AutoCloner

Multiple sequence alignment - TraesCS2B01G451500

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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	TraesCS2B01G451500	chr2B	100.000	2583	0	0	1	2583	645134805	645132223	0.000000e+00	4771.0
1	TraesCS2B01G451500	chr2B	83.422	187	26	4	608	791	398574437	398574621	4.420000e-38	169.0
2	TraesCS2B01G451500	chr5D	93.553	2606	144	5	1	2583	462797333	462794729	0.000000e+00	3860.0
3	TraesCS2B01G451500	chr5D	100.000	28	0	0	767	794	317283405	317283378	5.000000e-03	52.8
4	TraesCS2B01G451500	chr3D	93.250	1363	83	3	1	1360	283967579	283966223	0.000000e+00	1999.0
5	TraesCS2B01G451500	chr3D	96.074	866	30	3	1720	2583	283965217	283964354	0.000000e+00	1408.0
6	TraesCS2B01G451500	chr3D	94.203	276	16	0	1422	1697	283966214	283965939	3.070000e-114	422.0
7	TraesCS2B01G451500	chr6D	95.520	1183	49	2	1405	2583	288467007	288468189	0.000000e+00	1888.0
8	TraesCS2B01G451500	chr6D	91.685	1371	93	3	1	1352	288465641	288467009	0.000000e+00	1881.0
9	TraesCS2B01G451500	chr7A	87.512	1009	104	5	796	1782	22920190	22919182	0.000000e+00	1146.0
10	TraesCS2B01G451500	chr7D	87.500	992	109	11	804	1782	22530289	22529300	0.000000e+00	1131.0
11	TraesCS2B01G451500	chr4A	89.441	805	75	6	1787	2582	18745895	18746698	0.000000e+00	1007.0
12	TraesCS2B01G451500	chr4A	87.014	901	102	14	894	1782	705180497	705179600	0.000000e+00	1002.0
13	TraesCS2B01G451500	chr2A	89.335	797	79	4	1790	2582	453508536	453507742	0.000000e+00	996.0
14	TraesCS2B01G451500	chr5A	89.166	803	80	4	1787	2582	4799395	4800197	0.000000e+00	994.0
15	TraesCS2B01G451500	chr5A	92.355	484	34	2	1955	2436	554339940	554339458	0.000000e+00	686.0
16	TraesCS2B01G451500	chr5A	95.413	109	5	0	2475	2583	554339457	554339349	9.500000e-40	174.0
17	TraesCS2B01G451500	chr3A	89.624	665	64	4	1775	2436	454087983	454088645	0.000000e+00	841.0
18	TraesCS2B01G451500	chr2D	85.204	196	18	9	606	794	330453728	330453919	9.430000e-45	191.0
19	TraesCS2B01G451500	chr2D	100.000	28	0	0	767	794	92613493	92613466	5.000000e-03	52.8
20	TraesCS2B01G451500	chr4D	100.000	28	0	0	767	794	69539729	69539702	5.000000e-03	52.8
21	TraesCS2B01G451500	chr4D	100.000	28	0	0	767	794	261986679	261986706	5.000000e-03	52.8

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	TraesCS2B01G451500	chr2B	645132223	645134805	2582	True	4771.000000	4771	100.0000	1	2583	1	chr2B.!!$R1	2582
1	TraesCS2B01G451500	chr5D	462794729	462797333	2604	True	3860.000000	3860	93.5530	1	2583	1	chr5D.!!$R2	2582
2	TraesCS2B01G451500	chr3D	283964354	283967579	3225	True	1276.333333	1999	94.5090	1	2583	3	chr3D.!!$R1	2582
3	TraesCS2B01G451500	chr6D	288465641	288468189	2548	False	1884.500000	1888	93.6025	1	2583	2	chr6D.!!$F1	2582
4	TraesCS2B01G451500	chr7A	22919182	22920190	1008	True	1146.000000	1146	87.5120	796	1782	1	chr7A.!!$R1	986
5	TraesCS2B01G451500	chr7D	22529300	22530289	989	True	1131.000000	1131	87.5000	804	1782	1	chr7D.!!$R1	978
6	TraesCS2B01G451500	chr4A	18745895	18746698	803	False	1007.000000	1007	89.4410	1787	2582	1	chr4A.!!$F1	795
7	TraesCS2B01G451500	chr4A	705179600	705180497	897	True	1002.000000	1002	87.0140	894	1782	1	chr4A.!!$R1	888
8	TraesCS2B01G451500	chr2A	453507742	453508536	794	True	996.000000	996	89.3350	1790	2582	1	chr2A.!!$R1	792
9	TraesCS2B01G451500	chr5A	4799395	4800197	802	False	994.000000	994	89.1660	1787	2582	1	chr5A.!!$F1	795
10	TraesCS2B01G451500	chr5A	554339349	554339940	591	True	430.000000	686	93.8840	1955	2583	2	chr5A.!!$R1	628
11	TraesCS2B01G451500	chr3A	454087983	454088645	662	False	841.000000	841	89.6240	1775	2436	1	chr3A.!!$F1	661

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
297	301	2.443887	ATGCACACACTTTCCATTGC	57.556	45.0	0.0	0.0	0.0	3.56	F
1230	1279	0.541764	ATTTTGCAGGCTCGGGGAAA	60.542	50.0	0.0	0.0	0.0	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1254	1303	0.183492	TGCTGACTCAAAGCCTGGTT	59.817	50.0	0.00	0.00	40.06	3.67	R
2460	3305	0.820891	ATCACCTTCCGGATGCATGC	60.821	55.0	11.82	11.82	0.00	4.06	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
68	69	5.197451	TGGAAGTTATGTGGTTCAACTGTT	58.803	37.500	0.00	0.00	32.96	3.16
79	80	5.298276	GTGGTTCAACTGTTTCAGGTATGAA	59.702	40.000	0.00	6.34	43.72	2.57
90	91	6.042781	TGTTTCAGGTATGAACTCACCTAAGT	59.957	38.462	0.00	0.00	45.07	2.24
100	101	6.848451	TGAACTCACCTAAGTTTGTTTCAAC	58.152	36.000	0.00	0.00	39.55	3.18
105	106	7.973944	ACTCACCTAAGTTTGTTTCAACATTTC	59.026	33.333	0.00	0.00	38.95	2.17
122	123	7.981225	TCAACATTTCGATCTAGAACATCATGA	59.019	33.333	0.00	0.00	0.00	3.07
123	124	8.606602	CAACATTTCGATCTAGAACATCATGAA	58.393	33.333	0.00	0.00	0.00	2.57
159	160	8.007405	TCTTTGCTAATACTGATGTACTGCTA	57.993	34.615	0.00	0.00	0.00	3.49
163	164	7.371159	TGCTAATACTGATGTACTGCTATCAC	58.629	38.462	0.00	0.00	30.66	3.06
189	190	3.537580	TGGTAATTACGCTTTAGCAGGG	58.462	45.455	9.46	0.00	42.21	4.45
216	217	4.292977	GGATTGACCTAGCCAAATTTCG	57.707	45.455	0.00	0.00	35.41	3.46
291	295	8.662781	TTCCTATATAGAATGCACACACTTTC	57.337	34.615	11.53	0.00	0.00	2.62
297	301	2.443887	ATGCACACACTTTCCATTGC	57.556	45.000	0.00	0.00	0.00	3.56
443	485	6.918022	ACTTCTTCCAAATCAAATTGAACGAC	59.082	34.615	0.00	0.00	31.84	4.34
445	487	5.300539	TCTTCCAAATCAAATTGAACGACCA	59.699	36.000	0.00	0.00	31.84	4.02
447	489	6.095432	TCCAAATCAAATTGAACGACCATT	57.905	33.333	0.00	0.00	31.84	3.16
465	507	7.280205	ACGACCATTTTTAGATGTTAGGATGAC	59.720	37.037	0.00	0.00	0.00	3.06
467	509	8.877864	ACCATTTTTAGATGTTAGGATGACAA	57.122	30.769	0.00	0.00	0.00	3.18
499	541	9.689976	TTTATGTTGTGTCATTTACCAAGAATG	57.310	29.630	0.00	0.00	36.15	2.67
517	559	8.950210	CCAAGAATGTTGTTTACAGAGATGTAT	58.050	33.333	0.00	0.00	40.83	2.29
645	687	3.940852	GTGACACATCCTATGCATGAACA	59.059	43.478	10.16	0.00	0.00	3.18
655	697	9.669353	CATCCTATGCATGAACAAAGTTTATAC	57.331	33.333	10.16	0.00	0.00	1.47
864	909	5.944007	AGGCACGTTTATTAGTTTCCTGATT	59.056	36.000	0.00	0.00	0.00	2.57
925	972	5.680619	ACGATGCATCTATTTGGTTTCCTA	58.319	37.500	23.73	0.00	0.00	2.94
957	1004	9.551734	CATCCTAGATTGATCACATTTCTGTTA	57.448	33.333	0.00	0.00	31.62	2.41
1030	1077	1.869754	GCAGCTTGTTCTGTGACTCGA	60.870	52.381	0.00	0.00	36.49	4.04
1031	1078	2.681706	CAGCTTGTTCTGTGACTCGAT	58.318	47.619	0.00	0.00	0.00	3.59
1038	1085	5.835113	TGTTCTGTGACTCGATATCATCA	57.165	39.130	3.12	0.56	0.00	3.07
1049	1096	8.253810	TGACTCGATATCATCAGAGAACTTTTT	58.746	33.333	11.06	0.00	35.45	1.94
1084	1131	0.841961	TGAGAGATGCCCATTCCTGG	59.158	55.000	0.00	0.00	42.73	4.45
1159	1206	6.045318	GCTGTAAGATCTGCTTCTTATGTCA	58.955	40.000	0.00	2.53	39.65	3.58
1208	1257	7.444299	AGTGCATTTTTCCTTGACAATATGTT	58.556	30.769	0.00	0.00	0.00	2.71
1230	1279	0.541764	ATTTTGCAGGCTCGGGGAAA	60.542	50.000	0.00	0.00	0.00	3.13
1231	1280	0.541764	TTTTGCAGGCTCGGGGAAAT	60.542	50.000	0.00	0.00	0.00	2.17
1254	1303	1.492176	GGGCCTGATCTTTGAGGATGA	59.508	52.381	0.84	0.00	0.00	2.92
1270	1319	2.553028	GGATGAACCAGGCTTTGAGTCA	60.553	50.000	0.00	0.00	38.79	3.41
1280	1329	2.816087	GGCTTTGAGTCAGCATTCAAGA	59.184	45.455	6.69	0.00	39.21	3.02
1290	1339	5.713389	AGTCAGCATTCAAGATTTTCCATGA	59.287	36.000	0.00	0.00	0.00	3.07
1327	1376	5.104318	AGTTCCCCTTTCAGGAAGATCATAC	60.104	44.000	0.00	0.00	43.99	2.39
1334	1383	3.562182	TCAGGAAGATCATACGTGCCTA	58.438	45.455	0.00	0.00	0.00	3.93
1336	1385	4.404394	TCAGGAAGATCATACGTGCCTAAA	59.596	41.667	0.00	0.00	0.00	1.85
1381	1485	3.173151	TGTCAATCCTGAACCTGCTCTA	58.827	45.455	0.00	0.00	31.88	2.43
1402	1506	3.444029	ACCCTTTAATCCATTTGCTGCT	58.556	40.909	0.00	0.00	0.00	4.24
1429	1533	3.367498	CCGCTACCATAAGTCTATCAGCC	60.367	52.174	0.00	0.00	0.00	4.85
1488	1592	3.451526	GCAAAAAGCAGAACAAGAAGCT	58.548	40.909	0.00	0.00	44.79	3.74
1504	1608	5.690464	AGAAGCTCAACAATCTAGACCAT	57.310	39.130	0.00	0.00	0.00	3.55
1516	1620	7.170965	ACAATCTAGACCATTCACACAAGAAT	58.829	34.615	0.00	0.00	38.72	2.40
1546	1650	4.462133	AGCCAGATCAGAATTCCATGAAG	58.538	43.478	0.65	0.00	0.00	3.02
1662	1775	3.135348	AGCCACATGACACACAGCTATAT	59.865	43.478	0.00	0.00	0.00	0.86
1785	2619	9.685276	TTCATTAACCACATTCAGATAGTCAAT	57.315	29.630	0.00	0.00	0.00	2.57
1812	2646	9.028284	AGAGATGAATTTGACCATGTTTACAAT	57.972	29.630	0.00	0.00	0.00	2.71
1821	2655	8.777865	TTGACCATGTTTACAATCTCTTAGAG	57.222	34.615	2.23	2.23	0.00	2.43
1858	2692	9.364653	TGAAAAGGTAGTCTTAGTTTCTAGAGT	57.635	33.333	0.00	0.00	34.78	3.24
1888	2722	5.450818	TGATGGAGGCTACTACCAAATTT	57.549	39.130	0.00	0.00	37.24	1.82
1938	2774	6.823689	ACAAGAATCTAATTACGCCATGTTCT	59.176	34.615	0.00	0.00	0.00	3.01
2368	3209	6.959904	AGATAGCCGAATACATCTACCTCTA	58.040	40.000	0.00	0.00	0.00	2.43
2430	3275	4.491676	TGATCGGGTCTTCTTTTACTTCG	58.508	43.478	0.00	0.00	0.00	3.79
2459	3304	6.040054	CCTCAATTGTATTCATTGGCTGATCA	59.960	38.462	5.13	0.00	32.72	2.92
2460	3305	7.034685	TCAATTGTATTCATTGGCTGATCAG	57.965	36.000	18.84	18.84	32.72	2.90
2512	3357	7.744733	TGCATCTATCAACATGGGTTATAGAA	58.255	34.615	0.00	0.00	35.59	2.10
2514	3359	7.661437	GCATCTATCAACATGGGTTATAGAACA	59.339	37.037	2.17	0.00	35.59	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	6.207025	GTCTACAGAATCCTCGGCTCTAAATA	59.793	42.308	0.00	0.00	0.00	1.40
68	69	6.681729	AACTTAGGTGAGTTCATACCTGAA	57.318	37.500	6.20	0.00	46.40	3.02
79	80	7.404671	AATGTTGAAACAAACTTAGGTGAGT	57.595	32.000	0.00	0.00	43.03	3.41
90	91	8.616942	TGTTCTAGATCGAAATGTTGAAACAAA	58.383	29.630	0.00	0.00	43.03	2.83
100	101	8.134905	TGTTCATGATGTTCTAGATCGAAATG	57.865	34.615	0.00	0.00	0.00	2.32
105	106	6.202379	AGCAATGTTCATGATGTTCTAGATCG	59.798	38.462	0.00	0.00	0.00	3.69
122	123	9.793252	CAGTATTAGCAAAGAATAAGCAATGTT	57.207	29.630	0.00	0.00	0.00	2.71
123	124	9.177608	TCAGTATTAGCAAAGAATAAGCAATGT	57.822	29.630	0.00	0.00	0.00	2.71
145	146	5.620738	AATGGTGATAGCAGTACATCAGT	57.379	39.130	0.00	0.00	31.99	3.41
163	164	5.885881	TGCTAAAGCGTAATTACCAAATGG	58.114	37.500	10.01	0.00	45.83	3.16
214	215	9.784680	TGCTTTTTATACTGTTTACAAAAACGA	57.215	25.926	0.00	0.00	46.63	3.85
237	241	7.603180	TCTGTATAGGAAACATCATACTGCT	57.397	36.000	0.00	0.00	0.00	4.24
291	295	3.931468	TGGATTTTATTTGCACGCAATGG	59.069	39.130	5.11	0.00	35.70	3.16
297	301	5.789512	GCATTGTTTGGATTTTATTTGCACG	59.210	36.000	0.00	0.00	0.00	5.34
443	485	8.960591	AGTTGTCATCCTAACATCTAAAAATGG	58.039	33.333	0.00	0.00	0.00	3.16
445	487	9.965902	AGAGTTGTCATCCTAACATCTAAAAAT	57.034	29.630	0.00	0.00	29.17	1.82
467	509	9.733556	TGGTAAATGACACAACATAAATAGAGT	57.266	29.630	0.00	0.00	0.00	3.24
571	613	0.108615	CGACTCTTGCCGACTGGAAT	60.109	55.000	0.00	0.00	37.49	3.01
794	836	6.069088	TCAGGAAACATATTATCACCAGGGTT	60.069	38.462	0.00	0.00	0.00	4.11
842	887	8.609176	TGATAATCAGGAAACTAATAAACGTGC	58.391	33.333	0.00	0.00	40.21	5.34
864	909	6.798427	AGTTCCAGAGAAGCATAACTGATA	57.202	37.500	0.00	0.00	30.91	2.15
925	972	6.566079	TGTGATCAATCTAGGATGAGGTTT	57.434	37.500	0.00	0.00	0.00	3.27
978	1025	7.716123	AGCATTTTCAATCTAGGAGAAGAGATG	59.284	37.037	0.00	0.90	32.66	2.90
981	1028	7.274447	AGAGCATTTTCAATCTAGGAGAAGAG	58.726	38.462	0.00	0.00	0.00	2.85
1015	1062	6.095440	TCTGATGATATCGAGTCACAGAACAA	59.905	38.462	20.41	8.87	34.22	2.83
1049	1096	2.038952	CTCTCAACACCAGGATGACCAA	59.961	50.000	0.00	0.00	39.69	3.67
1059	1106	0.994247	ATGGGCATCTCTCAACACCA	59.006	50.000	0.00	0.00	0.00	4.17
1084	1131	1.106285	GTGGCTCCATTGATGTTCCC	58.894	55.000	0.00	0.00	0.00	3.97
1159	1206	3.576078	TTGGTCAGAGTGTCACCAAAT	57.424	42.857	0.00	0.00	45.29	2.32
1169	1216	1.717032	TGCACTACCTTGGTCAGAGT	58.283	50.000	0.00	0.00	0.00	3.24
1171	1219	3.788227	AAATGCACTACCTTGGTCAGA	57.212	42.857	0.00	0.00	0.00	3.27
1172	1220	4.321230	GGAAAAATGCACTACCTTGGTCAG	60.321	45.833	0.00	0.00	0.00	3.51
1208	1257	1.181786	CCCCGAGCCTGCAAAATAAA	58.818	50.000	0.00	0.00	0.00	1.40
1230	1279	3.397527	TCCTCAAAGATCAGGCCCTTAT	58.602	45.455	0.00	0.00	0.00	1.73
1231	1280	2.845659	TCCTCAAAGATCAGGCCCTTA	58.154	47.619	0.00	0.00	0.00	2.69
1254	1303	0.183492	TGCTGACTCAAAGCCTGGTT	59.817	50.000	0.00	0.00	40.06	3.67
1270	1319	6.349243	TGTTCATGGAAAATCTTGAATGCT	57.651	33.333	0.00	0.00	34.72	3.79
1280	1329	4.335735	TCCCATCCTGTTCATGGAAAAT	57.664	40.909	0.00	0.00	43.32	1.82
1327	1376	3.865745	CACTATGGTTCTCTTTAGGCACG	59.134	47.826	0.00	0.00	0.00	5.34
1381	1485	3.444029	AGCAGCAAATGGATTAAAGGGT	58.556	40.909	0.00	0.00	0.00	4.34
1402	1506	3.225177	AGACTTATGGTAGCGGCTCTA	57.775	47.619	5.39	0.00	0.00	2.43
1488	1592	5.863965	TGTGTGAATGGTCTAGATTGTTGA	58.136	37.500	0.00	0.00	0.00	3.18
1504	1608	3.068024	GCTTGTTGGGATTCTTGTGTGAA	59.932	43.478	0.00	0.00	0.00	3.18
1516	1620	1.361204	TCTGATCTGGCTTGTTGGGA	58.639	50.000	0.00	0.00	0.00	4.37
1568	1672	5.876651	ATTGCAAATTAAGAGGGGGAATC	57.123	39.130	1.71	0.00	0.00	2.52
1573	1677	4.157656	TCGACAATTGCAAATTAAGAGGGG	59.842	41.667	1.71	0.00	0.00	4.79
1785	2619	9.513906	TTGTAAACATGGTCAAATTCATCTCTA	57.486	29.630	0.00	0.00	0.00	2.43
1788	2622	9.028284	AGATTGTAAACATGGTCAAATTCATCT	57.972	29.630	0.00	0.00	0.00	2.90
1821	2655	8.779354	AAGACTACCTTTTCATCAAGATGTAC	57.221	34.615	9.66	0.00	39.72	2.90
1832	2666	9.364653	ACTCTAGAAACTAAGACTACCTTTTCA	57.635	33.333	0.00	0.00	36.34	2.69
1858	2692	8.270137	TGGTAGTAGCCTCCATCAATTTTATA	57.730	34.615	0.00	0.00	0.00	0.98
1888	2722	4.161189	TGCTTTTCAAATTGGAACAGTGGA	59.839	37.500	9.87	0.00	42.39	4.02
2045	2883	1.228862	GCACCAACCATCCCAAGGT	60.229	57.895	0.00	0.00	42.34	3.50
2169	3008	1.212616	GCCTGCTTGTCTATGTAGCG	58.787	55.000	0.00	0.00	37.73	4.26
2175	3014	1.690219	CCCTCGGCCTGCTTGTCTAT	61.690	60.000	0.00	0.00	0.00	1.98
2176	3015	2.359169	CCCTCGGCCTGCTTGTCTA	61.359	63.158	0.00	0.00	0.00	2.59
2203	3042	3.716195	CCATCTGTGGCACCCGGA	61.716	66.667	16.26	11.03	39.01	5.14
2340	3181	6.946583	AGGTAGATGTATTCGGCTATCTTACA	59.053	38.462	0.00	0.00	32.54	2.41
2430	3275	5.127682	AGCCAATGAATACAATTGAGGAACC	59.872	40.000	13.59	0.00	0.00	3.62
2459	3304	1.452651	CACCTTCCGGATGCATGCT	60.453	57.895	20.33	4.11	0.00	3.79
2460	3305	0.820891	ATCACCTTCCGGATGCATGC	60.821	55.000	11.82	11.82	0.00	4.06
2469	3314	1.945387	CATCAGGACATCACCTTCCG	58.055	55.000	0.00	0.00	38.32	4.30
2470	3315	1.065199	TGCATCAGGACATCACCTTCC	60.065	52.381	0.00	0.00	38.32	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.