AutoCloner

Multiple sequence alignment - TraesCS7A01G163000

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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	TraesCS7A01G163000	chr7A	100.000	3809	0	0	1	3809	119127121	119130929	0.000000e+00	7035.0
1	TraesCS7A01G163000	chr7A	83.465	1391	207	17	626	2007	119691911	119693287	0.000000e+00	1273.0
2	TraesCS7A01G163000	chr7A	85.302	1143	159	9	872	2011	119602475	119603611	0.000000e+00	1171.0
3	TraesCS7A01G163000	chr7A	78.827	1091	210	18	902	1986	119695236	119696311	0.000000e+00	715.0
4	TraesCS7A01G163000	chr7A	85.227	704	90	11	2083	2779	119603686	119604382	0.000000e+00	712.0
5	TraesCS7A01G163000	chr7A	86.252	611	72	10	2083	2687	119693606	119694210	0.000000e+00	652.0
6	TraesCS7A01G163000	chr7D	95.624	3816	124	13	1	3809	113984104	113987883	0.000000e+00	6082.0
7	TraesCS7A01G163000	chr7D	83.832	1404	203	21	626	2020	114822312	114823700	0.000000e+00	1314.0
8	TraesCS7A01G163000	chr7D	79.659	1057	186	22	938	1984	114826005	114827042	0.000000e+00	734.0
9	TraesCS7A01G163000	chr7D	83.263	711	85	17	2083	2782	114823714	114824401	1.160000e-174	623.0
10	TraesCS7A01G163000	chr7D	78.251	423	63	21	5	414	114821895	114822301	1.060000e-60	244.0
11	TraesCS7A01G163000	chr7B	92.343	3239	211	19	466	3691	73683277	73686491	0.000000e+00	4573.0
12	TraesCS7A01G163000	chr7B	84.057	1405	203	20	626	2020	74345128	74346521	0.000000e+00	1334.0
13	TraesCS7A01G163000	chr7B	85.431	707	86	12	2083	2782	74346535	74347231	0.000000e+00	719.0
14	TraesCS7A01G163000	chr7B	78.012	1137	224	22	858	1986	74353326	74354444	0.000000e+00	691.0
15	TraesCS7A01G163000	chr7B	92.842	475	26	5	1	467	73682643	73683117	0.000000e+00	682.0
16	TraesCS7A01G163000	chr7B	81.852	270	25	10	3541	3809	73686479	73686725	4.990000e-49	206.0
17	TraesCS7A01G163000	chr1B	79.268	82	17	0	1272	1353	319527025	319526944	1.480000e-04	58.4

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	TraesCS7A01G163000	chr7A	119127121	119130929	3808	False	7035.000000	7035	100.000000	1	3809	1	chr7A.!!$F1	3808
1	TraesCS7A01G163000	chr7A	119602475	119604382	1907	False	941.500000	1171	85.264500	872	2779	2	chr7A.!!$F2	1907
2	TraesCS7A01G163000	chr7A	119691911	119696311	4400	False	880.000000	1273	82.848000	626	2687	3	chr7A.!!$F3	2061
3	TraesCS7A01G163000	chr7D	113984104	113987883	3779	False	6082.000000	6082	95.624000	1	3809	1	chr7D.!!$F1	3808
4	TraesCS7A01G163000	chr7D	114821895	114827042	5147	False	728.750000	1314	81.251250	5	2782	4	chr7D.!!$F2	2777
5	TraesCS7A01G163000	chr7B	73682643	73686725	4082	False	1820.333333	4573	89.012333	1	3809	3	chr7B.!!$F2	3808
6	TraesCS7A01G163000	chr7B	74345128	74347231	2103	False	1026.500000	1334	84.744000	626	2782	2	chr7B.!!$F3	2156
7	TraesCS7A01G163000	chr7B	74353326	74354444	1118	False	691.000000	691	78.012000	858	1986	1	chr7B.!!$F1	1128

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	Hairpin	End Stability	Orientation
110	113	1.285078	TCCGATTCCTCTCCTGAGTCA	59.715	52.381	38.61	3.41	F
1172	1357	1.004918	ACGCTGTAAGGACTGGCAC	60.005	57.895	0.00	5.01	F
1443	1631	1.309499	TTGCCCTTGATTTACCGCCG	61.309	55.000	0.00	6.46	F
2125	2556	1.065199	TCAGATGCCCTTGTGGATGAC	60.065	52.381	35.39	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1443	1631	1.798087	CGGTACCAACAAATCGCCC	59.202	57.895	13.54	0.00	0.00	6.13	R
2125	2556	0.961753	GGAGAACTTGCAAGGGGTTG	59.038	55.000	29.18	5.47	0.00	3.77	R
2729	3170	2.223433	GCATAACACAATGAGGCAGCTC	60.223	50.000	0.00	0.00	0.00	4.09	R
3659	5034	1.252215	TGGCCTCATCGGTGTCGTAA	61.252	55.000	3.32	0.00	37.69	3.18	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
110	113	1.285078	TCCGATTCCTCTCCTGAGTCA	59.715	52.381	0.00	0.00	38.61	3.41
144	147	7.093992	GTCTAATCTAGATCGGAGAATTTGGG	58.906	42.308	5.51	0.00	43.58	4.12
438	450	7.681168	TCCTCCACCTTAGTTTTCTAATTCCTA	59.319	37.037	0.00	0.00	40.95	2.94
514	687	3.675348	TCCCCTTCCACGAACTAGATA	57.325	47.619	0.00	0.00	0.00	1.98
562	736	2.034879	CCAAACTCAGGCGCATCGT	61.035	57.895	10.83	0.00	0.00	3.73
596	770	2.181125	TCCTATTCACCTGTGGCGTTA	58.819	47.619	0.00	0.00	0.00	3.18
611	785	3.449737	TGGCGTTACTGCTATCTTAACCT	59.550	43.478	0.00	0.00	34.52	3.50
613	787	5.221130	GGCGTTACTGCTATCTTAACCTAG	58.779	45.833	0.00	0.00	34.52	3.02
691	868	6.875948	AAATTCCACAAATTAACTTTGGGC	57.124	33.333	12.13	0.00	45.31	5.36
724	901	5.816258	CACAATGAGCACACAATCTAGATCT	59.184	40.000	5.51	0.00	0.00	2.75
769	946	9.458727	CCCATGCTCTTATGTATCATTCTAATT	57.541	33.333	0.00	0.00	0.00	1.40
1013	1198	1.766494	ATCAAAATGGGCAGCGATCA	58.234	45.000	0.00	0.00	0.00	2.92
1172	1357	1.004918	ACGCTGTAAGGACTGGCAC	60.005	57.895	0.00	0.00	0.00	5.01
1225	1410	7.724061	GGAAGATATGCCCCAAACTAAGATTTA	59.276	37.037	0.00	0.00	0.00	1.40
1443	1631	1.309499	TTGCCCTTGATTTACCGCCG	61.309	55.000	0.00	0.00	0.00	6.46
1466	1654	1.533731	CGATTTGTTGGTACCGCAAGT	59.466	47.619	17.45	15.75	0.00	3.16
1478	1666	3.066291	ACCGCAAGTGGATCAATACAA	57.934	42.857	6.67	0.00	0.00	2.41
1486	1674	7.099120	GCAAGTGGATCAATACAAATTTCCTT	58.901	34.615	0.00	0.00	0.00	3.36
1572	1760	7.890127	TCATTTGAACTACCTCCTCAATTCAAT	59.110	33.333	0.00	0.00	36.32	2.57
2125	2556	1.065199	TCAGATGCCCTTGTGGATGAC	60.065	52.381	0.00	0.00	35.39	3.06
2172	2603	9.981114	ACTTAAAATGTTTAGATTTGAGGTTGG	57.019	29.630	0.00	0.00	0.00	3.77
2578	3019	3.118454	GCCGTCGTGTGGACCATG	61.118	66.667	0.00	0.00	42.99	3.66
2691	3132	5.906113	TCTCTCGGGAATATAGAATGCTC	57.094	43.478	0.00	0.00	0.00	4.26
2704	3145	9.906660	AATATAGAATGCTCGAACTAGAGAAAG	57.093	33.333	0.00	0.00	40.57	2.62
2729	3170	4.439305	TGAATTTTCTGGCAGAAATCCG	57.561	40.909	35.58	2.25	43.06	4.18
2808	3529	4.269603	CGCATGGATGAAGAACTTGAGTAG	59.730	45.833	0.00	0.00	0.00	2.57
2878	3602	5.938322	TGTAATGCTCCTTTTTCGAACATC	58.062	37.500	0.00	0.00	0.00	3.06
2888	3612	8.036273	TCCTTTTTCGAACATCAACCTTATAC	57.964	34.615	0.00	0.00	0.00	1.47
2915	3641	8.893727	AGTCCCTTCTTAATAAATGATGAAACG	58.106	33.333	0.00	0.00	0.00	3.60
2939	3665	4.457834	TCTTTTGCCTCCGTTTCAAAAA	57.542	36.364	0.00	0.00	38.65	1.94
3245	3979	6.314896	CAGAGGATAAGAAAAAGCTGGTACTG	59.685	42.308	0.00	0.00	0.00	2.74
3358	4093	4.565652	GGACATGGGTATCTCACACAAAGT	60.566	45.833	0.00	0.00	45.85	2.66
3432	4170	5.770685	ACAGGGCTTTCTTTATCTTCTCT	57.229	39.130	0.00	0.00	0.00	3.10
3460	4198	6.712095	GCTAATCAAGATTGATGTATGGTGGA	59.288	38.462	8.76	0.00	46.60	4.02
3659	5034	5.521696	TGATTGGAATGATGGGATTCTTGT	58.478	37.500	0.00	0.00	33.52	3.16
3685	5060	0.620556	ACCGATGAGGCCATTCACTT	59.379	50.000	5.01	0.00	46.52	3.16
3802	5845	2.812619	GGGATAAGGCGCCAGAGCT	61.813	63.158	31.54	3.61	36.60	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	113	2.860009	TCTAGATTAGACGTCGGCCAT	58.140	47.619	10.46	0.60	0.00	4.40
438	450	9.525826	GATTCAAGGATCATTAATACTGGGAAT	57.474	33.333	0.00	0.00	36.53	3.01
514	687	3.392616	GGTTGAGGTGGAGGTGATGATAT	59.607	47.826	0.00	0.00	0.00	1.63
562	736	3.181480	TGAATAGGAACGATGATGTGCGA	60.181	43.478	0.00	0.00	0.00	5.10
596	770	7.483580	AAGTTGACTAGGTTAAGATAGCAGT	57.516	36.000	0.00	0.00	0.00	4.40
643	819	6.228258	TGTAAGGTTTAGACAGTGATTGGAC	58.772	40.000	0.00	0.00	0.00	4.02
654	830	9.758651	ATTTGTGGAATTTTGTAAGGTTTAGAC	57.241	29.630	0.00	0.00	0.00	2.59
724	901	2.406130	GGTTTACGTCGGTGAACATCA	58.594	47.619	0.00	0.00	42.61	3.07
769	946	8.167605	TCAAGAACCGTAAAATGAAACCATTA	57.832	30.769	0.00	0.00	33.43	1.90
845	1025	8.757307	ATCCCTCATACCCAATTAAGAATAGA	57.243	34.615	0.00	0.00	0.00	1.98
973	1158	7.407393	TGATTCTACATGAAAATGATGCCAA	57.593	32.000	0.00	0.00	38.29	4.52
1013	1198	6.930722	CCTATGTCTTTTTCTTGTGCCATTTT	59.069	34.615	0.00	0.00	0.00	1.82
1225	1410	2.872245	CGTTGGACACTGTGAGAACATT	59.128	45.455	15.86	0.00	0.00	2.71
1443	1631	1.798087	CGGTACCAACAAATCGCCC	59.202	57.895	13.54	0.00	0.00	6.13
1572	1760	5.455612	AAGTGTTCTTAGATTCGGGAAACCA	60.456	40.000	0.00	0.00	40.79	3.67
2125	2556	0.961753	GGAGAACTTGCAAGGGGTTG	59.038	55.000	29.18	5.47	0.00	3.77
2172	2603	8.761575	TTGCCATCTTCTTTGTCATTTAAATC	57.238	30.769	0.00	0.00	0.00	2.17
2225	2656	5.890424	ACTTTTCAACGAAAGGAGAAACA	57.110	34.783	5.69	0.00	40.19	2.83
2318	2759	7.110043	TGTTAAGCAATGGCATAATTCATGA	57.890	32.000	0.00	0.00	44.61	3.07
2691	3132	8.930760	AGAAAATTCATGTCTTTCTCTAGTTCG	58.069	33.333	11.26	0.00	35.03	3.95
2704	3145	5.809051	GGATTTCTGCCAGAAAATTCATGTC	59.191	40.000	22.64	13.58	46.08	3.06
2729	3170	2.223433	GCATAACACAATGAGGCAGCTC	60.223	50.000	0.00	0.00	0.00	4.09
2808	3529	5.875359	AGATTTTACTCTCCCAACATCGAAC	59.125	40.000	0.00	0.00	0.00	3.95
2874	3598	5.726793	AGAAGGGACTGTATAAGGTTGATGT	59.273	40.000	0.00	0.00	40.86	3.06
2915	3641	3.915437	TGAAACGGAGGCAAAAGATTC	57.085	42.857	0.00	0.00	0.00	2.52
3014	3742	7.617225	TCGATGATGGAAAGAGTAAAAGGTAA	58.383	34.615	0.00	0.00	0.00	2.85
3089	3823	4.717233	TCAAGCATTCACACAACTTGTT	57.283	36.364	0.00	0.00	38.99	2.83
3245	3979	4.092091	CCAGTTCTTTCTTATCGTCTGTGC	59.908	45.833	0.00	0.00	0.00	4.57
3432	4170	9.223099	CACCATACATCAATCTTGATTAGCATA	57.777	33.333	2.68	0.00	45.13	3.14
3455	4193	4.083164	CGTATTTTGTTACCCTTGTCCACC	60.083	45.833	0.00	0.00	0.00	4.61
3460	4198	6.991531	TGAAGTACGTATTTTGTTACCCTTGT	59.008	34.615	4.71	0.00	0.00	3.16
3548	4286	8.896744	AGATGATTTGAGCGATAGAAAAATTGA	58.103	29.630	0.00	0.00	39.76	2.57
3659	5034	1.252215	TGGCCTCATCGGTGTCGTAA	61.252	55.000	3.32	0.00	37.69	3.18
3685	5060	3.054139	AGCTCAAGTGCCTCCATATTGAA	60.054	43.478	0.00	0.00	32.58	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.