AutoCloner

Multiple sequence alignment - TraesCS7B01G171300

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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	TraesCS7B01G171300	chr7B	100.000	2435	0	0	1	2435	244270873	244268439	0.000000e+00	4497
1	TraesCS7B01G171300	chr7B	94.778	517	26	1	1920	2435	176228309	176228825	0.000000e+00	804
2	TraesCS7B01G171300	chr7B	94.778	517	26	1	1920	2435	689892695	689893211	0.000000e+00	804
3	TraesCS7B01G171300	chr7D	95.611	1162	34	8	742	1899	263958996	263957848	0.000000e+00	1847
4	TraesCS7B01G171300	chr7D	96.680	753	22	2	1	751	263960154	263959403	0.000000e+00	1249
5	TraesCS7B01G171300	chr7D	80.973	946	132	35	696	1624	263956377	263955463	0.000000e+00	706
6	TraesCS7B01G171300	chr7D	79.719	784	130	17	772	1544	263952837	263952072	7.660000e-150	540
7	TraesCS7B01G171300	chr7A	94.844	1183	37	10	720	1899	287215543	287214382	0.000000e+00	1825
8	TraesCS7B01G171300	chr7A	81.924	946	124	33	696	1624	287212912	287211997	0.000000e+00	756
9	TraesCS7B01G171300	chr7A	80.093	216	19	13	519	724	287216235	287216034	3.260000e-29	139
10	TraesCS7B01G171300	chr6B	95.753	518	20	2	1920	2435	18830384	18829867	0.000000e+00	833
11	TraesCS7B01G171300	chr6B	94.971	517	25	1	1920	2435	28177967	28177451	0.000000e+00	809
12	TraesCS7B01G171300	chr3B	95.745	517	21	1	1920	2435	716319278	716318762	0.000000e+00	832
13	TraesCS7B01G171300	chr3B	94.584	517	26	2	1920	2435	675670908	675671423	0.000000e+00	798
14	TraesCS7B01G171300	chr1B	95.358	517	23	1	1920	2435	449714510	449713994	0.000000e+00	821
15	TraesCS7B01G171300	chr1B	94.584	517	27	1	1920	2435	813110	812594	0.000000e+00	798
16	TraesCS7B01G171300	chr5B	95.164	517	24	1	1920	2435	690255323	690255839	0.000000e+00	815
17	TraesCS7B01G171300	chr5B	80.755	265	49	2	1106	1369	528537672	528537935	3.170000e-49	206
18	TraesCS7B01G171300	chr5B	80.597	268	44	8	1106	1369	528524850	528525113	1.480000e-47	200
19	TraesCS7B01G171300	chr5A	79.924	264	53	0	1106	1369	549153940	549154203	6.870000e-46	195
20	TraesCS7B01G171300	chr5A	78.947	247	50	2	1124	1369	549214942	549214697	1.500000e-37	167

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	TraesCS7B01G171300	chr7B	244268439	244270873	2434	True	4497.000000	4497	100.000000	1	2435	1	chr7B.!!$R1	2434
1	TraesCS7B01G171300	chr7B	176228309	176228825	516	False	804.000000	804	94.778000	1920	2435	1	chr7B.!!$F1	515
2	TraesCS7B01G171300	chr7B	689892695	689893211	516	False	804.000000	804	94.778000	1920	2435	1	chr7B.!!$F2	515
3	TraesCS7B01G171300	chr7D	263952072	263960154	8082	True	1085.500000	1847	88.245750	1	1899	4	chr7D.!!$R1	1898
4	TraesCS7B01G171300	chr7A	287211997	287216235	4238	True	906.666667	1825	85.620333	519	1899	3	chr7A.!!$R1	1380
5	TraesCS7B01G171300	chr6B	18829867	18830384	517	True	833.000000	833	95.753000	1920	2435	1	chr6B.!!$R1	515
6	TraesCS7B01G171300	chr6B	28177451	28177967	516	True	809.000000	809	94.971000	1920	2435	1	chr6B.!!$R2	515
7	TraesCS7B01G171300	chr3B	716318762	716319278	516	True	832.000000	832	95.745000	1920	2435	1	chr3B.!!$R1	515
8	TraesCS7B01G171300	chr3B	675670908	675671423	515	False	798.000000	798	94.584000	1920	2435	1	chr3B.!!$F1	515
9	TraesCS7B01G171300	chr1B	449713994	449714510	516	True	821.000000	821	95.358000	1920	2435	1	chr1B.!!$R2	515
10	TraesCS7B01G171300	chr1B	812594	813110	516	True	798.000000	798	94.584000	1920	2435	1	chr1B.!!$R1	515
11	TraesCS7B01G171300	chr5B	690255323	690255839	516	False	815.000000	815	95.164000	1920	2435	1	chr5B.!!$F3	515

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
359	360	0.179056	AATTGTATCACCCGAGGGCG	60.179	55.0	8.33	0.00	39.32	6.13	F
1026	1951	0.104671	GCTCCAGGAAGCTAGCTCAG	59.895	60.0	19.65	8.12	39.27	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1417	2345	0.469494	TTTCAGGAGCTGTGCACAGA	59.531	50.0	43.32	23.37	46.59	3.41	R
1969	2903	0.675633	GCTGAAGCTGCCCAGAAAAA	59.324	50.0	19.57	0.00	38.21	1.94	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
89	90	5.518812	TGAAATTGATCGTTGTTGGAAGTG	58.481	37.500	0.00	0.00	0.00	3.16
238	239	5.769662	AGCTGTTTGTGATTAATGTCTTCCA	59.230	36.000	0.00	0.00	0.00	3.53
255	256	9.851686	ATGTCTTCCAAATCTAAATATGCTGTA	57.148	29.630	0.00	0.00	0.00	2.74
353	354	6.183360	GGTTTACTGGTTAATTGTATCACCCG	60.183	42.308	0.00	0.00	0.00	5.28
359	360	0.179056	AATTGTATCACCCGAGGGCG	60.179	55.000	8.33	0.00	39.32	6.13
383	384	3.202906	TCGAAGCTGCAAGTTAACTGTT	58.797	40.909	9.34	0.00	35.30	3.16
386	387	1.956477	AGCTGCAAGTTAACTGTTGGG	59.044	47.619	9.34	0.64	35.30	4.12
398	399	9.975218	AAGTTAACTGTTGGGACATTTCTATAT	57.025	29.630	9.34	0.00	39.30	0.86
482	483	0.560688	AACAAAAAGGGGCAGGAGGA	59.439	50.000	0.00	0.00	0.00	3.71
495	496	3.244181	GGCAGGAGGAAAATCAGCAAAAA	60.244	43.478	0.00	0.00	0.00	1.94
506	507	9.780413	GGAAAATCAGCAAAAACAACATAAAAA	57.220	25.926	0.00	0.00	0.00	1.94
624	627	5.493133	ACGTTGCTTCAAACACAATTCTA	57.507	34.783	0.00	0.00	0.00	2.10
625	628	5.270853	ACGTTGCTTCAAACACAATTCTAC	58.729	37.500	0.00	0.00	0.00	2.59
686	700	3.840666	TCTCAAAGCTCAACCCACTATCT	59.159	43.478	0.00	0.00	0.00	1.98
816	1741	2.838202	GAGTTCATGGTCTTGTCCCCTA	59.162	50.000	0.00	0.00	0.00	3.53
824	1749	3.268330	GGTCTTGTCCCCTAACGATTTC	58.732	50.000	0.00	0.00	0.00	2.17
848	1773	9.793259	TTCCTATCTATGATAATTGTGGAAACC	57.207	33.333	0.00	0.00	0.00	3.27
865	1790	1.755179	ACCAAGATGCAGATTTCCCG	58.245	50.000	0.00	0.00	0.00	5.14
916	1841	0.517316	GGCACAAACCATCGACAGAC	59.483	55.000	0.00	0.00	0.00	3.51
983	1908	1.028868	GTCACAGCCCATCTCCTTGC	61.029	60.000	0.00	0.00	0.00	4.01
1026	1951	0.104671	GCTCCAGGAAGCTAGCTCAG	59.895	60.000	19.65	8.12	39.27	3.35
1251	2179	1.523154	TTGGGTTCACAAGCGATGGC	61.523	55.000	0.00	0.00	40.37	4.40
1260	2188	0.463295	CAAGCGATGGCAGGATCACT	60.463	55.000	1.50	0.00	43.41	3.41
1305	2233	4.002982	TGGAGTATGTGATGTGTTTGCTC	58.997	43.478	0.00	0.00	0.00	4.26
1417	2345	2.084546	GCGGACTTAACCAGCAATTCT	58.915	47.619	0.00	0.00	32.76	2.40
1899	2832	7.009815	CCAAATGCTGTATGAAATTGTAAGCAG	59.990	37.037	0.00	0.00	41.96	4.24
1901	2834	5.252547	TGCTGTATGAAATTGTAAGCAGGA	58.747	37.500	0.00	0.00	34.46	3.86
1902	2835	5.709631	TGCTGTATGAAATTGTAAGCAGGAA	59.290	36.000	0.00	0.00	34.46	3.36
1903	2836	6.208402	TGCTGTATGAAATTGTAAGCAGGAAA	59.792	34.615	0.00	0.00	34.46	3.13
1904	2837	7.090173	GCTGTATGAAATTGTAAGCAGGAAAA	58.910	34.615	0.00	0.00	0.00	2.29
1905	2838	7.598493	GCTGTATGAAATTGTAAGCAGGAAAAA	59.402	33.333	0.00	0.00	0.00	1.94
1907	2840	9.638239	TGTATGAAATTGTAAGCAGGAAAAATC	57.362	29.630	0.00	0.00	0.00	2.17
1909	2842	8.767478	ATGAAATTGTAAGCAGGAAAAATCAG	57.233	30.769	0.00	0.00	0.00	2.90
1911	2844	8.855110	TGAAATTGTAAGCAGGAAAAATCAGTA	58.145	29.630	0.00	0.00	0.00	2.74
1912	2845	9.129209	GAAATTGTAAGCAGGAAAAATCAGTAC	57.871	33.333	0.00	0.00	0.00	2.73
1913	2846	6.569179	TTGTAAGCAGGAAAAATCAGTACC	57.431	37.500	0.00	0.00	0.00	3.34
1914	2847	5.626142	TGTAAGCAGGAAAAATCAGTACCA	58.374	37.500	0.00	0.00	0.00	3.25
1917	2850	5.453567	AGCAGGAAAAATCAGTACCAAAC	57.546	39.130	0.00	0.00	0.00	2.93
1918	2851	4.280929	AGCAGGAAAAATCAGTACCAAACC	59.719	41.667	0.00	0.00	0.00	3.27
1969	2903	8.814038	ATCTGTTGCCTCTGTTTAATAATCTT	57.186	30.769	0.00	0.00	0.00	2.40
1972	2906	9.696917	CTGTTGCCTCTGTTTAATAATCTTTTT	57.303	29.630	0.00	0.00	0.00	1.94
2008	2942	4.137849	GCTTTTTCAGCTGAATTTTGGC	57.862	40.909	28.89	22.06	46.27	4.52
2122	3159	4.310769	CAAGATTGGGACTAATAGGCTCG	58.689	47.826	0.00	0.00	0.00	5.03
2125	3162	1.040646	TGGGACTAATAGGCTCGCAG	58.959	55.000	0.00	0.00	0.00	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	78	3.013921	TGACCTTGTCACTTCCAACAAC	58.986	45.455	0.00	0.00	37.67	3.32
89	90	1.838112	TCATTGCCCATGACCTTGTC	58.162	50.000	0.00	0.00	36.94	3.18
203	204	2.292569	CACAAACAGCTTCACATCTGCT	59.707	45.455	0.00	0.00	37.56	4.24
255	256	7.613801	TGGTGTTCTAGTTGCCATAACAATATT	59.386	33.333	0.00	0.00	32.32	1.28
353	354	2.279784	CAGCTTCGATCCGCCCTC	60.280	66.667	0.00	0.00	0.00	4.30
359	360	3.003480	AGTTAACTTGCAGCTTCGATCC	58.997	45.455	1.12	0.00	0.00	3.36
383	384	7.201702	TGGTGTGTAATATAGAAATGTCCCA	57.798	36.000	0.00	0.00	0.00	4.37
434	435	4.463539	TGCTATGTGATTGGCTCAAAATGT	59.536	37.500	0.00	0.00	35.07	2.71
438	439	2.754552	GGTGCTATGTGATTGGCTCAAA	59.245	45.455	0.00	0.00	35.07	2.69
482	483	9.288124	GCTTTTTATGTTGTTTTTGCTGATTTT	57.712	25.926	0.00	0.00	0.00	1.82
542	543	2.210116	CCTTCCGTGCGTTATTATGCT	58.790	47.619	0.00	0.00	37.19	3.79
624	627	2.029020	GGACCCGTCCTTTAGTTTACGT	60.029	50.000	6.63	0.00	46.16	3.57
625	628	2.610433	GGACCCGTCCTTTAGTTTACG	58.390	52.381	6.63	0.00	46.16	3.18
686	700	4.430007	CATCTTTGCTAGCTTGGTACGTA	58.570	43.478	17.23	0.00	0.00	3.57
824	1749	9.573166	TTGGTTTCCACAATTATCATAGATAGG	57.427	33.333	0.00	0.00	30.78	2.57
848	1773	3.932459	GCGGGAAATCTGCATCTTG	57.068	52.632	0.00	0.00	46.73	3.02
916	1841	0.459411	TCGGTCTGTGTGTGTGTGTG	60.459	55.000	0.00	0.00	0.00	3.82
983	1908	4.809958	TGATCATGGTTGCTTGTTTTGTTG	59.190	37.500	0.00	0.00	0.00	3.33
1065	1990	2.413453	GTCTGATGTTGCGAACCTTCTC	59.587	50.000	0.00	0.00	0.00	2.87
1066	1991	2.224281	TGTCTGATGTTGCGAACCTTCT	60.224	45.455	0.00	0.00	0.00	2.85
1067	1992	2.143122	TGTCTGATGTTGCGAACCTTC	58.857	47.619	0.00	0.00	0.00	3.46
1251	2179	1.277273	TCACAAGGCAGAGTGATCCTG	59.723	52.381	3.10	0.00	39.65	3.86
1260	2188	4.650734	TCATTGTTGTATCACAAGGCAGA	58.349	39.130	0.00	0.00	39.00	4.26
1417	2345	0.469494	TTTCAGGAGCTGTGCACAGA	59.531	50.000	43.32	23.37	46.59	3.41
1728	2661	3.067106	TCGTTTGTTTTGCCTTTTTGCA	58.933	36.364	0.00	0.00	40.07	4.08
1836	2769	5.411831	TCTCTGATGGCATCCATACATAC	57.588	43.478	23.92	0.00	45.26	2.39
1899	2832	5.983118	CACTTGGTTTGGTACTGATTTTTCC	59.017	40.000	0.00	0.00	0.00	3.13
1901	2834	6.538945	ACACTTGGTTTGGTACTGATTTTT	57.461	33.333	0.00	0.00	0.00	1.94
1902	2835	6.337356	CAACACTTGGTTTGGTACTGATTTT	58.663	36.000	0.00	0.00	37.72	1.82
1903	2836	5.163457	CCAACACTTGGTTTGGTACTGATTT	60.163	40.000	0.00	0.00	45.93	2.17
1904	2837	4.340950	CCAACACTTGGTTTGGTACTGATT	59.659	41.667	0.00	0.00	45.93	2.57
1905	2838	3.888930	CCAACACTTGGTTTGGTACTGAT	59.111	43.478	0.00	0.00	45.93	2.90
1907	2840	3.708563	CCAACACTTGGTTTGGTACTG	57.291	47.619	0.00	0.00	45.93	2.74
1918	2851	5.301805	CCCCTTAATAATAGGCCAACACTTG	59.698	44.000	5.01	0.00	0.00	3.16
1929	2862	5.946377	GGCAACAGATCCCCCTTAATAATAG	59.054	44.000	0.00	0.00	0.00	1.73
1969	2903	0.675633	GCTGAAGCTGCCCAGAAAAA	59.324	50.000	19.57	0.00	38.21	1.94
2008	2942	3.958798	TCTTAGGGAGAAGGGTTATCGTG	59.041	47.826	0.00	0.00	0.00	4.35
2104	3039	2.037772	CTGCGAGCCTATTAGTCCCAAT	59.962	50.000	0.00	0.00	0.00	3.16
2122	3159	1.989966	ACAGCATGCGCAATCTCTGC	61.990	55.000	22.04	22.04	44.00	4.26
2125	3162	1.063649	CCACAGCATGCGCAATCTC	59.936	57.895	17.11	3.56	42.53	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.