AutoCloner

Multiple sequence alignment - TraesCS5B01G551000

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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	TraesCS5B01G551000	chr5B	100.000	2882	0	0	1	2882	702480329	702477448	0.000000e+00	5323.0
1	TraesCS5B01G551000	chr5B	84.864	1579	197	20	762	2310	702552821	702551255	0.000000e+00	1554.0
2	TraesCS5B01G551000	chr5B	86.102	1252	149	16	724	1967	702558103	702556869	0.000000e+00	1325.0
3	TraesCS5B01G551000	chr5B	83.575	207	24	4	2685	2881	702550862	702550656	4.900000e-43	185.0
4	TraesCS5B01G551000	chr5D	95.975	2236	70	6	397	2621	550301588	550299362	0.000000e+00	3613.0
5	TraesCS5B01G551000	chr5D	86.656	1259	150	14	724	1979	550402753	550401510	0.000000e+00	1378.0
6	TraesCS5B01G551000	chr5D	91.729	399	25	3	14	404	550302027	550301629	5.430000e-152	547.0
7	TraesCS5B01G551000	chr5D	87.940	199	3	10	2684	2882	550299194	550299017	6.250000e-52	215.0
8	TraesCS5B01G551000	chr5D	83.571	140	14	6	73	205	550403404	550403267	3.900000e-24	122.0
9	TraesCS5B01G551000	chr5D	82.482	137	13	5	73	204	550375258	550375128	3.040000e-20	110.0
10	TraesCS5B01G551000	chr4A	92.201	1654	88	13	765	2403	617360181	617361808	0.000000e+00	2302.0
11	TraesCS5B01G551000	chr4A	84.560	1658	212	24	682	2310	617288745	617290387	0.000000e+00	1604.0
12	TraesCS5B01G551000	chr4A	84.318	1658	217	22	682	2310	617348814	617350457	0.000000e+00	1581.0
13	TraesCS5B01G551000	chr4A	86.240	1468	166	17	724	2171	617281327	617282778	0.000000e+00	1559.0
14	TraesCS5B01G551000	chr4A	90.934	364	21	10	401	756	617359558	617359917	2.010000e-131	479.0
15	TraesCS5B01G551000	chr4A	85.470	351	20	5	62	404	617359187	617359514	1.280000e-88	337.0
16	TraesCS5B01G551000	chr4A	83.557	298	32	7	2431	2724	617361806	617362090	2.200000e-66	263.0
17	TraesCS5B01G551000	chr4A	89.119	193	20	1	2690	2881	617353211	617353403	3.710000e-59	239.0
18	TraesCS5B01G551000	chr4A	90.789	76	5	2	130	205	617280696	617280769	1.830000e-17	100.0
19	TraesCS5B01G551000	chr4A	93.939	66	4	0	2817	2882	617362123	617362188	1.830000e-17	100.0
20	TraesCS5B01G551000	chr4A	87.500	56	6	1	2674	2728	617283321	617283376	2.400000e-06	63.9
21	TraesCS5B01G551000	chr4A	90.476	42	4	0	89	130	617280532	617280573	4.010000e-04	56.5
22	TraesCS5B01G551000	chr1D	83.455	1366	188	23	784	2130	199020209	199021555	0.000000e+00	1236.0

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	TraesCS5B01G551000	chr5B	702477448	702480329	2881	True	5323.000000	5323	100.000000	1	2882	1	chr5B.!!$R1	2881
1	TraesCS5B01G551000	chr5B	702556869	702558103	1234	True	1325.000000	1325	86.102000	724	1967	1	chr5B.!!$R2	1243
2	TraesCS5B01G551000	chr5B	702550656	702552821	2165	True	869.500000	1554	84.219500	762	2881	2	chr5B.!!$R3	2119
3	TraesCS5B01G551000	chr5D	550299017	550302027	3010	True	1458.333333	3613	91.881333	14	2882	3	chr5D.!!$R2	2868
4	TraesCS5B01G551000	chr5D	550401510	550403404	1894	True	750.000000	1378	85.113500	73	1979	2	chr5D.!!$R3	1906
5	TraesCS5B01G551000	chr4A	617288745	617290387	1642	False	1604.000000	1604	84.560000	682	2310	1	chr4A.!!$F1	1628
6	TraesCS5B01G551000	chr4A	617348814	617353403	4589	False	910.000000	1581	86.718500	682	2881	2	chr4A.!!$F3	2199
7	TraesCS5B01G551000	chr4A	617359187	617362188	3001	False	696.200000	2302	89.220200	62	2882	5	chr4A.!!$F4	2820
8	TraesCS5B01G551000	chr4A	617280532	617283376	2844	False	444.850000	1559	88.751250	89	2728	4	chr4A.!!$F2	2639
9	TraesCS5B01G551000	chr1D	199020209	199021555	1346	False	1236.000000	1236	83.455000	784	2130	1	chr1D.!!$F1	1346

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
86	87	0.178964	TGCCCTTGGACTTTTGGAGG	60.179	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1971	2688	0.259356	TCATCCCTTCCATGCATGCA	59.741	50.0	25.04	25.04	0.0	3.96	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
21	22	3.476552	TGGGCTTGTGATCGATTAATCC	58.523	45.455	9.87	1.19	0.00	3.01
22	23	3.118075	TGGGCTTGTGATCGATTAATCCA	60.118	43.478	9.87	0.00	0.00	3.41
23	24	4.074970	GGGCTTGTGATCGATTAATCCAT	58.925	43.478	9.87	2.35	0.00	3.41
24	25	4.520492	GGGCTTGTGATCGATTAATCCATT	59.480	41.667	9.87	0.00	0.00	3.16
25	26	5.455392	GGCTTGTGATCGATTAATCCATTG	58.545	41.667	9.87	0.00	0.00	2.82
32	33	7.603784	TGTGATCGATTAATCCATTGATACCAG	59.396	37.037	9.87	0.00	28.65	4.00
35	36	6.156519	TCGATTAATCCATTGATACCAGTCG	58.843	40.000	9.87	0.00	0.00	4.18
86	87	0.178964	TGCCCTTGGACTTTTGGAGG	60.179	55.000	0.00	0.00	0.00	4.30
118	122	3.771577	AATTTCGGAAGTCAGACCTGT	57.228	42.857	0.00	0.00	0.00	4.00
123	127	2.035961	TCGGAAGTCAGACCTGTGAAAG	59.964	50.000	0.00	0.00	0.00	2.62
247	437	0.458716	GGAACGAGCTAGCTGGTGAC	60.459	60.000	29.88	24.49	35.25	3.67
258	448	1.134965	AGCTGGTGACTCTAATGCGAC	60.135	52.381	0.00	0.00	0.00	5.19
318	511	3.003378	TCACCGATCGACAGACATATGTC	59.997	47.826	25.47	25.47	45.01	3.06
335	528	3.116063	TGTCGTTAATTTGCATGCGAG	57.884	42.857	14.09	0.00	0.00	5.03
426	749	5.874810	GCTAATCCAAGTCAACACACTATGA	59.125	40.000	0.00	0.00	0.00	2.15
435	758	9.546909	CAAGTCAACACACTATGATTAATTCAC	57.453	33.333	0.00	0.00	37.11	3.18
463	786	3.119708	GCCACTGCCAGAAGATTAACTTG	60.120	47.826	0.00	0.00	39.13	3.16
464	787	3.441572	CCACTGCCAGAAGATTAACTTGG	59.558	47.826	0.00	0.00	39.13	3.61
498	850	2.611518	CACTGTCAAAGGATCCGAGTC	58.388	52.381	5.98	0.00	0.00	3.36
636	1023	0.179006	GTCAGGCCATGGGAATCTCC	60.179	60.000	15.13	4.65	35.23	3.71
1152	1866	4.394712	GCGTCTGGTGGGAGTGGG	62.395	72.222	0.00	0.00	0.00	4.61
1289	2003	2.511637	GAGGAGGATCAAAGGGTGGATT	59.488	50.000	0.00	0.00	36.25	3.01
1539	2253	1.593750	CTACTCTGATGCTGGCGGC	60.594	63.158	12.43	12.43	42.22	6.53
1888	2602	2.572290	GCGGATACCACTAAATTGCCT	58.428	47.619	0.00	0.00	0.00	4.75
1971	2688	5.011329	AGCATTTCACATCAAAGGACACATT	59.989	36.000	0.00	0.00	0.00	2.71
2072	2791	0.682532	TGTTCAGGCAGGTTTGTGCA	60.683	50.000	0.00	0.00	45.93	4.57
2114	2844	4.935808	AGTACCTCATTTGTAGCCTTTTCG	59.064	41.667	0.00	0.00	0.00	3.46
2183	2922	5.699458	GTCTTTCTGAGTTTCGACCCATTTA	59.301	40.000	0.00	0.00	0.00	1.40
2203	2942	7.759433	CCATTTAACATGTCCAAGTATGTTTCC	59.241	37.037	0.00	0.00	43.00	3.13
2218	2960	4.359434	TGTTTCCTGTGCATACCACTAA	57.641	40.909	0.00	0.00	44.92	2.24
2271	3020	7.961326	ATACCAACCTTGCTTTCTATTTGAT	57.039	32.000	0.00	0.00	0.00	2.57
2328	3094	5.643777	AGAATCAAACAGTCTTAACCATCGG	59.356	40.000	0.00	0.00	0.00	4.18
2333	3099	4.689612	ACAGTCTTAACCATCGGCATAT	57.310	40.909	0.00	0.00	0.00	1.78
2427	3238	9.950680	AACAAGTTGATAGTCAAAAGTGTTATG	57.049	29.630	10.54	0.00	38.22	1.90
2428	3239	9.120538	ACAAGTTGATAGTCAAAAGTGTTATGT	57.879	29.630	10.54	0.00	38.22	2.29
2568	3381	4.766891	AGGCCCCAATTTATTATCATGTCG	59.233	41.667	0.00	0.00	0.00	4.35
2647	3505	7.730084	TCTTGTGATTGATTGGTATAGGAGAG	58.270	38.462	0.00	0.00	0.00	3.20
2773	5976	8.693542	AAAGTGAATTTATGATGCACTTAAGC	57.306	30.769	14.33	0.00	45.84	3.09
2775	5978	6.316140	AGTGAATTTATGATGCACTTAAGCGA	59.684	34.615	1.29	0.00	36.49	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.118075	TGGATTAATCGATCACAAGCCCA	60.118	43.478	15.11	10.78	0.00	5.36
1	2	3.476552	TGGATTAATCGATCACAAGCCC	58.523	45.455	15.11	9.03	0.00	5.19
2	3	5.239306	TCAATGGATTAATCGATCACAAGCC	59.761	40.000	12.69	12.32	0.00	4.35
3	4	6.304356	TCAATGGATTAATCGATCACAAGC	57.696	37.500	12.69	0.00	0.00	4.01
4	5	8.446273	GGTATCAATGGATTAATCGATCACAAG	58.554	37.037	12.69	3.08	34.89	3.16
5	6	7.936301	TGGTATCAATGGATTAATCGATCACAA	59.064	33.333	12.69	1.83	34.89	3.33
7	8	7.604164	ACTGGTATCAATGGATTAATCGATCAC	59.396	37.037	12.69	8.81	34.89	3.06
8	9	7.679783	ACTGGTATCAATGGATTAATCGATCA	58.320	34.615	12.69	4.63	34.89	2.92
9	10	7.009631	CGACTGGTATCAATGGATTAATCGATC	59.990	40.741	12.69	1.44	34.89	3.69
10	11	6.813649	CGACTGGTATCAATGGATTAATCGAT	59.186	38.462	9.32	8.19	34.89	3.59
11	12	6.015772	TCGACTGGTATCAATGGATTAATCGA	60.016	38.462	9.32	5.99	34.89	3.59
12	13	6.156519	TCGACTGGTATCAATGGATTAATCG	58.843	40.000	9.32	0.00	34.89	3.34
13	14	7.962964	TTCGACTGGTATCAATGGATTAATC	57.037	36.000	6.93	6.93	34.89	1.75
14	15	8.746052	TTTTCGACTGGTATCAATGGATTAAT	57.254	30.769	0.00	0.00	34.89	1.40
15	16	8.746052	ATTTTCGACTGGTATCAATGGATTAA	57.254	30.769	0.00	0.00	34.89	1.40
16	17	9.839817	TTATTTTCGACTGGTATCAATGGATTA	57.160	29.630	0.00	0.00	34.89	1.75
17	18	8.746052	TTATTTTCGACTGGTATCAATGGATT	57.254	30.769	0.00	0.00	34.89	3.01
18	19	8.746052	TTTATTTTCGACTGGTATCAATGGAT	57.254	30.769	0.00	0.00	37.55	3.41
19	20	8.746052	ATTTATTTTCGACTGGTATCAATGGA	57.254	30.769	0.00	0.00	0.00	3.41
23	24	9.878667	TGTCTATTTATTTTCGACTGGTATCAA	57.121	29.630	0.00	0.00	0.00	2.57
24	25	9.309516	GTGTCTATTTATTTTCGACTGGTATCA	57.690	33.333	0.00	0.00	0.00	2.15
25	26	9.530633	AGTGTCTATTTATTTTCGACTGGTATC	57.469	33.333	0.00	0.00	0.00	2.24
59	60	4.096003	TCCAAGGGCAGCGCTACC	62.096	66.667	19.02	19.02	0.00	3.18
60	61	2.804828	AAGTCCAAGGGCAGCGCTAC	62.805	60.000	10.99	3.45	0.00	3.58
86	87	3.435105	TCCGAAATTAATGCACATGGC	57.565	42.857	0.00	0.00	45.13	4.40
118	122	9.856488	GTATCAATAATACTAGATCGCCTTTCA	57.144	33.333	0.00	0.00	37.78	2.69
244	434	1.746470	TCGAGGTCGCATTAGAGTCA	58.254	50.000	0.00	0.00	39.60	3.41
247	437	1.531578	TCGATCGAGGTCGCATTAGAG	59.468	52.381	15.15	0.00	41.22	2.43
258	448	2.186532	TGACCTAGGATCGATCGAGG	57.813	55.000	29.84	29.84	36.91	4.63
318	511	4.032900	AGTCTACTCGCATGCAAATTAACG	59.967	41.667	19.57	0.00	0.00	3.18
335	528	2.748532	ACGCACTCTGGTTCTAGTCTAC	59.251	50.000	0.00	0.00	0.00	2.59
426	749	3.613910	GCAGTGGCAAACGGTGAATTAAT	60.614	43.478	0.00	0.00	40.72	1.40
435	758	2.133742	CTTCTGGCAGTGGCAAACGG	62.134	60.000	20.97	9.02	43.71	4.44
464	787	1.130561	GACAGTGGCATTTTACCGAGC	59.869	52.381	0.00	0.00	0.00	5.03
480	832	3.697045	ACTAGACTCGGATCCTTTGACAG	59.303	47.826	10.75	3.13	0.00	3.51
513	869	0.387878	GCTAGGCGATCCGATCACAG	60.388	60.000	9.07	1.25	37.47	3.66
595	951	0.512952	AGACATGTGAAAGAACGCGC	59.487	50.000	5.73	0.00	0.00	6.86
636	1023	8.253113	AGGCCTGACAAATTAATTAACAAGATG	58.747	33.333	3.11	0.00	0.00	2.90
813	1508	8.000709	AGAAGTTTCCTATGATCATAATGCCAA	58.999	33.333	16.08	3.35	0.00	4.52
968	1666	1.202964	TGGGTGGAGTGAGACGAGTTA	60.203	52.381	0.00	0.00	0.00	2.24
1152	1866	1.278413	GACCCAGACCCTCTACCAAAC	59.722	57.143	0.00	0.00	0.00	2.93
1289	2003	0.546747	AGATCCGGAACCAGACCCAA	60.547	55.000	9.01	0.00	0.00	4.12
1491	2205	4.335647	CCACCGGCAACAGGAGCT	62.336	66.667	0.00	0.00	34.83	4.09
1539	2253	0.882927	CACCACCACCGTTACCACTG	60.883	60.000	0.00	0.00	0.00	3.66
1824	2538	2.282462	CCACCACTGCCAGTTCCC	60.282	66.667	0.00	0.00	0.00	3.97
1888	2602	5.301551	TCCAATTCTAGCTTGCTCAACAAAA	59.698	36.000	0.00	0.00	37.96	2.44
1971	2688	0.259356	TCATCCCTTCCATGCATGCA	59.741	50.000	25.04	25.04	0.00	3.96
2072	2791	8.554490	AGGTACTCCTTCACATATGTCTATTT	57.446	34.615	5.07	0.00	42.12	1.40
2137	2867	1.634702	TGCAAACAAAACGGCAGAAC	58.365	45.000	0.00	0.00	0.00	3.01
2183	2922	5.241506	CACAGGAAACATACTTGGACATGTT	59.758	40.000	0.00	0.00	45.03	2.71
2218	2960	9.203163	ACCTAGAAACTATAGAGTTGCATACTT	57.797	33.333	10.83	0.00	45.50	2.24
2271	3020	6.126420	ACCCAAATTAACACGGAGGGAATATA	60.126	38.462	0.00	0.00	38.21	0.86
2277	3026	2.209690	ACCCAAATTAACACGGAGGG	57.790	50.000	0.00	0.00	40.66	4.30
2756	5952	6.093357	TCAATGTCGCTTAAGTGCATCATAAA	59.907	34.615	19.34	10.18	0.00	1.40
2769	5972	6.700081	GGTGATATACTGTTCAATGTCGCTTA	59.300	38.462	0.00	0.00	0.00	3.09
2773	5976	6.902224	TTGGTGATATACTGTTCAATGTCG	57.098	37.500	0.00	0.00	0.00	4.35
2811	6014	6.555463	ATTAACGGAAAGACATCCTCCTAA	57.445	37.500	0.00	0.00	37.34	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.