AutoCloner

Multiple sequence alignment - TraesCS3A01G104300

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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	TraesCS3A01G104300	chr3A	100.000	1553	0	0	1457	3009	67383501	67385053	0.000000e+00	2868
1	TraesCS3A01G104300	chr3A	100.000	1026	0	0	1	1026	67382045	67383070	0.000000e+00	1895
2	TraesCS3A01G104300	chr3A	83.871	155	15	8	452	597	725959772	725959925	4.040000e-29	139
3	TraesCS3A01G104300	chr3A	82.500	160	18	7	453	603	681558512	681558670	6.770000e-27	132
4	TraesCS3A01G104300	chr3A	84.800	125	16	2	287	408	57269839	57269715	4.070000e-24	122
5	TraesCS3A01G104300	chr3B	96.647	1551	46	3	1459	3009	92604739	92606283	0.000000e+00	2571
6	TraesCS3A01G104300	chr3B	96.821	346	9	1	681	1026	92604399	92604742	7.230000e-161	577
7	TraesCS3A01G104300	chr3B	81.236	437	54	16	1	409	92603661	92604097	8.040000e-86	327
8	TraesCS3A01G104300	chr3B	83.007	153	18	6	453	597	605273000	605273152	6.770000e-27	132
9	TraesCS3A01G104300	chr3D	96.647	1551	34	2	1459	3009	58428424	58429956	0.000000e+00	2560
10	TraesCS3A01G104300	chr3D	91.679	673	48	6	1	667	58404867	58405537	0.000000e+00	926
11	TraesCS3A01G104300	chr3D	91.353	266	12	4	761	1026	58428173	58428427	1.330000e-93	353
12	TraesCS3A01G104300	chr3D	96.190	105	4	0	665	769	58427893	58427997	3.990000e-39	172
13	TraesCS3A01G104300	chr7B	86.508	126	15	1	290	413	727387014	727386889	1.450000e-28	137
14	TraesCS3A01G104300	chr7B	82.500	160	18	8	453	603	112107826	112107668	6.770000e-27	132
15	TraesCS3A01G104300	chr6B	86.885	122	14	1	290	409	55006992	55007113	5.230000e-28	135
16	TraesCS3A01G104300	chr7A	83.117	154	16	8	453	597	134625443	134625595	6.770000e-27	132
17	TraesCS3A01G104300	chr7A	85.246	122	16	1	290	409	134625442	134625563	1.130000e-24	124
18	TraesCS3A01G104300	chr5B	83.117	154	16	8	453	597	40480777	40480929	6.770000e-27	132
19	TraesCS3A01G104300	chr5B	84.426	122	17	1	290	409	8364237	8364116	5.270000e-23	119
20	TraesCS3A01G104300	chr5A	83.007	153	18	7	453	597	91625618	91625770	6.770000e-27	132
21	TraesCS3A01G104300	chr2A	78.469	209	33	8	453	649	691659809	691659601	3.150000e-25	126
22	TraesCS3A01G104300	chr2A	85.124	121	16	1	291	409	459017076	459017196	4.070000e-24	122
23	TraesCS3A01G104300	chr1B	84.426	122	17	1	290	409	589545624	589545503	5.270000e-23	119

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	TraesCS3A01G104300	chr3A	67382045	67385053	3008	False	2381.500000	2868	100.000	1	3009	2	chr3A.!!$F3	3008
1	TraesCS3A01G104300	chr3B	92603661	92606283	2622	False	1158.333333	2571	91.568	1	3009	3	chr3B.!!$F2	3008
2	TraesCS3A01G104300	chr3D	58427893	58429956	2063	False	1028.333333	2560	94.730	665	3009	3	chr3D.!!$F2	2344
3	TraesCS3A01G104300	chr3D	58404867	58405537	670	False	926.000000	926	91.679	1	667	1	chr3D.!!$F1	666

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
421	451	0.034059	GGGCATCATCGATCGAACCT	59.966	55.0	23.5	2.26	0.0	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2088	2356	1.198713	ACACCATCCAGCAGTAGGAG	58.801	55.0	0.0	0.0	38.83	3.69	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
21	22	2.025793	AGATCTCTGACAGGAAGACCGA	60.026	50.000	1.81	0.00	41.83	4.69
90	91	1.270907	AGATCGAAGAACAGCAGGGT	58.729	50.000	0.00	0.00	43.58	4.34
242	270	1.305297	TGCCTCCACCTGAGATCGT	60.305	57.895	0.00	0.00	44.42	3.73
248	276	1.811266	CACCTGAGATCGTTGGCCG	60.811	63.158	0.00	0.00	38.13	6.13
259	287	4.337177	TTGGCCGGCATCGAACCA	62.337	61.111	30.85	12.44	39.46	3.67
305	335	2.364579	CCGCACACCCTACCCCTA	60.365	66.667	0.00	0.00	0.00	3.53
317	347	2.307686	CCTACCCCTAAGCACCTTCAAA	59.692	50.000	0.00	0.00	0.00	2.69
355	385	7.386299	GCATATCATCTTGAGATTTACGGAGTT	59.614	37.037	0.00	0.00	35.39	3.01
421	451	0.034059	GGGCATCATCGATCGAACCT	59.966	55.000	23.50	2.26	0.00	3.50
428	458	1.135139	CATCGATCGAACCTCCACACT	59.865	52.381	23.50	0.00	0.00	3.55
476	506	2.308866	CACCCTACCCCTGAACATCTTT	59.691	50.000	0.00	0.00	0.00	2.52
481	511	3.710209	ACCCCTGAACATCTTTGAGAG	57.290	47.619	0.00	0.00	0.00	3.20
552	582	6.035866	GTCTAGTAGTCGACGAAATCTTCTCA	59.964	42.308	10.46	0.00	0.00	3.27
553	583	4.972201	AGTAGTCGACGAAATCTTCTCAC	58.028	43.478	10.46	0.00	0.00	3.51
559	594	3.314553	GACGAAATCTTCTCACCGAACA	58.685	45.455	0.00	0.00	0.00	3.18
561	596	3.005472	ACGAAATCTTCTCACCGAACAGA	59.995	43.478	0.00	0.00	0.00	3.41
578	613	2.416547	ACAGACATCGCCGAAAATTCTG	59.583	45.455	13.02	13.02	36.02	3.02
581	616	3.372206	AGACATCGCCGAAAATTCTGAAG	59.628	43.478	0.00	0.00	0.00	3.02
629	696	9.213777	TGAGATACCACTATTCTTCTAACCATT	57.786	33.333	0.00	0.00	0.00	3.16
635	702	7.824779	ACCACTATTCTTCTAACCATTCAACTC	59.175	37.037	0.00	0.00	0.00	3.01
669	736	6.379386	TCGCTACTACCATGAGAATTTATCG	58.621	40.000	0.00	0.00	0.00	2.92
798	1065	1.131638	TCGCCATCTAGAATGCCCTT	58.868	50.000	10.31	0.00	0.00	3.95
803	1070	3.067320	GCCATCTAGAATGCCCTTGAAAC	59.933	47.826	0.00	0.00	0.00	2.78
846	1113	3.628646	GAACCCATCCAGCACGGCT	62.629	63.158	0.00	0.00	40.77	5.52
1779	2047	1.682394	GCTCGTCCTCTACTTCCTCCA	60.682	57.143	0.00	0.00	0.00	3.86
2071	2339	4.213482	GTCCATATTATTGTTCAGTCCCGC	59.787	45.833	0.00	0.00	0.00	6.13
2088	2356	0.315869	CGCGTATGCATTTCGGTTCC	60.316	55.000	19.91	7.34	42.97	3.62
2146	2414	3.920446	TCTTGCTGTGCTATTGTCGTTA	58.080	40.909	0.00	0.00	0.00	3.18
2147	2415	4.311606	TCTTGCTGTGCTATTGTCGTTAA	58.688	39.130	0.00	0.00	0.00	2.01
2255	2523	2.364002	TCTCAAACAGTCACGGTCATGA	59.636	45.455	0.00	0.00	0.00	3.07
2305	2573	1.225704	CCTGGTCAGGCAGATTCCC	59.774	63.158	3.86	0.00	42.44	3.97
2310	2578	1.821136	GGTCAGGCAGATTCCCTTTTG	59.179	52.381	0.00	0.00	0.00	2.44
2316	2584	2.247358	GCAGATTCCCTTTTGGTTCCA	58.753	47.619	0.00	0.00	38.10	3.53
2333	2601	4.580580	GGTTCCATGGGTAATTGAGATGTC	59.419	45.833	13.02	0.00	0.00	3.06
2399	2667	4.042311	TCCCTTAAACTGCATTGTACCTGA	59.958	41.667	0.00	0.00	0.00	3.86
2414	2682	7.781548	TTGTACCTGACTTTTCACTAACTTC	57.218	36.000	0.00	0.00	0.00	3.01
2417	2685	8.698210	TGTACCTGACTTTTCACTAACTTCTAA	58.302	33.333	0.00	0.00	0.00	2.10
2536	2804	6.618287	TGTAGTTTGATTGACAGAGTTTGG	57.382	37.500	0.00	0.00	0.00	3.28
2698	2966	1.340248	CATGGAGGGCAGAATCATTGC	59.660	52.381	0.00	0.00	40.80	3.56
2899	3167	5.133941	TGTTTGTTGGGTGCAGAGTATTTA	58.866	37.500	0.00	0.00	0.00	1.40
2989	3257	4.655186	TGGTAGGTACTTACACCACACTTT	59.345	41.667	16.10	0.00	41.40	2.66
2993	3261	5.365619	AGGTACTTACACCACACTTTTGAG	58.634	41.667	0.00	0.00	41.40	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	1.000607	CGAGTTTCGGTCTTCCTGTCA	60.001	52.381	0.00	0.00	36.00	3.58
21	22	1.874345	ATCTGGACGCCGACGAGTTT	61.874	55.000	0.00	0.00	43.93	2.66
32	33	2.725008	GCCTCCTCGATCTGGACG	59.275	66.667	0.83	0.00	0.00	4.79
57	58	7.042051	TGTTCTTCGATCTTCAAAACTTCGATT	60.042	33.333	0.00	0.00	38.47	3.34
90	91	1.203001	GGGATCCCCACTGTGTTTTGA	60.203	52.381	21.42	0.00	44.65	2.69
120	121	1.689233	TGCCCAGATCTAGCCCGTT	60.689	57.895	12.95	0.00	0.00	4.44
242	270	4.337177	TGGTTCGATGCCGGCCAA	62.337	61.111	26.77	6.41	37.92	4.52
248	276	2.332654	GGTGTGGTGGTTCGATGCC	61.333	63.158	0.00	0.00	0.00	4.40
259	287	0.252012	CTCTCCTCTCCAGGTGTGGT	60.252	60.000	9.05	0.00	45.28	4.16
320	350	8.964847	ATCTCAAGATGATATGCTGGCTCAGC	62.965	46.154	17.27	17.27	44.27	4.26
355	385	2.479275	CGACTTCGAGACGCCTATGATA	59.521	50.000	0.00	0.00	43.02	2.15
421	451	0.034960	CTCTCCTCTCCGAGTGTGGA	60.035	60.000	0.00	2.03	36.37	4.02
428	458	2.598467	GCCCTCTCTCCTCTCCGA	59.402	66.667	0.00	0.00	0.00	4.55
476	506	4.723309	TGATATGCTAGCTCAGTCTCTCA	58.277	43.478	17.23	4.97	0.00	3.27
481	511	6.023357	TCAAGATGATATGCTAGCTCAGTC	57.977	41.667	17.23	9.32	0.00	3.51
543	573	4.499183	GATGTCTGTTCGGTGAGAAGATT	58.501	43.478	0.00	0.00	39.95	2.40
545	575	2.095212	CGATGTCTGTTCGGTGAGAAGA	60.095	50.000	0.00	0.00	39.95	2.87
547	577	1.668919	GCGATGTCTGTTCGGTGAGAA	60.669	52.381	0.00	0.00	37.10	2.87
552	582	2.126071	CGGCGATGTCTGTTCGGT	60.126	61.111	0.00	0.00	37.10	4.69
553	583	1.011968	TTTCGGCGATGTCTGTTCGG	61.012	55.000	11.76	0.00	37.10	4.30
559	594	2.972625	TCAGAATTTTCGGCGATGTCT	58.027	42.857	11.76	8.34	0.00	3.41
561	596	3.074412	ACTTCAGAATTTTCGGCGATGT	58.926	40.909	11.76	0.00	0.00	3.06
590	625	9.717942	ATAGTGGTATCTCAGCTCATATTTTTC	57.282	33.333	0.00	0.00	0.00	2.29
597	632	6.782000	AGAAGAATAGTGGTATCTCAGCTCAT	59.218	38.462	0.00	0.00	0.00	2.90
635	702	3.792401	TGGTAGTAGCGAATCAACATGG	58.208	45.455	0.00	0.00	0.00	3.66
669	736	4.326548	CGGTGTTCGGAAAACTTCTCTATC	59.673	45.833	10.70	0.00	34.75	2.08
784	1051	5.189180	GTGAGTTTCAAGGGCATTCTAGAT	58.811	41.667	0.00	0.00	0.00	1.98
871	1138	2.445682	TGGGATTAACGAATTGGGGG	57.554	50.000	0.00	0.00	0.00	5.40
872	1139	2.552315	CGATGGGATTAACGAATTGGGG	59.448	50.000	0.00	0.00	0.00	4.96
1456	1724	3.151022	GCGGAGGAGGAGGAGGTG	61.151	72.222	0.00	0.00	0.00	4.00
1457	1725	4.467107	GGCGGAGGAGGAGGAGGT	62.467	72.222	0.00	0.00	0.00	3.85
1993	2261	2.357396	CACTACTGCGCTGGCACA	60.357	61.111	18.98	0.07	46.21	4.57
2071	2339	1.597663	GGAGGAACCGAAATGCATACG	59.402	52.381	15.97	15.97	0.00	3.06
2088	2356	1.198713	ACACCATCCAGCAGTAGGAG	58.801	55.000	0.00	0.00	38.83	3.69
2146	2414	6.275494	TCATCACTTGCATTCATGTTCATT	57.725	33.333	0.00	0.00	0.00	2.57
2147	2415	5.907866	TCATCACTTGCATTCATGTTCAT	57.092	34.783	0.00	0.00	0.00	2.57
2305	2573	5.480073	TCTCAATTACCCATGGAACCAAAAG	59.520	40.000	15.22	3.31	0.00	2.27
2310	2578	4.536765	ACATCTCAATTACCCATGGAACC	58.463	43.478	15.22	0.00	0.00	3.62
2316	2584	2.439507	AGGCGACATCTCAATTACCCAT	59.560	45.455	0.00	0.00	0.00	4.00
2333	2601	4.690748	TCTCAATCTCACTTTGTAAAGGCG	59.309	41.667	9.00	0.59	40.31	5.52
2536	2804	0.811281	GACAACTGCTTGCCATACCC	59.189	55.000	0.00	0.00	0.00	3.69
2698	2966	0.879765	CTTCTTCTGGCTGGCACTTG	59.120	55.000	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.