AutoCloner

Multiple sequence alignment - TraesCS1B01G142700

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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	TraesCS1B01G142700	chr1B	100.000	3922	0	0	1	3922	192277238	192273317	0.000000e+00	7243.0
1	TraesCS1B01G142700	chr1B	99.614	259	1	0	146	404	192282230	192281972	1.280000e-129	473.0
2	TraesCS1B01G142700	chr1B	93.750	64	3	1	768	830	470588418	470588481	1.160000e-15	95.3
3	TraesCS1B01G142700	chr1A	97.232	2746	61	4	405	3140	146944105	146946845	0.000000e+00	4636.0
4	TraesCS1B01G142700	chr1A	94.192	792	25	5	3143	3922	146946908	146947690	0.000000e+00	1188.0
5	TraesCS1B01G142700	chr1D	97.115	1664	38	3	1387	3049	143258445	143256791	0.000000e+00	2798.0
6	TraesCS1B01G142700	chr1D	97.368	988	25	1	405	1391	143264015	143263028	0.000000e+00	1679.0
7	TraesCS1B01G142700	chr1D	94.304	790	29	3	3143	3922	143256665	143255882	0.000000e+00	1195.0
8	TraesCS1B01G142700	chr1D	99.259	405	2	1	1	404	207159247	207159651	0.000000e+00	730.0
9	TraesCS1B01G142700	chr1D	97.674	215	3	2	191	404	207149174	207149387	6.190000e-98	368.0
10	TraesCS1B01G142700	chr1D	93.069	101	6	1	3054	3154	143256814	143256715	3.160000e-31	147.0
11	TraesCS1B01G142700	chr7D	88.825	2085	178	21	547	2592	113448692	113446624	0.000000e+00	2508.0
12	TraesCS1B01G142700	chr7D	86.534	453	41	11	2653	3101	113446630	113446194	7.620000e-132	481.0
13	TraesCS1B01G142700	chr7D	92.793	111	6	2	408	516	113448801	113448691	4.060000e-35	159.0
14	TraesCS1B01G142700	chr7B	88.506	2088	169	31	547	2592	73137267	73135209	0.000000e+00	2460.0
15	TraesCS1B01G142700	chr7A	90.263	1253	102	10	1355	2592	118464060	118462813	0.000000e+00	1620.0
16	TraesCS1B01G142700	chr7A	85.669	956	82	20	408	1317	118465011	118464065	0.000000e+00	955.0
17	TraesCS1B01G142700	chr7A	85.055	455	46	10	2653	3101	118462819	118462381	1.000000e-120	444.0
18	TraesCS1B01G142700	chr7A	80.110	181	34	2	1	180	540902540	540902361	2.460000e-27	134.0
19	TraesCS1B01G142700	chr6A	85.126	874	82	18	475	1318	588864300	588863445	0.000000e+00	850.0
20	TraesCS1B01G142700	chr6A	99.257	404	3	0	1	404	574487146	574487549	0.000000e+00	730.0
21	TraesCS1B01G142700	chr6A	99.225	258	2	0	147	404	574482090	574482347	2.130000e-127	466.0
22	TraesCS1B01G142700	chr6B	98.515	404	6	0	1	404	144806584	144806181	0.000000e+00	713.0
23	TraesCS1B01G142700	chr6B	98.456	259	4	0	146	404	144811638	144811380	1.280000e-124	457.0
24	TraesCS1B01G142700	chr6B	91.791	268	18	3	141	405	32568942	32568676	1.720000e-98	370.0
25	TraesCS1B01G142700	chr6B	97.386	153	4	0	4	156	32569107	32568955	1.080000e-65	261.0
26	TraesCS1B01G142700	chr6B	93.750	64	3	1	768	830	22744494	22744557	1.160000e-15	95.3
27	TraesCS1B01G142700	chr6B	86.170	94	3	3	768	860	71751603	71751687	4.170000e-15	93.5
28	TraesCS1B01G142700	chr5A	88.070	285	15	6	144	409	653369938	653370222	1.760000e-83	320.0
29	TraesCS1B01G142700	chr5A	92.308	156	12	0	1	156	653369411	653369566	5.100000e-54	222.0
30	TraesCS1B01G142700	chr5A	86.170	188	8	6	147	320	653302386	653302569	1.860000e-43	187.0
31	TraesCS1B01G142700	chr4B	81.868	182	29	3	1	180	42918036	42918215	2.440000e-32	150.0
32	TraesCS1B01G142700	chr5D	81.356	177	33	0	4	180	33699804	33699628	1.140000e-30	145.0
33	TraesCS1B01G142700	chr3B	82.530	166	27	2	16	180	152486423	152486259	1.140000e-30	145.0

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	TraesCS1B01G142700	chr1B	192273317	192277238	3921	True	7243.000000	7243	100.000000	1	3922	1	chr1B.!!$R1	3921
1	TraesCS1B01G142700	chr1A	146944105	146947690	3585	False	2912.000000	4636	95.712000	405	3922	2	chr1A.!!$F1	3517
2	TraesCS1B01G142700	chr1D	143263028	143264015	987	True	1679.000000	1679	97.368000	405	1391	1	chr1D.!!$R1	986
3	TraesCS1B01G142700	chr1D	143255882	143258445	2563	True	1380.000000	2798	94.829333	1387	3922	3	chr1D.!!$R2	2535
4	TraesCS1B01G142700	chr7D	113446194	113448801	2607	True	1049.333333	2508	89.384000	408	3101	3	chr7D.!!$R1	2693
5	TraesCS1B01G142700	chr7B	73135209	73137267	2058	True	2460.000000	2460	88.506000	547	2592	1	chr7B.!!$R1	2045
6	TraesCS1B01G142700	chr7A	118462381	118465011	2630	True	1006.333333	1620	86.995667	408	3101	3	chr7A.!!$R2	2693
7	TraesCS1B01G142700	chr6A	588863445	588864300	855	True	850.000000	850	85.126000	475	1318	1	chr6A.!!$R1	843
8	TraesCS1B01G142700	chr5A	653369411	653370222	811	False	271.000000	320	90.189000	1	409	2	chr5A.!!$F2	408

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	End Stability	Orientation
371	372	0.033405	TCCTCGTCCCTTACCTCTGG	60.033	60.0	0.00	0.0	3.86	F
377	378	0.044092	TCCCTTACCTCTGGCCATGA	59.956	55.0	5.51	5.2	3.07	F
392	393	0.471617	CATGAAGCCGATCCCCTCTT	59.528	55.0	0.00	0.0	2.85	F
1156	1201	1.055849	GGCCCCTTTGACAAATTGGT	58.944	50.0	14.13	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1331	1386	2.331893	TGGATGCGCAAGAAACCCG	61.332	57.895	17.11	43.02	5.28	R
1953	2027	3.003480	GGCTACTCGATTGGAATATGCC	58.997	50.000	0.00	0.00	4.40	R
1954	2028	3.931578	AGGCTACTCGATTGGAATATGC	58.068	45.455	0.00	0.00	3.14	R
2956	3039	0.036671	AACTACAACTAGGCACGCCC	60.037	55.000	3.95	36.58	6.13	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)

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Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
32	33	3.996150	ATTGTGCAGGTCAAAGTTCAG	57.004	42.857	0.00	3.02
35	36	1.334869	GTGCAGGTCAAAGTTCAGTGG	59.665	52.381	0.00	4.00
41	42	2.544267	GGTCAAAGTTCAGTGGTCTTCG	59.456	50.000	0.00	3.79
49	50	1.544691	TCAGTGGTCTTCGTTAGCTCC	59.455	52.381	0.00	4.70
57	58	2.431057	TCTTCGTTAGCTCCTGAATCCC	59.569	50.000	0.00	3.85
64	65	1.826024	CTCCTGAATCCCCGACCTG	59.174	63.158	0.00	4.00
77	78	2.330216	CCGACCTGGGAGGATTATTCT	58.670	52.381	37.67	2.40
125	126	0.674895	GCTGTTGGGATGAAGACGCT	60.675	55.000	0.00	5.07
156	157	0.883833	GGAGGCAAATGTCACACCTG	59.116	55.000	0.00	4.00
157	158	1.545428	GGAGGCAAATGTCACACCTGA	60.545	52.381	0.00	3.86
159	160	3.609853	GAGGCAAATGTCACACCTGATA	58.390	45.455	0.00	2.15
160	161	3.347216	AGGCAAATGTCACACCTGATAC	58.653	45.455	0.00	2.24
161	162	3.081061	GGCAAATGTCACACCTGATACA	58.919	45.455	0.00	2.29
162	163	3.696051	GGCAAATGTCACACCTGATACAT	59.304	43.478	34.11	2.29
163	164	4.439153	GGCAAATGTCACACCTGATACATG	60.439	45.833	33.04	3.21
164	165	4.395854	GCAAATGTCACACCTGATACATGA	59.604	41.667	33.04	3.07
165	166	5.448225	GCAAATGTCACACCTGATACATGAG	60.448	44.000	33.04	2.90
166	167	5.426689	AATGTCACACCTGATACATGAGT	57.573	39.130	33.04	3.41
167	168	6.544928	AATGTCACACCTGATACATGAGTA	57.455	37.500	33.04	2.59
168	169	6.737720	ATGTCACACCTGATACATGAGTAT	57.262	37.500	43.49	2.12
177	178	4.175787	GATACATGAGTATCGGTGGACC	57.824	50.000	45.03	4.46
178	179	2.160721	ACATGAGTATCGGTGGACCT	57.839	50.000	38.61	3.85
179	180	1.757118	ACATGAGTATCGGTGGACCTG	59.243	52.381	38.61	4.00
180	181	1.069204	CATGAGTATCGGTGGACCTGG	59.931	57.143	38.61	4.45
181	182	0.333652	TGAGTATCGGTGGACCTGGA	59.666	55.000	38.61	3.86

Showing 1 to 25 of 207 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
7	8	3.290710	ACTTTGACCTGCACAATTGAGT	58.709	40.909	13.59	0.00	3.41
14	15	2.016318	CACTGAACTTTGACCTGCACA	58.984	47.619	0.00	0.00	4.57
32	33	1.544691	TCAGGAGCTAACGAAGACCAC	59.455	52.381	0.00	0.00	4.16
35	36	3.449632	GGATTCAGGAGCTAACGAAGAC	58.550	50.000	0.00	0.00	3.01
41	42	1.120530	TCGGGGATTCAGGAGCTAAC	58.879	55.000	0.00	0.00	2.34
57	58	2.037772	CAGAATAATCCTCCCAGGTCGG	59.962	54.545	0.00	36.53	4.79
64	65	2.548920	CGGAGCACAGAATAATCCTCCC	60.549	54.545	0.00	36.39	4.30
94	95	3.570212	AACAGCTTGCCTCCGGGT	61.570	61.111	0.00	34.45	5.28
137	138	0.883833	CAGGTGTGACATTTGCCTCC	59.116	55.000	0.00	0.00	4.30
157	158	3.574396	CAGGTCCACCGATACTCATGTAT	59.426	47.826	0.00	41.65	2.29
159	160	1.757118	CAGGTCCACCGATACTCATGT	59.243	52.381	0.00	42.08	3.21
160	161	1.069204	CCAGGTCCACCGATACTCATG	59.931	57.143	0.00	42.08	3.07
161	162	1.063190	TCCAGGTCCACCGATACTCAT	60.063	52.381	0.00	42.08	2.90
162	163	0.333652	TCCAGGTCCACCGATACTCA	59.666	55.000	0.00	42.08	3.41
163	164	1.409427	CTTCCAGGTCCACCGATACTC	59.591	57.143	0.00	42.08	2.59
164	165	1.486211	CTTCCAGGTCCACCGATACT	58.514	55.000	0.00	42.08	2.12
165	166	0.464452	CCTTCCAGGTCCACCGATAC	59.536	60.000	0.00	42.08	2.24
166	167	2.910579	CCTTCCAGGTCCACCGATA	58.089	57.895	0.00	42.08	2.92
167	168	3.727387	CCTTCCAGGTCCACCGAT	58.273	61.111	0.00	42.08	4.18
176	177	6.995091	CCTTTCTATCTATTTCACCTTCCAGG	59.005	42.308	0.00	42.49	4.45
177	178	6.995091	CCCTTTCTATCTATTTCACCTTCCAG	59.005	42.308	0.00	0.00	3.86
178	179	6.126478	CCCCTTTCTATCTATTTCACCTTCCA	60.126	42.308	0.00	0.00	3.53
179	180	6.126449	ACCCCTTTCTATCTATTTCACCTTCC	60.126	42.308	0.00	0.00	3.46
180	181	6.768381	CACCCCTTTCTATCTATTTCACCTTC	59.232	42.308	0.00	0.00	3.46
181	182	6.447084	TCACCCCTTTCTATCTATTTCACCTT	59.553	38.462	0.00	0.00	3.50

Showing 1 to 25 of 222 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.