AutoCloner

Multiple sequence alignment - TraesCS7D01G510300

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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	TraesCS7D01G510300	chr7D	100.000	3303	0	0	1	3303	613405284	613408586	0.000000e+00	6100
1	TraesCS7D01G510300	chr7D	89.232	1003	90	10	1112	2110	613394582	613395570	0.000000e+00	1238
2	TraesCS7D01G510300	chr7D	77.247	712	98	41	249	944	613393761	613394424	3.130000e-95	359
3	TraesCS7D01G510300	chr7D	87.432	183	13	6	2107	2287	613396122	613396296	5.590000e-48	202
4	TraesCS7D01G510300	chr7A	96.070	3333	97	14	1	3303	704791196	704794524	0.000000e+00	5398
5	TraesCS7D01G510300	chr7A	89.033	1003	92	10	1112	2110	704776826	704777814	0.000000e+00	1227
6	TraesCS7D01G510300	chr7A	87.432	183	13	6	2107	2287	704778366	704778540	5.590000e-48	202
7	TraesCS7D01G510300	chr7A	90.909	77	6	1	249	324	704691559	704691635	5.830000e-18	102
8	TraesCS7D01G510300	chr7B	95.202	3293	119	8	30	3303	703245083	703248355	0.000000e+00	5169
9	TraesCS7D01G510300	chr7B	89.133	1003	91	9	1112	2110	703165853	703166841	0.000000e+00	1232
10	TraesCS7D01G510300	chr7B	78.837	430	56	27	249	658	703165093	703165507	1.180000e-64	257
11	TraesCS7D01G510300	chr7B	88.950	181	11	3	2107	2285	703167393	703167566	7.180000e-52	215

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	TraesCS7D01G510300	chr7D	613405284	613408586	3302	False	6100.000000	6100	100.0000	1	3303	1	chr7D.!!$F1	3302
1	TraesCS7D01G510300	chr7D	613393761	613396296	2535	False	599.666667	1238	84.6370	249	2287	3	chr7D.!!$F2	2038
2	TraesCS7D01G510300	chr7A	704791196	704794524	3328	False	5398.000000	5398	96.0700	1	3303	1	chr7A.!!$F2	3302
3	TraesCS7D01G510300	chr7A	704776826	704778540	1714	False	714.500000	1227	88.2325	1112	2287	2	chr7A.!!$F3	1175
4	TraesCS7D01G510300	chr7B	703245083	703248355	3272	False	5169.000000	5169	95.2020	30	3303	1	chr7B.!!$F1	3273
5	TraesCS7D01G510300	chr7B	703165093	703167566	2473	False	568.000000	1232	85.6400	249	2285	3	chr7B.!!$F2	2036

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
497	547	1.208052	ACACTGTCATTCCCCTCATCG	59.792	52.381	0.0	0.0	0.0	3.84	F
693	765	1.509548	CCATCCCATCCCATACCCCC	61.510	65.000	0.0	0.0	0.0	5.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2013	2126	1.154016	ACGGTCGTTCAGCTGATCG	60.154	57.895	31.86	31.86	44.04	3.69	R
2432	3105	7.621832	TTGTCTGCAAAATCATAACGAAAAG	57.378	32.000	0.00	0.00	0.00	2.27	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
90	96	3.336138	AGTAGTTTGTCAAGCTAGGGC	57.664	47.619	9.20	0.00	39.06	5.19
123	129	8.110612	GCTTCTTTCTTTTTCTTTTTACAGCAC	58.889	33.333	0.00	0.00	0.00	4.40
143	149	4.695455	GCACATCCTGCTCTTGTTTTAGTA	59.305	41.667	0.00	0.00	43.33	1.82
144	150	5.390991	GCACATCCTGCTCTTGTTTTAGTAC	60.391	44.000	0.00	0.00	43.33	2.73
154	160	7.147983	TGCTCTTGTTTTAGTACCACATTGTTT	60.148	33.333	0.00	0.00	0.00	2.83
156	162	8.282455	TCTTGTTTTAGTACCACATTGTTTCA	57.718	30.769	0.00	0.00	0.00	2.69
157	163	8.402472	TCTTGTTTTAGTACCACATTGTTTCAG	58.598	33.333	0.00	0.00	0.00	3.02
195	223	7.359264	GCATTGCAATACCTTGTAGTATCTACG	60.359	40.741	12.53	0.00	34.69	3.51
407	456	1.864711	TCTGAACGTTGCCTCTTTTCG	59.135	47.619	5.00	0.00	0.00	3.46
497	547	1.208052	ACACTGTCATTCCCCTCATCG	59.792	52.381	0.00	0.00	0.00	3.84
509	577	2.354704	CCCCTCATCGCTGTCAGTTTTA	60.355	50.000	0.93	0.00	0.00	1.52
614	686	2.408704	CGTTCGATTCGCTCTCTTGTTT	59.591	45.455	0.00	0.00	0.00	2.83
688	760	1.826340	CGACGCCATCCCATCCCATA	61.826	60.000	0.00	0.00	0.00	2.74
693	765	1.509548	CCATCCCATCCCATACCCCC	61.510	65.000	0.00	0.00	0.00	5.40
714	787	5.390613	CCCGTTTTGCAACTTCAATACTAG	58.609	41.667	0.00	0.00	0.00	2.57
783	858	2.396590	TTCGCAATTCCTGGGTAGAC	57.603	50.000	0.00	0.00	39.04	2.59
910	985	8.202461	TCTTTTTAGAGTAACAGGGAGATCAA	57.798	34.615	0.00	0.00	0.00	2.57
912	987	6.546428	TTTAGAGTAACAGGGAGATCAAGG	57.454	41.667	0.00	0.00	0.00	3.61
999	1074	3.480470	AGGTGTTTGATCACAGGTTGAG	58.520	45.455	0.00	0.00	37.77	3.02
1998	2111	3.138283	AGGTCCTTCAGGTGATTCACAAA	59.862	43.478	18.09	8.34	35.86	2.83
2377	3050	4.378459	GGATTAGTTGCAGAGTTGTTTCCG	60.378	45.833	0.00	0.00	0.00	4.30
2425	3098	7.775561	ACCTAAAATTTGAGTCTTTCTGTCACT	59.224	33.333	1.77	0.00	0.00	3.41
2812	3486	3.648067	TGCCCACCCAAACATTCAAAATA	59.352	39.130	0.00	0.00	0.00	1.40
2816	3490	5.642919	CCCACCCAAACATTCAAAATACATG	59.357	40.000	0.00	0.00	0.00	3.21
2924	3598	2.023673	TGCAGTGTTTTTCCTCCTGTG	58.976	47.619	0.00	0.00	0.00	3.66
3029	3703	6.108687	TGCCGGATAGATCATATTGACATTC	58.891	40.000	5.05	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.089874	CGGAAGGATCTGCCCCCA	61.090	66.667	0.00	0.00	37.37	4.96
90	96	5.268118	AGAAAAAGAAAGAAGCAAGGGTG	57.732	39.130	0.00	0.00	0.00	4.61
123	129	5.122396	GTGGTACTAAAACAAGAGCAGGATG	59.878	44.000	0.00	0.00	40.87	3.51
143	149	7.173218	CAGACAAGTATACTGAAACAATGTGGT	59.827	37.037	6.06	0.00	34.07	4.16
144	150	7.521529	CAGACAAGTATACTGAAACAATGTGG	58.478	38.462	6.06	0.00	34.07	4.17
154	160	4.831107	TGCAATGCAGACAAGTATACTGA	58.169	39.130	2.72	0.00	33.32	3.41
156	162	6.260936	GGTATTGCAATGCAGACAAGTATACT	59.739	38.462	25.81	0.00	40.61	2.12
157	163	6.260936	AGGTATTGCAATGCAGACAAGTATAC	59.739	38.462	25.81	16.10	40.61	1.47
195	223	5.623673	CACGGTAACAACATAGCAACTTTTC	59.376	40.000	0.00	0.00	0.00	2.29
264	292	1.302285	CCTGCTGAAGCCATGGACT	59.698	57.895	18.40	9.58	41.18	3.85
407	456	7.727181	TCTATTATTAAACTGACTGAGAGGGC	58.273	38.462	0.00	0.00	0.00	5.19
497	547	1.807142	GCTCTGGGTAAAACTGACAGC	59.193	52.381	1.25	0.00	0.00	4.40
509	577	0.036022	GAGACTGCTTTGCTCTGGGT	59.964	55.000	0.00	0.00	0.00	4.51
614	686	7.229306	ACAGATTTAATTGTTCACAGCAGAGAA	59.771	33.333	0.00	0.00	0.00	2.87
688	760	0.684805	TGAAGTTGCAAAACGGGGGT	60.685	50.000	0.00	0.00	0.00	4.95
693	765	5.565259	CAGCTAGTATTGAAGTTGCAAAACG	59.435	40.000	0.00	0.00	32.37	3.60
714	787	0.030235	GTGAACAAAACCCGGTCAGC	59.970	55.000	0.00	0.00	0.00	4.26
767	842	4.423625	ACTATGTCTACCCAGGAATTGC	57.576	45.455	0.00	0.00	0.00	3.56
783	858	0.321671	CGCCCCTGGATGGTACTATG	59.678	60.000	0.00	0.00	0.00	2.23
955	1030	3.503827	AGATGCATGACAAGCAACATG	57.496	42.857	9.71	0.00	46.27	3.21
1998	2111	2.486592	CTGATCGGCCGTAAAACCTTTT	59.513	45.455	27.15	0.00	0.00	2.27
2013	2126	1.154016	ACGGTCGTTCAGCTGATCG	60.154	57.895	31.86	31.86	44.04	3.69
2146	2818	9.903682	ATGTTCAGTCTATTCATTTGTTTCAAG	57.096	29.630	0.00	0.00	0.00	3.02
2427	3100	9.307121	TCTGCAAAATCATAACGAAAAGAAAAA	57.693	25.926	0.00	0.00	0.00	1.94
2432	3105	7.621832	TTGTCTGCAAAATCATAACGAAAAG	57.378	32.000	0.00	0.00	0.00	2.27
2438	3111	9.282247	CTAACTGATTGTCTGCAAAATCATAAC	57.718	33.333	15.60	0.00	40.89	1.89
2812	3486	5.243060	CAGGATTCATATGGCATGAACATGT	59.757	40.000	10.98	0.00	40.37	3.21
2816	3490	5.779529	AACAGGATTCATATGGCATGAAC	57.220	39.130	10.98	3.08	40.37	3.18
2924	3598	4.691860	ACAACATGAGCTACAAATCAGC	57.308	40.909	0.00	0.00	39.41	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.