AutoCloner

Multiple sequence alignment - TraesCS4D01G358800

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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	TraesCS4D01G358800	chr4D	100.000	3845	0	0	1	3845	506288383	506284539	0.000000e+00	7101.0
1	TraesCS4D01G358800	chr4D	84.984	939	89	22	425	1338	506050331	506051242	0.000000e+00	905.0
2	TraesCS4D01G358800	chr4D	78.011	905	142	38	2251	3139	506052027	506052890	2.050000e-142	516.0
3	TraesCS4D01G358800	chr4D	91.389	360	30	1	1404	1763	506051363	506051721	3.450000e-135	492.0
4	TraesCS4D01G358800	chr4D	89.333	75	8	0	2084	2158	506051827	506051901	1.140000e-15	95.3
5	TraesCS4D01G358800	chr3B	93.231	2024	83	16	9	1993	799813682	799811674	0.000000e+00	2929.0
6	TraesCS4D01G358800	chr3B	93.684	1520	59	8	2029	3544	799811678	799810192	0.000000e+00	2241.0
7	TraesCS4D01G358800	chr3B	85.902	610	60	10	1153	1752	720219238	720218645	9.070000e-176	627.0
8	TraesCS4D01G358800	chr3B	96.104	308	11	1	3539	3845	799800202	799799895	5.730000e-138	501.0
9	TraesCS4D01G358800	chr3B	75.796	785	116	50	2292	3030	720218542	720217786	2.860000e-86	329.0
10	TraesCS4D01G358800	chr3B	83.333	252	42	0	9	260	214443110	214442859	2.310000e-57	233.0
11	TraesCS4D01G358800	chr4B	95.363	1833	64	9	2029	3845	662420402	662418575	0.000000e+00	2894.0
12	TraesCS4D01G358800	chr4B	86.680	1479	111	40	565	1989	662421851	662420405	0.000000e+00	1561.0
13	TraesCS4D01G358800	chr4B	85.860	1372	125	36	427	1763	661303530	661304867	0.000000e+00	1395.0
14	TraesCS4D01G358800	chr4B	77.233	1019	154	50	2251	3248	661305208	661306169	3.400000e-145	525.0
15	TraesCS4D01G358800	chr5A	84.830	2116	212	59	1404	3464	702522352	702520291	0.000000e+00	2028.0
16	TraesCS4D01G358800	chr5A	84.099	1459	141	44	355	1764	702225562	702226978	0.000000e+00	1325.0
17	TraesCS4D01G358800	chr5A	87.898	785	58	20	573	1338	702523221	702522455	0.000000e+00	889.0
18	TraesCS4D01G358800	chr5A	78.046	1034	147	54	2251	3255	702227570	702228552	2.580000e-161	579.0
19	TraesCS4D01G358800	chr5A	83.824	68	6	4	1799	1866	659321416	659321354	4.150000e-05	60.2
20	TraesCS4D01G358800	chr5A	97.143	35	1	0	1832	1866	709215816	709215850	4.150000e-05	60.2
21	TraesCS4D01G358800	chr3D	86.084	618	64	9	1153	1756	544361097	544360488	0.000000e+00	645.0
22	TraesCS4D01G358800	chr3D	79.907	428	65	11	2292	2707	544360405	544359987	1.040000e-75	294.0
23	TraesCS4D01G358800	chr3D	85.156	256	38	0	1	256	140411907	140411652	2.950000e-66	263.0
24	TraesCS4D01G358800	chr3D	83.200	250	33	4	9	258	511735102	511734862	1.800000e-53	220.0
25	TraesCS4D01G358800	chr3A	85.600	625	62	17	1153	1764	681343656	681343047	7.010000e-177	630.0
26	TraesCS4D01G358800	chr3A	83.594	256	39	2	5	258	78183879	78184133	1.790000e-58	237.0
27	TraesCS4D01G358800	chr6A	86.873	259	29	3	1	258	608085682	608085428	6.290000e-73	285.0
28	TraesCS4D01G358800	chr6B	87.264	212	27	0	1	212	82528184	82528395	3.840000e-60	243.0
29	TraesCS4D01G358800	chr2D	83.984	256	38	3	3	257	30677835	30677582	3.840000e-60	243.0
30	TraesCS4D01G358800	chr7D	83.200	250	42	0	9	258	59870477	59870228	2.990000e-56	230.0
31	TraesCS4D01G358800	chr1A	85.294	68	5	1	1799	1866	27310880	27310942	8.920000e-07	65.8

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	TraesCS4D01G358800	chr4D	506284539	506288383	3844	True	7101.000	7101	100.00000	1	3845	1	chr4D.!!$R1	3844
1	TraesCS4D01G358800	chr4D	506050331	506052890	2559	False	502.075	905	85.92925	425	3139	4	chr4D.!!$F1	2714
2	TraesCS4D01G358800	chr3B	799810192	799813682	3490	True	2585.000	2929	93.45750	9	3544	2	chr3B.!!$R4	3535
3	TraesCS4D01G358800	chr3B	720217786	720219238	1452	True	478.000	627	80.84900	1153	3030	2	chr3B.!!$R3	1877
4	TraesCS4D01G358800	chr4B	662418575	662421851	3276	True	2227.500	2894	91.02150	565	3845	2	chr4B.!!$R1	3280
5	TraesCS4D01G358800	chr4B	661303530	661306169	2639	False	960.000	1395	81.54650	427	3248	2	chr4B.!!$F1	2821
6	TraesCS4D01G358800	chr5A	702520291	702523221	2930	True	1458.500	2028	86.36400	573	3464	2	chr5A.!!$R2	2891
7	TraesCS4D01G358800	chr5A	702225562	702228552	2990	False	952.000	1325	81.07250	355	3255	2	chr5A.!!$F2	2900
8	TraesCS4D01G358800	chr3D	544359987	544361097	1110	True	469.500	645	82.99550	1153	2707	2	chr3D.!!$R3	1554
9	TraesCS4D01G358800	chr3A	681343047	681343656	609	True	630.000	630	85.60000	1153	1764	1	chr3A.!!$R1	611

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	Hairpin	End Stability	Orientation
234	235	0.810031	CGACCGAATCCCGCAAGATT	60.810	55.000	0.0	39.19	2.40	F
487	497	1.495878	GCGCATCTGATAGGACACAG	58.504	55.000	0.3	35.72	3.66	F
1173	1253	2.045340	CGCCCCATCCCGAACTTT	60.045	61.111	0.0	0.00	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1836	1977	0.107643	GGGGATCTGCTAGTTGGCTC	59.892	60.0	0.00	4.70	R
1838	1979	1.424638	TAGGGGATCTGCTAGTTGGC	58.575	55.0	0.00	4.52	R
2877	3481	0.526211	AGTAGTCGTCGATTGCAGCA	59.474	50.0	8.43	4.41	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
35	36	2.523412	TCCCTTATCGGAGCCGGG	60.523	66.667	9.29	1.99	40.25	5.73
45	46	2.597510	GAGCCGGGCAAACCTTGT	60.598	61.111	23.09	0.00	36.97	3.16
70	71	7.482169	TGTAATAGACAGTCAGGAAGATGTT	57.518	36.000	2.66	0.00	32.86	2.71
79	80	3.686726	GTCAGGAAGATGTTGTGCTAAGG	59.313	47.826	0.00	0.00	0.00	2.69
127	128	2.892640	TCGCCACCGATGAAGAGG	59.107	61.111	0.00	0.00	38.82	3.69
130	131	1.522580	GCCACCGATGAAGAGGAGC	60.523	63.158	0.00	0.00	0.00	4.70
173	174	2.432510	TGTACACACATGGACACAGACA	59.567	45.455	0.00	0.00	45.28	3.41
180	181	2.872245	ACATGGACACAGACAAACGAAG	59.128	45.455	0.00	0.00	0.00	3.79
215	216	0.893727	ATCCACCAAAGACCAACGCC	60.894	55.000	0.00	0.00	0.00	5.68
227	228	4.807039	AACGCCGACCGAATCCCG	62.807	66.667	0.00	0.00	41.02	5.14
234	235	0.810031	CGACCGAATCCCGCAAGATT	60.810	55.000	0.00	0.00	39.19	2.40
261	262	2.295349	GAGACAAACCTCCACACGTCTA	59.705	50.000	0.00	0.00	34.02	2.59
461	471	8.576442	CATGTTTACTTAAAATCCACTCCACTT	58.424	33.333	0.00	0.00	0.00	3.16
487	497	1.495878	GCGCATCTGATAGGACACAG	58.504	55.000	0.30	0.00	35.72	3.66
504	514	5.986135	GGACACAGATCTTGATTACGCTAAT	59.014	40.000	10.61	0.00	0.00	1.73
693	712	4.078537	CACATACCCATTTCCACTTGTGA	58.921	43.478	1.89	0.00	36.26	3.58
707	732	6.957631	TCCACTTGTGATTTGGAGTATATGT	58.042	36.000	1.89	0.00	34.35	2.29
755	783	3.891422	AGCAGAGAGGAGACATGAAAG	57.109	47.619	0.00	0.00	0.00	2.62
811	839	3.243359	TCCACCAAAGCAATCCTTTCT	57.757	42.857	0.00	0.00	41.75	2.52
881	920	4.264253	CGGTATCACCATGCCATCATTAT	58.736	43.478	0.00	0.00	38.47	1.28
892	931	3.575256	TGCCATCATTATTTGATCCAGGC	59.425	43.478	7.93	7.93	45.31	4.85
1173	1253	2.045340	CGCCCCATCCCGAACTTT	60.045	61.111	0.00	0.00	0.00	2.66
1389	1516	6.746364	GTGAGCAGATGATTTCTTTTGCTTAG	59.254	38.462	11.23	0.00	40.08	2.18
1784	1925	2.700353	AGGGCATCTCTAGCAGATCT	57.300	50.000	0.00	0.00	40.20	2.75
1934	2097	3.623060	GGATAGAGAGCATTTTTCGCACA	59.377	43.478	0.00	0.00	0.00	4.57
2013	2196	3.231818	AGTTACACTGCACAGGTAGTCT	58.768	45.455	2.21	2.81	37.94	3.24
2114	2314	8.202811	TGTCAATGAAATCCACTGAATTTCAAA	58.797	29.630	7.43	0.00	44.30	2.69
2192	2393	9.698309	TTTCAGTTGTACAAAAGAAATCAAACA	57.302	25.926	22.74	8.22	0.00	2.83
2337	2873	2.586792	GAGCGCCCTCTGAATGGT	59.413	61.111	2.29	0.00	35.16	3.55
2619	3187	0.465705	CCATGAGGACCACTATGCGT	59.534	55.000	0.00	0.00	36.89	5.24
2670	3238	2.825836	GTTGGCTGCTCCATCCGG	60.826	66.667	0.00	0.00	46.04	5.14
2737	3308	5.304101	ACATTTTCTTGCTCCACAACCAATA	59.696	36.000	0.00	0.00	33.68	1.90
2837	3435	2.906389	ACATCAACTGTGAGCCCTTCTA	59.094	45.455	0.00	0.00	37.14	2.10
2871	3475	1.736645	CGTGGGTTCATCGTCGCTT	60.737	57.895	0.00	0.00	0.00	4.68
2872	3476	1.787847	GTGGGTTCATCGTCGCTTG	59.212	57.895	0.00	0.00	0.00	4.01
2873	3477	0.949105	GTGGGTTCATCGTCGCTTGT	60.949	55.000	0.00	0.00	0.00	3.16
2874	3478	0.669318	TGGGTTCATCGTCGCTTGTC	60.669	55.000	0.00	0.00	0.00	3.18
2875	3479	1.683790	GGGTTCATCGTCGCTTGTCG	61.684	60.000	0.00	0.00	40.15	4.35
2876	3480	1.057361	GTTCATCGTCGCTTGTCGC	59.943	57.895	0.00	0.00	38.27	5.19
2877	3481	1.080772	TTCATCGTCGCTTGTCGCT	60.081	52.632	0.00	0.00	38.27	4.93
3064	3687	0.603975	AAGGCACTCCAAGAACTCGC	60.604	55.000	0.00	0.00	38.49	5.03
3072	3695	4.096532	CACTCCAAGAACTCGCTATCTACA	59.903	45.833	0.00	0.00	0.00	2.74
3081	3704	4.138290	ACTCGCTATCTACAGTACTGCAT	58.862	43.478	22.90	14.09	0.00	3.96
3167	3796	8.651588	GCTCGATGTCCTCTTAATAAACATATG	58.348	37.037	0.00	0.00	31.04	1.78
3414	4053	2.083774	ACACACAACAGACACCACAAG	58.916	47.619	0.00	0.00	0.00	3.16
3659	4299	1.448985	CAAACACCATCCTACCACCG	58.551	55.000	0.00	0.00	0.00	4.94
3662	4302	1.153369	CACCATCCTACCACCGCTG	60.153	63.158	0.00	0.00	0.00	5.18
3827	4467	1.516386	CCCACGAGAATCACCGTCG	60.516	63.158	0.00	0.00	36.83	5.12
3842	4482	1.436336	GTCGTATGCGCCTACCACT	59.564	57.895	15.88	0.00	38.14	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.585990	GGGGCAATGATGACGGCG	61.586	66.667	4.80	4.80	34.32	6.46
1	2	2.124151	AGGGGCAATGATGACGGC	60.124	61.111	0.00	0.00	34.32	5.68
2	3	1.526917	GGAGGGGCAATGATGACGG	60.527	63.158	0.00	0.00	34.32	4.79
3	4	1.526917	GGGAGGGGCAATGATGACG	60.527	63.158	0.00	0.00	34.32	4.35
4	5	0.259938	AAGGGAGGGGCAATGATGAC	59.740	55.000	0.00	0.00	0.00	3.06
5	6	1.905839	TAAGGGAGGGGCAATGATGA	58.094	50.000	0.00	0.00	0.00	2.92
6	7	2.800250	GATAAGGGAGGGGCAATGATG	58.200	52.381	0.00	0.00	0.00	3.07
7	8	1.352352	CGATAAGGGAGGGGCAATGAT	59.648	52.381	0.00	0.00	0.00	2.45
12	13	2.700149	TCCGATAAGGGAGGGGCA	59.300	61.111	0.00	0.00	41.52	5.36
35	36	6.017440	TGACTGTCTATTACAACAAGGTTTGC	60.017	38.462	9.51	0.00	37.74	3.68
45	46	7.482169	ACATCTTCCTGACTGTCTATTACAA	57.518	36.000	9.51	0.00	37.74	2.41
70	71	1.762957	GTCCTATGGAGCCTTAGCACA	59.237	52.381	4.38	0.00	43.56	4.57
120	121	1.134189	TCCGATCTACGCTCCTCTTCA	60.134	52.381	0.00	0.00	41.07	3.02
143	144	4.154195	GTCCATGTGTGTACAAGTTGGATC	59.846	45.833	16.56	9.80	42.41	3.36
151	152	3.118592	TGTCTGTGTCCATGTGTGTACAA	60.119	43.478	0.00	0.00	40.84	2.41
169	170	1.067071	GGATCCGGTCTTCGTTTGTCT	60.067	52.381	0.00	0.00	37.11	3.41
173	174	0.389426	CGTGGATCCGGTCTTCGTTT	60.389	55.000	7.39	0.00	37.11	3.60
206	207	2.433664	ATTCGGTCGGCGTTGGTC	60.434	61.111	6.85	0.00	0.00	4.02
209	210	3.192922	GGGATTCGGTCGGCGTTG	61.193	66.667	6.85	0.00	0.00	4.10
215	216	0.810031	AATCTTGCGGGATTCGGTCG	60.810	55.000	0.00	0.00	39.69	4.79
227	228	1.808411	TTGTCTCCGGTGAATCTTGC	58.192	50.000	7.99	0.00	0.00	4.01
228	229	2.484264	GGTTTGTCTCCGGTGAATCTTG	59.516	50.000	7.99	0.00	0.00	3.02
229	230	2.372172	AGGTTTGTCTCCGGTGAATCTT	59.628	45.455	7.99	0.00	0.00	2.40
234	235	2.055299	GGAGGTTTGTCTCCGGTGA	58.945	57.895	0.00	0.06	43.19	4.02
261	262	7.716998	ACGCTCATTCAGTGAATAATAGGATTT	59.283	33.333	17.86	0.00	36.14	2.17
282	283	5.888105	TGAAACTACCACTAATCTACGCTC	58.112	41.667	0.00	0.00	0.00	5.03
359	360	7.654923	TCATTATATGCAGTTGTAGAAGCTGAG	59.345	37.037	0.00	0.00	32.39	3.35
461	471	1.202568	CCTATCAGATGCGCCTGACAA	60.203	52.381	17.03	8.83	44.93	3.18
487	497	7.148557	GCCCTTAAGATTAGCGTAATCAAGATC	60.149	40.741	3.36	0.00	45.41	2.75
707	732	6.270064	TCAAGAGAACGCGATTGATGTTATA	58.730	36.000	15.93	0.00	0.00	0.98
832	863	8.765219	GTGCACTAGGATTTGTACAGTATATTG	58.235	37.037	10.32	0.00	0.00	1.90
839	870	2.930040	CGGTGCACTAGGATTTGTACAG	59.070	50.000	17.98	0.00	30.59	2.74
840	871	2.354303	CCGGTGCACTAGGATTTGTACA	60.354	50.000	21.86	0.00	30.59	2.90
841	872	2.277084	CCGGTGCACTAGGATTTGTAC	58.723	52.381	21.86	0.00	0.00	2.90
842	873	1.903860	ACCGGTGCACTAGGATTTGTA	59.096	47.619	29.35	0.00	0.00	2.41
843	874	0.690762	ACCGGTGCACTAGGATTTGT	59.309	50.000	29.35	11.09	0.00	2.83
844	875	2.684001	TACCGGTGCACTAGGATTTG	57.316	50.000	29.35	10.35	0.00	2.32
881	920	5.245531	CCTTTATATAGCGCCTGGATCAAA	58.754	41.667	2.29	0.00	0.00	2.69
892	931	2.832129	TCCTCCTGCCCTTTATATAGCG	59.168	50.000	0.00	0.00	0.00	4.26
1389	1516	0.231279	CACCAACAAGCACGTACGTC	59.769	55.000	19.94	13.38	0.00	4.34
1784	1925	7.581213	TGCTTCTCAAACTTGAATTTTAGGA	57.419	32.000	0.00	0.00	36.64	2.94
1834	1975	1.488393	GGGATCTGCTAGTTGGCTCTT	59.512	52.381	0.00	0.00	0.00	2.85
1836	1977	0.107643	GGGGATCTGCTAGTTGGCTC	59.892	60.000	0.00	0.00	0.00	4.70
1838	1979	1.424638	TAGGGGATCTGCTAGTTGGC	58.575	55.000	0.00	0.00	0.00	4.52
1934	2097	7.023120	TGGAGGTTAGGGCATCTATACTTAAT	58.977	38.462	0.00	0.00	0.00	1.40
2020	2203	9.398538	AGCGGATGGTTTATTAAGTTTGTATAA	57.601	29.630	0.00	0.00	0.00	0.98
2117	2317	8.710239	AGGTAAACATTTTGGTTTCCACTAAAT	58.290	29.630	4.14	0.00	41.07	1.40
2670	3238	1.264288	CCACTGAAGTTTGCGACCTTC	59.736	52.381	4.32	4.32	0.00	3.46
2737	3308	2.634600	TGTGAGTAAACACTTGCCGTT	58.365	42.857	0.00	0.00	40.87	4.44
2837	3435	2.508439	CGCGCGGGTTCTACATGT	60.508	61.111	24.84	2.69	0.00	3.21
2871	3475	2.048316	TCGATTGCAGCAGCGACA	60.048	55.556	15.87	0.00	46.23	4.35
2872	3476	2.397252	GTCGATTGCAGCAGCGAC	59.603	61.111	26.68	26.68	46.23	5.19
2873	3477	3.181290	CGTCGATTGCAGCAGCGA	61.181	61.111	15.87	15.87	46.23	4.93
2874	3478	3.181290	TCGTCGATTGCAGCAGCG	61.181	61.111	12.16	12.16	46.23	5.18
2875	3479	0.802222	TAGTCGTCGATTGCAGCAGC	60.802	55.000	0.00	0.00	42.57	5.25
2876	3480	0.917259	GTAGTCGTCGATTGCAGCAG	59.083	55.000	0.00	0.00	0.00	4.24
2877	3481	0.526211	AGTAGTCGTCGATTGCAGCA	59.474	50.000	8.43	0.00	0.00	4.41
3064	3687	6.203145	ACGTAGACATGCAGTACTGTAGATAG	59.797	42.308	23.44	12.86	0.00	2.08
3072	3695	3.005554	ACGTACGTAGACATGCAGTACT	58.994	45.455	21.41	0.00	36.48	2.73
3167	3796	4.801516	GGAGACGAAGCAGAATAGAACTTC	59.198	45.833	0.00	0.00	36.11	3.01
3177	3806	1.048601	ACTTTGGGAGACGAAGCAGA	58.951	50.000	0.00	0.00	43.26	4.26
3241	3870	4.681074	TCATCACACTTCACACCACTTA	57.319	40.909	0.00	0.00	0.00	2.24
3355	3991	7.065324	TCTGAACTTTGTAACGTGTTCTTCATT	59.935	33.333	13.33	0.00	39.38	2.57
3414	4053	0.402121	AGACCTCCTTGCCCTTGTTC	59.598	55.000	0.00	0.00	0.00	3.18
3604	4243	0.541392	TTCTCGATCATGTGGTGGGG	59.459	55.000	0.00	0.00	0.00	4.96
3659	4299	0.324943	TCAGTTTAGGAGTGGCCAGC	59.675	55.000	5.11	0.00	40.02	4.85
3662	4302	1.383523	GCATCAGTTTAGGAGTGGCC	58.616	55.000	0.00	0.00	0.00	5.36
3754	4394	3.624861	CGGCATGATAGCTTCTTCACTTT	59.375	43.478	0.00	0.00	34.17	2.66
3799	4439	1.808411	TTCTCGTGGGCATTCACTTC	58.192	50.000	0.00	0.00	35.63	3.01
3803	4443	1.678728	GGTGATTCTCGTGGGCATTCA	60.679	52.381	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.