555036	0.000000e+00	1105
24	TraesCS5A01G471300	chr6A	98.413	630	7	1	2628	3254	499375485	499374856	0.000000e+00	1105
25	TraesCS5A01G471300	chr6A	81.163	1290	204	25	992	2248	22200989	22199706	0.000000e+00	1000
26	TraesCS5A01G471300	chr4A	98.413	630	7	1	2628	3254	167230981	167230352	0.000000e+00	1105
27	TraesCS5A01G471300	chr2A	98.413	630	7	1	2628	3254	618840298	618840927	0.000000e+00	1105
28	TraesCS5A01G471300	chr6D	83.069	1134	185	5	1117	2248	23632011	23630883	0.000000e+00	1024
29	TraesCS5A01G471300	chr6D	82.953	1138	182	7	1117	2248	23642055	23640924	0.000000e+00	1016
30	TraesCS5A01G471300	chr3B	86.234	632	76	7	69	693	778184583	778185210	0.000000e+00	675
31	TraesCS5A01G471300	chr3B	85.443	632	84	5	69	693	778214717	778215347	0.000000e+00	651
32	TraesCS5A01G471300	chr7B	81.575	635	106	7	63	688	711736572	711737204	6.230000e-142	514
33	TraesCS5A01G471300	chr7B	79.790	668	125	8	33	691	715365436	715364770	8.170000e-131	477
34	TraesCS5A01G471300	chr2D	79.844	640	122	4	53	691	544205227	544204594	8.230000e-126	460

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	TraesCS5A01G471300	chr5A	647964975	647968228	3253	True	6010.0	6010	100.000000	1	3254	1	chr5A.!!$R1	3253
1	TraesCS5A01G471300	chr5A	648227253	648228523	1270	True	1496.0	1496	87.888000	995	2280	1	chr5A.!!$R2	1285
2	TraesCS5A01G471300	chr5A	137317878	137318507	629	False	1110.0	1110	98.571000	2628	3254	1	chr5A.!!$F1	626
3	TraesCS5A01G471300	chr5A	624424558	624425187	629	False	1110.0	1110	98.571000	2628	3254	1	chr5A.!!$F4	626
4	TraesCS5A01G471300	chr5A	624417578	624418219	641	False	1094.0	1094	97.508000	2617	3254	1	chr5A.!!$F3	637
5	TraesCS5A01G471300	chr5A	648176234	648177121	887	True	567.5	885	92.222000	4	852	2	chr5A.!!$R4	848
6	TraesCS5A01G471300	chr5A	471401925	471402587	662	False	503.0	503	80.572000	33	688	1	chr5A.!!$F2	655
7	TraesCS5A01G471300	chrUn	294623284	294625045	1761	True	2549.0	2549	92.877000	874	2628	1	chrUn.!!$R3	1754
8	TraesCS5A01G471300	chrUn	98340207	98340871	664	True	531.0	531	81.259000	33	691	1	chrUn.!!$R2	658
9	TraesCS5A01G471300	chr5D	520300355	520301969	1614	True	2224.0	2224	91.397000	990	2628	1	chr5D.!!$R2	1638
10	TraesCS5A01G471300	chr5D	434572064	434572674	610	True	475.0	475	80.719000	29	640	1	chr5D.!!$R1	611
11	TraesCS5A01G471300	chr5B	655278870	655280162	1292	False	1676.0	1676	89.992000	970	2277	1	chr5B.!!$F1	1307
12	TraesCS5A01G471300	chr5B	655391166	655392854	1688	False	914.5	1655	88.566000	692	2280	2	chr5B.!!$F3	1588
13	TraesCS5A01G471300	chr5B	655322177	655323855	1678	False	655.0	1598	87.731667	990	2628	3	chr5B.!!$F2	1638
14	TraesCS5A01G471300	chr1A	572176577	572177206	629	False	1110.0	1110	98.571000	2628	3254	1	chr1A.!!$F1	626
15	TraesCS5A01G471300	chr6A	499381679	499382319	640	True	1109.0	1109	97.972000	2618	3254	1	chr6A.!!$R3	636
16	TraesCS5A01G471300	chr6A	7554407	7555036	629	False	1105.0	1105	98.413000	2628	3254	1	chr6A.!!$F1	626
17	TraesCS5A01G471300	chr6A	499374856	499375485	629	True	1105.0	1105	98.413000	2628	3254	1	chr6A.!!$R2	626
18	TraesCS5A01G471300	chr6A	22199706	22200989	1283	True	1000.0	1000	81.163000	992	2248	1	chr6A.!!$R1	1256
19	TraesCS5A01G471300	chr4A	167230352	167230981	629	True	1105.0	1105	98.413000	2628	3254	1	chr4A.!!$R1	626
20	TraesCS5A01G471300	chr2A	618840298	618840927	629	False	1105.0	1105	98.413000	2628	3254	1	chr2A.!!$F1	626
21	TraesCS5A01G471300	chr6D	23630883	23632011	1128	True	1024.0	1024	83.069000	1117	2248	1	chr6D.!!$R1	1131
22	TraesCS5A01G471300	chr6D	23640924	23642055	1131	True	1016.0	1016	82.953000	1117	2248	1	chr6D.!!$R2	1131
23	TraesCS5A01G471300	chr3B	778184583	778185210	627	False	675.0	675	86.234000	69	693	1	chr3B.!!$F1	624
24	TraesCS5A01G471300	chr3B	778214717	778215347	630	False	651.0	651	85.443000	69	693	1	chr3B.!!$F2	624
25	TraesCS5A01G471300	chr7B	711736572	711737204	632	False	514.0	514	81.575000	63	688	1	chr7B.!!$F1	625
26	TraesCS5A01G471300	chr7B	715364770	715365436	666	True	477.0	477	79.790000	33	691	1	chr7B.!!$R1	658
27	TraesCS5A01G471300	chr2D	544204594	544205227	633	True	460.0	460	79.844000	53	691	1	chr2D.!!$R1	638

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
363	366	0.033503	TCTGGGATCTAGCGGACACA	60.034	55.0	0.00	0.0	0.0	3.72	F
1415	1636	0.108138	CTAAGGCCAGAGTTCACGGG	60.108	60.0	5.01	0.0	0.0	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1991	2215	0.035630	AGTCACCATGCCAGAGAAGC	60.036	55.0	0.00	0.00	0.0	3.86	R
2421	2686	0.174845	CCTAAACCACTGATCGGCGA	59.825	55.0	13.87	13.87	0.0	5.54	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
31	32	5.147865	CGATCATCATCTTGGTACGTAGAC	58.852	45.833	0.00	0.00	0.00	2.59
184	185	0.818296	TCTTCTTGCCGGTCTCTAGC	59.182	55.000	1.90	0.00	0.00	3.42
211	212	2.301583	TGAGATTTGTGTCCGATGGTCA	59.698	45.455	0.00	0.00	0.00	4.02
223	224	1.897398	GATGGTCAACGCACGACACC	61.897	60.000	0.00	0.09	34.97	4.16
312	315	1.200716	CGGCAAGCAGTGACATTCATT	59.799	47.619	0.00	0.00	33.13	2.57
333	336	3.469008	TTCTTCAACCACGTCTGATGT	57.531	42.857	0.00	0.00	0.00	3.06
363	366	0.033503	TCTGGGATCTAGCGGACACA	60.034	55.000	0.00	0.00	0.00	3.72
545	548	3.252974	AGATGAAGGTGGACGATGTTC	57.747	47.619	0.00	0.00	0.00	3.18
688	700	7.862372	CCGTTTTTCTCATGAAATATATGTGGG	59.138	37.037	0.00	0.00	41.24	4.61
693	705	9.778741	TTTCTCATGAAATATATGTGGGTACTC	57.221	33.333	0.00	0.00	37.27	2.59
873	961	0.699981	TTGCACCTAACCCTAACCCC	59.300	55.000	0.00	0.00	0.00	4.95
874	962	0.178855	TGCACCTAACCCTAACCCCT	60.179	55.000	0.00	0.00	0.00	4.79
875	963	0.255033	GCACCTAACCCTAACCCCTG	59.745	60.000	0.00	0.00	0.00	4.45
899	987	1.227089	CGCCTGTCTCCTGATTCCG	60.227	63.158	0.00	0.00	0.00	4.30
918	1006	2.099921	CCGGTCTGAATCTGATCGTCTT	59.900	50.000	18.78	0.00	34.87	3.01
943	1053	1.035923	TCTGATCGAGCTGTGATCCC	58.964	55.000	18.27	1.66	41.22	3.85
945	1055	1.411977	CTGATCGAGCTGTGATCCCTT	59.588	52.381	18.27	0.00	41.22	3.95
956	1066	4.813697	GCTGTGATCCCTTCTGAATCTTAC	59.186	45.833	0.00	0.00	0.00	2.34
1028	1216	1.258445	ATCGGGAGGTTCGTGCTCTT	61.258	55.000	0.00	0.00	0.00	2.85
1041	1229	2.576615	GTGCTCTTCTTGACCCTGTTT	58.423	47.619	0.00	0.00	0.00	2.83
1044	1232	2.856222	CTCTTCTTGACCCTGTTTGCT	58.144	47.619	0.00	0.00	0.00	3.91
1285	1506	2.448931	TGGGGTTCCTTGGGTCGT	60.449	61.111	0.00	0.00	0.00	4.34
1287	1508	2.222013	GGGGTTCCTTGGGTCGTCT	61.222	63.158	0.00	0.00	0.00	4.18
1415	1636	0.108138	CTAAGGCCAGAGTTCACGGG	60.108	60.000	5.01	0.00	0.00	5.28
1542	1763	3.260884	ACAAGCAAATCCTCGAAGTCCTA	59.739	43.478	0.00	0.00	0.00	2.94
1564	1785	3.691342	CGGGCTCCGTCAACTCCA	61.691	66.667	5.56	0.00	42.73	3.86
1572	1793	2.280797	GTCAACTCCAGCACGGCA	60.281	61.111	0.00	0.00	33.14	5.69
1626	1847	1.215647	GTGGACTCAGCCGTTCGAT	59.784	57.895	0.00	0.00	0.00	3.59
1719	1940	2.889617	CACATCGCGGTCTACCCA	59.110	61.111	6.13	0.00	0.00	4.51
1920	2144	2.286365	TCATGGTCCCCAAGTTCAAC	57.714	50.000	0.00	0.00	36.95	3.18
1984	2208	2.549349	GGTGTCACTAGGGCTTTCGAAA	60.549	50.000	10.71	10.71	0.00	3.46
2020	2244	1.383943	ATGGTGACTGGCGGGGATA	60.384	57.895	0.00	0.00	0.00	2.59
2021	2245	0.986019	ATGGTGACTGGCGGGGATAA	60.986	55.000	0.00	0.00	0.00	1.75
2022	2246	1.146263	GGTGACTGGCGGGGATAAG	59.854	63.158	0.00	0.00	0.00	1.73
2082	2309	2.181021	GTGGACGAGGTAGGCACG	59.819	66.667	0.00	0.00	0.00	5.34
2244	2471	3.653164	TGGTCATGTGGCTAATCCTCTA	58.347	45.455	0.00	0.00	35.26	2.43
2254	2481	6.270927	TGTGGCTAATCCTCTAGCTCATTAAT	59.729	38.462	0.00	0.00	43.28	1.40
2255	2482	7.454694	TGTGGCTAATCCTCTAGCTCATTAATA	59.545	37.037	0.00	0.00	43.28	0.98
2256	2483	8.314751	GTGGCTAATCCTCTAGCTCATTAATAA	58.685	37.037	0.00	0.00	43.28	1.40
2421	2686	8.350722	GTCATCAATGTGCTCAATATTCTCATT	58.649	33.333	0.00	0.00	0.00	2.57
2443	2708	1.656652	CCGATCAGTGGTTTAGGCAG	58.343	55.000	0.00	0.00	0.00	4.85
2447	2712	3.125316	CGATCAGTGGTTTAGGCAGAAAC	59.875	47.826	6.51	6.51	38.38	2.78
2528	2836	5.123344	GGTGGTTTTATGCTGTTAACTCGAT	59.877	40.000	7.22	0.00	0.00	3.59
2541	2849	5.048504	TGTTAACTCGATGAGGACTAACGTT	60.049	40.000	5.88	5.88	33.35	3.99
2558	2866	3.585862	ACGTTGTCGCTGAGATGTAAAT	58.414	40.909	0.00	0.00	41.18	1.40
2645	2953	6.013379	TGTTGTTGAAGGAAATATGCCCTAA	58.987	36.000	0.00	0.00	31.36	2.69
2772	3083	6.265649	AGACAAACAGAGTGTCACTAGTATGT	59.734	38.462	5.21	7.89	46.44	2.29
3070	3381	2.563179	GCTCTACAGGTGTCTCCAAAGA	59.437	50.000	0.00	0.00	39.02	2.52
3080	3391	5.485353	AGGTGTCTCCAAAGATAGATGTTGA	59.515	40.000	0.00	0.00	39.02	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.743938	ACGTACCAAGATGATGATCGC	58.256	47.619	0.00	0.00	33.34	4.58
12	13	4.338400	TCCTGTCTACGTACCAAGATGATG	59.662	45.833	0.00	0.00	0.00	3.07
16	17	5.071370	CCTATCCTGTCTACGTACCAAGAT	58.929	45.833	0.00	0.00	0.00	2.40
31	32	5.674525	TGACAGAAAACTATGCCTATCCTG	58.325	41.667	0.00	0.00	0.00	3.86
184	185	2.029020	TCGGACACAAATCTCACCAGAG	60.029	50.000	0.00	0.00	43.48	3.35
211	212	2.803817	AAGGAGGGTGTCGTGCGTT	61.804	57.895	0.00	0.00	0.00	4.84
223	224	0.331278	TACCAATGCCACCAAGGAGG	59.669	55.000	0.00	0.00	41.22	4.30
312	315	3.804036	ACATCAGACGTGGTTGAAGAAA	58.196	40.909	0.00	0.00	0.00	2.52
333	336	4.402793	GCTAGATCCCAGAGTTGTCAACTA	59.597	45.833	18.17	2.92	43.03	2.24
447	450	3.389329	CCTGTAGGAGCACCTTCACATAT	59.611	47.826	8.39	0.00	45.36	1.78
545	548	1.033746	AGAATCTTGTGCCATGCCGG	61.034	55.000	0.00	0.00	38.11	6.13
693	705	3.491619	CCTCCACGATTCATCTGTACTGG	60.492	52.174	0.00	0.00	0.00	4.00
699	758	3.533606	ACTTCCTCCACGATTCATCTG	57.466	47.619	0.00	0.00	0.00	2.90
849	913	5.205821	GGGTTAGGGTTAGGTGCAATTTAT	58.794	41.667	0.00	0.00	0.00	1.40
852	916	2.291996	GGGGTTAGGGTTAGGTGCAATT	60.292	50.000	0.00	0.00	0.00	2.32
853	917	1.286849	GGGGTTAGGGTTAGGTGCAAT	59.713	52.381	0.00	0.00	0.00	3.56
854	918	0.699981	GGGGTTAGGGTTAGGTGCAA	59.300	55.000	0.00	0.00	0.00	4.08
899	987	4.377839	TGAAGACGATCAGATTCAGACC	57.622	45.455	0.00	0.00	0.00	3.85
943	1053	2.860735	CCTTCGCGGTAAGATTCAGAAG	59.139	50.000	6.13	0.00	34.94	2.85
945	1055	1.470979	GCCTTCGCGGTAAGATTCAGA	60.471	52.381	6.13	0.00	34.25	3.27
1016	1201	1.149148	GGTCAAGAAGAGCACGAACC	58.851	55.000	0.00	0.00	44.14	3.62
1028	1216	0.106769	TGCAGCAAACAGGGTCAAGA	60.107	50.000	0.00	0.00	0.00	3.02
1626	1847	3.332493	GAACGGCGCGGTAGAGACA	62.332	63.158	21.59	0.00	0.00	3.41
1670	1891	1.447838	GTCGTCATGGATGGCACGT	60.448	57.895	0.00	0.00	32.13	4.49
1767	1988	4.993584	AGGATAAGCATGTAGAATTCAGCG	59.006	41.667	8.44	0.00	0.00	5.18
1920	2144	2.159787	CGCTTCAAACTCGGATGTGAAG	60.160	50.000	12.81	12.81	46.33	3.02
1991	2215	0.035630	AGTCACCATGCCAGAGAAGC	60.036	55.000	0.00	0.00	0.00	3.86
1998	2222	4.720902	CCGCCAGTCACCATGCCA	62.721	66.667	0.00	0.00	0.00	4.92
2020	2244	2.037847	GGTGATGGCAAGCCCCTT	59.962	61.111	8.89	0.00	34.56	3.95
2021	2245	3.267233	TGGTGATGGCAAGCCCCT	61.267	61.111	8.89	0.00	34.56	4.79
2022	2246	3.070576	GTGGTGATGGCAAGCCCC	61.071	66.667	8.89	2.85	34.56	5.80
2280	2507	0.385473	CACATGACCGGCGAACAAAC	60.385	55.000	9.30	0.00	0.00	2.93
2343	2608	1.369448	CGGTCGCGAGAGATAGCAC	60.369	63.158	10.24	0.00	43.49	4.40
2421	2686	0.174845	CCTAAACCACTGATCGGCGA	59.825	55.000	13.87	13.87	0.00	5.54
2487	2752	1.808945	CACCACATTGAAGGCTGACTC	59.191	52.381	0.00	0.00	0.00	3.36
2528	2836	0.956633	AGCGACAACGTTAGTCCTCA	59.043	50.000	18.71	0.00	41.98	3.86
2541	2849	6.801539	AGAAAAATTTACATCTCAGCGACA	57.198	33.333	0.00	0.00	0.00	4.35
2772	3083	6.822170	TGATTAACGAGCTAGTCAAGTAGAGA	59.178	38.462	0.00	0.00	0.00	3.10
3070	3381	5.234329	CGAAATACGCCAACTCAACATCTAT	59.766	40.000	0.00	0.00	34.51	1.98
3080	3391	4.098960	TCCTAATCTCGAAATACGCCAACT	59.901	41.667	0.00	0.00	42.26	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.