AutoCloner

Multiple sequence alignment - TraesCS6D01G367100

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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	TraesCS6D01G367100	chr6D	100.000	3263	0	0	1	3263	455087225	455083963	0.000000e+00	6026.0
1	TraesCS6D01G367100	chr6D	89.068	1802	125	27	533	2280	455311343	455313126	0.000000e+00	2170.0
2	TraesCS6D01G367100	chr6D	90.123	81	8	0	2502	2582	23102089	23102169	4.450000e-19	106.0
3	TraesCS6D01G367100	chr6D	91.045	67	1	4	2387	2453	455313405	455313466	5.800000e-13	86.1
4	TraesCS6D01G367100	chr6A	93.757	2531	120	10	1	2526	601399346	601396849	0.000000e+00	3764.0
5	TraesCS6D01G367100	chr6A	90.404	1782	123	18	533	2291	601967700	601969456	0.000000e+00	2300.0
6	TraesCS6D01G367100	chr6A	84.717	759	89	19	2524	3263	601395807	601395057	0.000000e+00	734.0
7	TraesCS6D01G367100	chr6A	78.000	250	46	9	2491	2737	12003881	12004124	7.290000e-32	148.0
8	TraesCS6D01G367100	chr6B	91.042	2534	153	33	1	2506	691862869	691865356	0.000000e+00	3354.0
9	TraesCS6D01G367100	chr6B	90.959	2533	155	37	1	2506	692195783	692193298	0.000000e+00	3341.0
10	TraesCS6D01G367100	chr6B	91.312	1715	107	20	571	2280	692488864	692490541	0.000000e+00	2303.0
11	TraesCS6D01G367100	chr6B	90.395	531	47	4	2733	3262	692192702	692192175	0.000000e+00	695.0
12	TraesCS6D01G367100	chr6B	90.207	531	51	1	2734	3263	691865953	691866483	0.000000e+00	691.0
13	TraesCS6D01G367100	chrUn	93.814	388	24	0	1666	2053	480245409	480245796	4.690000e-163	584.0
14	TraesCS6D01G367100	chr2A	82.227	512	86	4	2752	3259	707743866	707743356	1.390000e-118	436.0
15	TraesCS6D01G367100	chr5A	80.077	522	93	8	2746	3263	367779915	367780429	8.550000e-101	377.0
16	TraesCS6D01G367100	chr5A	84.211	114	17	1	2533	2645	537023267	537023154	3.440000e-20	110.0
17	TraesCS6D01G367100	chr5A	74.882	211	41	10	2499	2706	338452156	338452357	5.800000e-13	86.1
18	TraesCS6D01G367100	chr1D	79.887	532	87	10	2751	3263	247821525	247820995	3.980000e-99	372.0
19	TraesCS6D01G367100	chr1D	77.561	205	35	5	2502	2697	92965733	92965531	2.660000e-21	113.0
20	TraesCS6D01G367100	chr1D	75.980	204	46	2	2500	2701	488137622	488137824	5.760000e-18	102.0
21	TraesCS6D01G367100	chr7D	78.244	524	105	9	2746	3263	56075766	56076286	8.730000e-86	327.0
22	TraesCS6D01G367100	chr7D	77.863	524	106	10	2746	3263	56060243	56060762	1.890000e-82	316.0
23	TraesCS6D01G367100	chr7D	76.585	205	43	3	2500	2701	35266600	35266802	1.240000e-19	108.0
24	TraesCS6D01G367100	chr4A	77.419	527	104	13	2746	3263	672739437	672739957	1.900000e-77	300.0
25	TraesCS6D01G367100	chr2D	79.126	206	40	3	2501	2705	630628840	630628637	4.390000e-29	139.0
26	TraesCS6D01G367100	chr1A	80.420	143	28	0	2501	2643	513460284	513460142	3.440000e-20	110.0
27	TraesCS6D01G367100	chr1A	82.759	116	18	2	2502	2616	416518496	416518382	5.760000e-18	102.0

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	TraesCS6D01G367100	chr6D	455083963	455087225	3262	True	6026.00	6026	100.0000	1	3263	1	chr6D.!!$R1	3262
1	TraesCS6D01G367100	chr6D	455311343	455313466	2123	False	1128.05	2170	90.0565	533	2453	2	chr6D.!!$F2	1920
2	TraesCS6D01G367100	chr6A	601967700	601969456	1756	False	2300.00	2300	90.4040	533	2291	1	chr6A.!!$F2	1758
3	TraesCS6D01G367100	chr6A	601395057	601399346	4289	True	2249.00	3764	89.2370	1	3263	2	chr6A.!!$R1	3262
4	TraesCS6D01G367100	chr6B	692488864	692490541	1677	False	2303.00	2303	91.3120	571	2280	1	chr6B.!!$F1	1709
5	TraesCS6D01G367100	chr6B	691862869	691866483	3614	False	2022.50	3354	90.6245	1	3263	2	chr6B.!!$F2	3262
6	TraesCS6D01G367100	chr6B	692192175	692195783	3608	True	2018.00	3341	90.6770	1	3262	2	chr6B.!!$R1	3261
7	TraesCS6D01G367100	chr2A	707743356	707743866	510	True	436.00	436	82.2270	2752	3259	1	chr2A.!!$R1	507
8	TraesCS6D01G367100	chr5A	367779915	367780429	514	False	377.00	377	80.0770	2746	3263	1	chr5A.!!$F2	517
9	TraesCS6D01G367100	chr1D	247820995	247821525	530	True	372.00	372	79.8870	2751	3263	1	chr1D.!!$R2	512
10	TraesCS6D01G367100	chr7D	56075766	56076286	520	False	327.00	327	78.2440	2746	3263	1	chr7D.!!$F3	517
11	TraesCS6D01G367100	chr7D	56060243	56060762	519	False	316.00	316	77.8630	2746	3263	1	chr7D.!!$F2	517
12	TraesCS6D01G367100	chr4A	672739437	672739957	520	False	300.00	300	77.4190	2746	3263	1	chr4A.!!$F1	517

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
875	944	1.631898	ACCCCTATAAAACGCACACCT	59.368	47.619	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2731	4382	1.159285	CCGCTCAGACATGAAAGCAA	58.841	50.0	0.0	0.0	34.23	3.91	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
103	105	4.451900	AGGACCAGGAAAATAGTTATGCG	58.548	43.478	0.00	0.00	0.00	4.73
130	132	9.985730	CATTACCAATAATAGAATGGTTGCATT	57.014	29.630	1.57	0.00	44.92	3.56
166	168	9.118300	CAGGTTGCTAAATCTCAGATTTAATCT	57.882	33.333	18.54	10.28	41.15	2.40
461	481	9.748708	ACACCATTAATTTTATCCATTTGATCG	57.251	29.630	0.00	0.00	34.76	3.69
568	590	2.032030	CAGTGGCTAAACTTCAACGGTG	60.032	50.000	0.00	0.00	0.00	4.94
737	773	2.738521	CAGCTCAACACCGACCCG	60.739	66.667	0.00	0.00	0.00	5.28
762	803	3.165071	AGTCAATCCAATCCAACCCAAC	58.835	45.455	0.00	0.00	0.00	3.77
779	838	1.892441	AACCCAACCCAACCCAACCT	61.892	55.000	0.00	0.00	0.00	3.50
791	851	2.028876	ACCCAACCTGTTTTACTGTGC	58.971	47.619	0.00	0.00	0.00	4.57
813	878	3.689161	CCATTCCACGCAGTTTAATCTCA	59.311	43.478	0.00	0.00	41.61	3.27
826	891	7.961827	GCAGTTTAATCTCAAATCTCTTGTGAG	59.038	37.037	0.00	0.00	40.15	3.51
875	944	1.631898	ACCCCTATAAAACGCACACCT	59.368	47.619	0.00	0.00	0.00	4.00
1008	1105	3.224324	GCTACGGCGATGGAGGGA	61.224	66.667	16.62	0.00	0.00	4.20
1105	1202	2.183300	GCATCACCTACGACCGCA	59.817	61.111	0.00	0.00	0.00	5.69
1139	1236	4.373116	GCTCTCCGACGGCCACAA	62.373	66.667	9.66	0.00	0.00	3.33
1215	1312	4.891727	CATACGCTCCGCCGCCTT	62.892	66.667	0.00	0.00	0.00	4.35
1376	1473	1.888436	AAGGCCATCGTCGCTGAGAA	61.888	55.000	5.01	0.00	0.00	2.87
1438	1535	1.801983	GAGTTCCTCGTCTCCGTCC	59.198	63.158	0.00	0.00	35.01	4.79
1485	1591	2.863137	GTCGGCTGAAGATTTGCTAGAG	59.137	50.000	0.00	0.00	0.00	2.43
1576	1682	1.975327	CCGTCCAAGAAGAGCCTGA	59.025	57.895	0.00	0.00	0.00	3.86
1596	1702	3.388024	TGATCCGGATCCTCGAGAAAAAT	59.612	43.478	35.72	2.77	37.02	1.82
1615	1721	0.191064	TGGAGACTTCCTGGACACCT	59.809	55.000	0.00	0.00	44.36	4.00
1684	1790	1.519246	CTCCTGCTCAAGGCGATGA	59.481	57.895	0.00	0.00	46.92	2.92
1721	1827	2.434185	GCGTCTCATGGCGGTGAA	60.434	61.111	0.00	0.00	0.00	3.18
1797	1903	3.127533	GTGAAGGCGGCGCTGAAT	61.128	61.111	32.30	15.12	0.00	2.57
2199	2305	3.433314	CCAAGGAGCTACTCAAGATGCAT	60.433	47.826	0.00	0.00	33.79	3.96
2325	2438	9.125906	CACATTGCTCTCTTTTAAATTCTCTTG	57.874	33.333	0.00	0.00	0.00	3.02
2417	2695	4.337763	GCACATTGCTCTCTTTCAATACG	58.662	43.478	0.00	0.00	40.96	3.06
2418	2696	4.142816	GCACATTGCTCTCTTTCAATACGT	60.143	41.667	0.00	0.00	40.96	3.57
2419	2697	5.063438	GCACATTGCTCTCTTTCAATACGTA	59.937	40.000	0.00	0.00	40.96	3.57
2518	3125	1.568504	TCTAAGGGCATCTCCAACGT	58.431	50.000	0.00	0.00	36.21	3.99
2577	4228	0.591170	CCGAACGTGTTTTGCCATCT	59.409	50.000	0.00	0.00	0.00	2.90
2581	4232	3.303461	CGAACGTGTTTTGCCATCTAACA	60.303	43.478	0.00	0.00	0.00	2.41
2599	4250	0.390340	CATGGTCCAGTGTCGGTCTG	60.390	60.000	0.00	0.00	0.00	3.51
2626	4277	1.594331	GTCTGGACGCACTTTTTCCT	58.406	50.000	0.00	0.00	0.00	3.36
2693	4344	1.880894	CCACGTCCGCTTCTGACTA	59.119	57.895	0.00	0.00	0.00	2.59
2701	4352	1.608717	CGCTTCTGACTACCCTGGCT	61.609	60.000	0.00	0.00	0.00	4.75
2742	4437	2.127270	CGCGCGTTGCTTTCATGT	60.127	55.556	24.19	0.00	43.27	3.21
2744	4439	1.207593	GCGCGTTGCTTTCATGTCT	59.792	52.632	8.43	0.00	41.73	3.41
2786	4481	3.064324	GCCGGCATTGAAGTGGCT	61.064	61.111	24.80	0.00	42.44	4.75
2809	4504	2.350514	GCCAAGAGAGTGCTGCCT	59.649	61.111	0.00	0.00	0.00	4.75
2812	4507	2.039405	CAAGAGAGTGCTGCCTGCC	61.039	63.158	0.00	0.00	42.00	4.85
2879	4575	1.684869	CCGGTCCATTGCCCTACATTT	60.685	52.381	0.00	0.00	0.00	2.32
2917	4617	0.179205	GAACCTACTCCGACGTCACG	60.179	60.000	17.16	4.74	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	6.534059	CACGTCCTGAAATTAGTAACATGTG	58.466	40.000	0.00	0.00	0.00	3.21
26	27	3.795623	AATATACGAGTTGCACGTCCT	57.204	42.857	3.93	0.00	43.62	3.85
89	91	9.672086	TTATTGGTAATGCGCATAACTATTTTC	57.328	29.630	25.61	4.47	0.00	2.29
103	105	7.432869	TGCAACCATTCTATTATTGGTAATGC	58.567	34.615	9.83	9.83	41.51	3.56
130	132	6.872920	AGATTTAGCAACCTGTTTTGAAACA	58.127	32.000	8.81	8.81	45.88	2.83
166	168	5.063880	TGAGCATAGCATCGACTAAGACTA	58.936	41.667	0.00	0.00	0.00	2.59
168	170	4.230314	TGAGCATAGCATCGACTAAGAC	57.770	45.455	0.00	0.00	0.00	3.01
234	236	8.367156	AGTGGCATAGCAAATAAAGAAGAAAAA	58.633	29.630	0.00	0.00	0.00	1.94
235	237	7.895759	AGTGGCATAGCAAATAAAGAAGAAAA	58.104	30.769	0.00	0.00	0.00	2.29
236	238	7.466746	AGTGGCATAGCAAATAAAGAAGAAA	57.533	32.000	0.00	0.00	0.00	2.52
237	239	7.176515	TCAAGTGGCATAGCAAATAAAGAAGAA	59.823	33.333	0.00	0.00	0.00	2.52
238	240	6.658816	TCAAGTGGCATAGCAAATAAAGAAGA	59.341	34.615	0.00	0.00	0.00	2.87
239	241	6.749118	GTCAAGTGGCATAGCAAATAAAGAAG	59.251	38.462	0.00	0.00	0.00	2.85
240	242	6.434028	AGTCAAGTGGCATAGCAAATAAAGAA	59.566	34.615	0.00	0.00	0.00	2.52
241	243	5.945784	AGTCAAGTGGCATAGCAAATAAAGA	59.054	36.000	0.00	0.00	0.00	2.52
242	244	6.032094	CAGTCAAGTGGCATAGCAAATAAAG	58.968	40.000	0.00	0.00	0.00	1.85
248	266	2.302733	TCTCAGTCAAGTGGCATAGCAA	59.697	45.455	0.00	0.00	0.00	3.91
352	370	3.819564	ATCCTACACTGCGCTGAAATA	57.180	42.857	21.92	8.68	0.00	1.40
461	481	3.139029	GGAACGATATCGATGGCCC	57.861	57.895	30.75	17.94	43.02	5.80
568	590	2.988684	TGGGCATGAAACACCGGC	60.989	61.111	0.00	0.00	0.00	6.13
737	773	2.094026	GGTTGGATTGGATTGACTTGGC	60.094	50.000	0.00	0.00	0.00	4.52
762	803	1.836604	CAGGTTGGGTTGGGTTGGG	60.837	63.158	0.00	0.00	0.00	4.12
791	851	3.689161	TGAGATTAAACTGCGTGGAATGG	59.311	43.478	0.00	0.00	0.00	3.16
813	878	0.792640	CGCGTGCTCACAAGAGATTT	59.207	50.000	0.00	0.00	44.98	2.17
826	891	2.853914	GAAGAAGTCCACGCGTGC	59.146	61.111	33.17	20.52	0.00	5.34
875	944	1.149101	ACAAAGGGGAGAGGAAGCAA	58.851	50.000	0.00	0.00	0.00	3.91
1008	1105	3.771160	GGCACCTCCACCGACGAT	61.771	66.667	0.00	0.00	34.01	3.73
1138	1235	4.619227	CGTGACGGGGCAGGTGTT	62.619	66.667	0.00	0.00	0.00	3.32
1438	1535	1.669115	CAGTGGCGTGGTTCCTGAG	60.669	63.158	0.00	0.00	0.00	3.35
1485	1591	2.514824	GGGGAATCCAGCGACAGC	60.515	66.667	0.09	0.00	45.58	4.40
1576	1682	3.495100	CCATTTTTCTCGAGGATCCGGAT	60.495	47.826	19.21	19.21	0.00	4.18
1596	1702	0.191064	AGGTGTCCAGGAAGTCTCCA	59.809	55.000	0.00	0.00	45.24	3.86
1615	1721	2.331893	GCCGCAGCATGTACACCAA	61.332	57.895	0.00	0.00	39.31	3.67
1703	1809	2.723586	TTTCACCGCCATGAGACGCA	62.724	55.000	0.00	0.00	0.00	5.24
1923	2029	3.023949	GCAGAGGTGGTCGATGGCT	62.024	63.158	0.00	0.00	0.00	4.75
2017	2123	1.273606	CTCGGTTGTGGTCAGTGAGAT	59.726	52.381	0.00	0.00	0.00	2.75
2085	2191	3.709633	ATCTCCTGCAGCACGGCA	61.710	61.111	8.66	0.00	42.53	5.69
2136	2242	3.414700	GCGTCCACCTGCAGAACG	61.415	66.667	17.39	18.86	0.00	3.95
2172	2278	2.247699	TGAGTAGCTCCTTGGCCTTA	57.752	50.000	3.32	0.00	0.00	2.69
2187	2293	1.842562	ACCCTAGCATGCATCTTGAGT	59.157	47.619	21.98	4.69	0.00	3.41
2199	2305	1.628846	GAGTCCTTCCAAACCCTAGCA	59.371	52.381	0.00	0.00	0.00	3.49
2518	3125	1.594833	CGGGTGGTTTGAGGATCGA	59.405	57.895	0.00	0.00	38.61	3.59
2577	4228	1.274167	GACCGACACTGGACCATGTTA	59.726	52.381	9.89	0.00	0.00	2.41
2581	4232	1.975327	CAGACCGACACTGGACCAT	59.025	57.895	0.00	0.00	0.00	3.55
2626	4277	3.449737	CCCTAGTTTGTCTCCGGATTACA	59.550	47.826	3.57	10.40	0.00	2.41
2662	4313	4.717629	CGTGGCAGCGGTTCGAGA	62.718	66.667	0.00	0.00	0.00	4.04
2701	4352	1.829222	GAGGGAGACGGTTAATGGTGA	59.171	52.381	0.00	0.00	0.00	4.02
2731	4382	1.159285	CCGCTCAGACATGAAAGCAA	58.841	50.000	0.00	0.00	34.23	3.91
2742	4437	2.282251	AGGTCACGTCCGCTCAGA	60.282	61.111	0.00	0.00	0.00	3.27
2744	4439	2.282251	AGAGGTCACGTCCGCTCA	60.282	61.111	0.00	0.00	32.38	4.26
2786	4481	2.962569	CACTCTCTTGGCCGACGA	59.037	61.111	0.00	0.00	0.00	4.20
2879	4575	5.542635	AGGTTCCTCAGCAACCGATAATATA	59.457	40.000	0.00	0.00	46.98	0.86
3059	4759	2.873288	CTTTGGAGCGCAAGGAGC	59.127	61.111	11.47	0.00	40.87	4.70
3087	4787	0.537188	TTTGCTCCGATGAGAGGGTC	59.463	55.000	0.00	0.00	41.42	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.