AutoCloner

Multiple sequence alignment - TraesCS2D01G265600

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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	TraesCS2D01G265600	chr2D	100.000	2695	0	0	1	2695	324284378	324281684	0.000000e+00	4977
1	TraesCS2D01G265600	chr2A	90.307	1826	132	16	890	2695	394394996	394396796	0.000000e+00	2350
2	TraesCS2D01G265600	chr2A	92.422	607	28	6	3	606	394393799	394394390	0.000000e+00	850
3	TraesCS2D01G265600	chr2A	83.283	658	90	14	1942	2592	735925710	735926354	2.990000e-164	588
4	TraesCS2D01G265600	chr2A	83.013	624	93	10	1957	2575	70042221	70042836	1.090000e-153	553
5	TraesCS2D01G265600	chr2A	81.667	660	101	12	1943	2592	36005436	36004787	5.110000e-147	531
6	TraesCS2D01G265600	chr2A	95.130	308	8	3	615	916	394394671	394394977	1.880000e-131	479
7	TraesCS2D01G265600	chr2B	92.673	1283	34	14	735	1985	393024042	393022788	0.000000e+00	1794
8	TraesCS2D01G265600	chr2B	89.320	721	67	4	1977	2695	393022734	393022022	0.000000e+00	896
9	TraesCS2D01G265600	chr2B	95.238	147	5	1	376	522	393024625	393024481	5.800000e-57	231
10	TraesCS2D01G265600	chr2B	94.355	124	5	2	615	737	393024438	393024316	3.540000e-44	189
11	TraesCS2D01G265600	chr3D	85.780	654	78	9	1943	2592	300618713	300618071	0.000000e+00	678
12	TraesCS2D01G265600	chrUn	83.562	657	93	12	1942	2592	229275566	229276213	3.840000e-168	601
13	TraesCS2D01G265600	chr3B	83.548	620	84	13	1957	2571	719434123	719433517	5.040000e-157	564
14	TraesCS2D01G265600	chr7A	83.524	613	85	8	1981	2586	294322302	294321699	2.340000e-155	558
15	TraesCS2D01G265600	chr4A	81.975	638	98	9	1957	2586	729107846	729107218	2.380000e-145	525

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	TraesCS2D01G265600	chr2D	324281684	324284378	2694	True	4977.000000	4977	100.000000	1	2695	1	chr2D.!!$R1	2694
1	TraesCS2D01G265600	chr2A	394393799	394396796	2997	False	1226.333333	2350	92.619667	3	2695	3	chr2A.!!$F3	2692
2	TraesCS2D01G265600	chr2A	735925710	735926354	644	False	588.000000	588	83.283000	1942	2592	1	chr2A.!!$F2	650
3	TraesCS2D01G265600	chr2A	70042221	70042836	615	False	553.000000	553	83.013000	1957	2575	1	chr2A.!!$F1	618
4	TraesCS2D01G265600	chr2A	36004787	36005436	649	True	531.000000	531	81.667000	1943	2592	1	chr2A.!!$R1	649
5	TraesCS2D01G265600	chr2B	393022022	393024625	2603	True	777.500000	1794	92.896500	376	2695	4	chr2B.!!$R1	2319
6	TraesCS2D01G265600	chr3D	300618071	300618713	642	True	678.000000	678	85.780000	1943	2592	1	chr3D.!!$R1	649
7	TraesCS2D01G265600	chrUn	229275566	229276213	647	False	601.000000	601	83.562000	1942	2592	1	chrUn.!!$F1	650
8	TraesCS2D01G265600	chr3B	719433517	719434123	606	True	564.000000	564	83.548000	1957	2571	1	chr3B.!!$R1	614
9	TraesCS2D01G265600	chr7A	294321699	294322302	603	True	558.000000	558	83.524000	1981	2586	1	chr7A.!!$R1	605
10	TraesCS2D01G265600	chr4A	729107218	729107846	628	True	525.000000	525	81.975000	1957	2586	1	chr4A.!!$R1	629

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
581	584	0.251916	TGGCTACATGTTTCCCGGAG	59.748	55.0	2.3	0.0	0.0	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1794	2418	0.500178	CGCATGAGATTAGTGTCGCG	59.5	55.0	0.0	0.0	35.14	5.87	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
17	18	4.452733	GGGGGCGTCGAGAAGGTG	62.453	72.222	0.00	0.00	0.00	4.00
66	67	1.529010	CCACTTGGAGCTGCAACCA	60.529	57.895	17.55	13.05	37.39	3.67
109	110	0.457853	GCGACAGGATGCTACGACAA	60.458	55.000	14.81	0.00	42.53	3.18
111	112	1.402325	CGACAGGATGCTACGACAACA	60.402	52.381	7.07	0.00	42.53	3.33
213	215	2.369291	ATGGGGATGGAGGCTGCT	60.369	61.111	7.74	0.00	0.00	4.24
270	272	4.899239	GGCGAGGTCGGATGGCTG	62.899	72.222	0.89	0.00	40.23	4.85
324	327	0.731417	ATCGAGTCCTTACGTGGTCG	59.269	55.000	0.00	0.00	43.34	4.79
494	497	7.739498	TTTGTTCCTTCCATTTGTCTAGTAC	57.261	36.000	0.00	0.00	0.00	2.73
495	498	6.681729	TGTTCCTTCCATTTGTCTAGTACT	57.318	37.500	0.00	0.00	0.00	2.73
534	537	2.041081	ACTCCATGGGTTTTGATTCGGA	59.959	45.455	13.02	0.00	0.00	4.55
581	584	0.251916	TGGCTACATGTTTCCCGGAG	59.748	55.000	2.30	0.00	0.00	4.63
597	601	3.117046	CCGGAGAAAAGTTATCGCTCTC	58.883	50.000	0.00	0.00	33.28	3.20
627	904	3.312459	ACTTATCTTTCCCTCCCATCCCT	60.312	47.826	0.00	0.00	0.00	4.20
667	949	1.505353	CCCCTCGTACGTGTGTCTC	59.495	63.158	16.05	0.00	0.00	3.36
727	1009	2.031616	CGCATCATCCATCCGGCT	59.968	61.111	0.00	0.00	0.00	5.52
731	1013	2.440409	GCATCATCCATCCGGCTTTAT	58.560	47.619	0.00	0.00	0.00	1.40
934	1542	1.731433	TAGCTAGCCACCTTACGCGG	61.731	60.000	12.13	0.00	0.00	6.46
994	1602	2.796031	CCACACACACATACGTACGTTT	59.204	45.455	27.92	16.53	0.00	3.60
1452	2064	6.204688	TGCACTCACAAGTTAGGTTAATTCAG	59.795	38.462	0.00	0.00	31.71	3.02
1634	2247	0.250513	GGGTTGAGTACTGCAGGAGG	59.749	60.000	19.93	0.00	0.00	4.30
1698	2311	1.729586	AGAGGTGTTGGCTTAGTCCA	58.270	50.000	0.00	0.00	0.00	4.02
1747	2360	2.301346	CCAAAGACCAAACTGCTCACT	58.699	47.619	0.00	0.00	0.00	3.41
1794	2418	6.809196	TGTTTAATTGTTTATCCGCATGTTCC	59.191	34.615	0.00	0.00	0.00	3.62
1830	2454	2.740438	GTGCGTTGGGCCCAAAAT	59.260	55.556	38.70	0.00	42.61	1.82
1914	2538	5.534654	CCAGTTTGACAAATTTCTACTCCCA	59.465	40.000	3.49	0.00	0.00	4.37
1919	2543	4.070009	GACAAATTTCTACTCCCACCGTT	58.930	43.478	0.00	0.00	0.00	4.44
1920	2544	3.818773	ACAAATTTCTACTCCCACCGTTG	59.181	43.478	0.00	0.00	0.00	4.10
1921	2545	2.781681	ATTTCTACTCCCACCGTTGG	57.218	50.000	0.00	0.00	43.50	3.77
1970	2611	8.671384	TTTTCTCCAAGAAACTTTCGATCTAA	57.329	30.769	1.73	0.00	43.25	2.10
1989	2698	7.650504	CGATCTAATTATCAACGGTCAAGGTAA	59.349	37.037	0.00	0.00	0.00	2.85
2127	2837	3.365565	CCGGGCAAACATTGTTGTAGTAC	60.366	47.826	2.13	0.00	34.06	2.73
2156	2867	0.396811	AAGTTGTCGTGCTAAGGCCT	59.603	50.000	0.00	0.00	37.74	5.19
2170	2881	2.307153	GGCCTCATAGGACCAACCA	58.693	57.895	0.00	0.00	37.46	3.67
2171	2882	0.623723	GGCCTCATAGGACCAACCAA	59.376	55.000	0.00	0.00	37.46	3.67
2215	2929	2.352225	CGCCGATGAAGAGAAGGATAGG	60.352	54.545	0.00	0.00	0.00	2.57
2232	2946	1.290134	AGGTCAGAAGGATCCAACCC	58.710	55.000	15.82	4.73	33.25	4.11
2345	3060	0.836400	ACCTCCACACACCTTCCGAT	60.836	55.000	0.00	0.00	0.00	4.18
2368	3083	2.884012	ACGCTTGAAACATCACCATGAA	59.116	40.909	0.00	0.00	33.72	2.57
2415	3130	1.450312	ATCTTCAAGAAGCCGCCGG	60.450	57.895	0.00	0.00	38.28	6.13
2438	3156	0.534412	CTCGTCTTCCTGAGCATGGT	59.466	55.000	0.00	0.00	0.00	3.55
2477	3197	7.402811	AATTTAGAAAAGCACCTAAAAACGC	57.597	32.000	0.00	0.00	38.07	4.84
2598	3332	1.076632	CCTAGACGAGAGGCAGGGT	60.077	63.158	0.00	0.00	46.78	4.34
2647	3381	4.833478	ACCTGACAACATCTCTTGCTAT	57.167	40.909	0.00	0.00	0.00	2.97

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.452733	CACCTTCTCGACGCCCCC	62.453	72.222	0.00	0.00	0.00	5.40
46	47	1.656441	GTTGCAGCTCCAAGTGGTG	59.344	57.895	0.00	0.00	36.34	4.17
47	48	1.529244	GGTTGCAGCTCCAAGTGGT	60.529	57.895	0.00	0.00	36.34	4.16
48	49	1.521450	CTGGTTGCAGCTCCAAGTGG	61.521	60.000	0.00	0.00	33.06	4.00
49	50	1.954528	CTGGTTGCAGCTCCAAGTG	59.045	57.895	0.00	0.00	33.06	3.16
50	51	1.900498	GCTGGTTGCAGCTCCAAGT	60.900	57.895	0.00	0.00	44.31	3.16
51	52	2.633509	GGCTGGTTGCAGCTCCAAG	61.634	63.158	0.00	6.75	46.69	3.61
52	53	2.598394	GGCTGGTTGCAGCTCCAA	60.598	61.111	0.00	0.00	46.69	3.53
53	54	3.888460	TGGCTGGTTGCAGCTCCA	61.888	61.111	0.00	9.05	46.69	3.86
83	84	3.822192	CATCCTGTCGCGGGTCGA	61.822	66.667	6.13	0.00	46.29	4.20
88	89	2.655364	CGTAGCATCCTGTCGCGG	60.655	66.667	6.13	0.00	0.00	6.46
109	110	1.269448	GATTGCAACACCCGACATTGT	59.731	47.619	0.00	0.00	0.00	2.71
111	112	1.541147	CTGATTGCAACACCCGACATT	59.459	47.619	0.00	0.00	0.00	2.71
122	123	1.076841	TCCCCAACATCCTGATTGCAA	59.923	47.619	0.00	0.00	0.00	4.08
213	215	0.934496	GTACAACACTGTGCTTCGCA	59.066	50.000	7.90	0.00	36.96	5.10
259	261	2.409870	CCAAAGGCAGCCATCCGAC	61.410	63.158	15.80	0.00	0.00	4.79
324	327	4.440214	CAATGCTTTGCGTCGGTC	57.560	55.556	0.00	0.00	0.00	4.79
344	347	6.937392	AGCTAGGAGTACCAACTAAAGAAAG	58.063	40.000	0.00	0.00	35.56	2.62
348	351	7.878644	AGAAAAAGCTAGGAGTACCAACTAAAG	59.121	37.037	0.00	0.00	35.56	1.85
494	497	3.697045	GAGTCATGGAGATATACGGGGAG	59.303	52.174	0.00	0.00	0.00	4.30
495	498	3.563697	GGAGTCATGGAGATATACGGGGA	60.564	52.174	0.00	0.00	0.00	4.81
534	537	2.108952	AGAAAGCCTGTTGGAGTTGGAT	59.891	45.455	0.00	0.00	34.57	3.41
581	584	5.538067	AAGCAAGAGAGCGATAACTTTTC	57.462	39.130	0.00	0.00	40.15	2.29
597	601	5.590663	GGGAGGGAAAGATAAGTTAAGCAAG	59.409	44.000	0.00	0.00	0.00	4.01
667	949	1.278172	CGTGCACTCAACTGGACTCG	61.278	60.000	16.19	0.00	30.62	4.18
727	1009	5.583061	ACAGTGAAGTGTCGTTGACAATAAA	59.417	36.000	0.49	0.00	44.49	1.40
731	1013	2.967362	ACAGTGAAGTGTCGTTGACAA	58.033	42.857	0.49	0.00	44.49	3.18
791	1349	4.466370	TGTTATATAATGGCGGAGAGAGGG	59.534	45.833	0.00	0.00	0.00	4.30
934	1542	0.179070	GTTAGCCAGCCAGGTAGCTC	60.179	60.000	0.00	0.00	42.61	4.09
994	1602	5.131642	AGCTGATAGATTCCTCCATTTGACA	59.868	40.000	0.00	0.00	0.00	3.58
1029	1637	3.435186	GAAGCTGAAGCACCCGGC	61.435	66.667	4.90	0.00	45.16	6.13
1452	2064	1.478510	ACACCCTGATCAGTGATCGAC	59.521	52.381	24.52	6.05	41.51	4.20
1634	2247	0.665298	GAGAAGAATCCCATTGGCGC	59.335	55.000	0.00	0.00	0.00	6.53
1698	2311	3.888930	CTGGTCCACCAACAGTTTAACAT	59.111	43.478	0.00	0.00	46.97	2.71
1747	2360	8.958119	AACAAGAAGAACTACACAATTCAGTA	57.042	30.769	0.00	0.00	0.00	2.74
1794	2418	0.500178	CGCATGAGATTAGTGTCGCG	59.500	55.000	0.00	0.00	35.14	5.87
1830	2454	2.291209	ATTGCACATGACAACAGGGA	57.709	45.000	0.00	0.00	31.68	4.20
1914	2538	0.608582	ACGCTACTCTCTCCAACGGT	60.609	55.000	0.00	0.00	0.00	4.83
1919	2543	1.751351	CCATCAACGCTACTCTCTCCA	59.249	52.381	0.00	0.00	0.00	3.86
1920	2544	2.025155	TCCATCAACGCTACTCTCTCC	58.975	52.381	0.00	0.00	0.00	3.71
1921	2545	3.784701	TTCCATCAACGCTACTCTCTC	57.215	47.619	0.00	0.00	0.00	3.20
2127	2837	1.781429	CACGACAACTTCTCGACTGTG	59.219	52.381	0.00	0.00	35.08	3.66
2156	2867	3.886505	GTGTGTTTTGGTTGGTCCTATGA	59.113	43.478	0.00	0.00	37.07	2.15
2166	2877	2.094234	GCTGTTCTGGTGTGTTTTGGTT	60.094	45.455	0.00	0.00	0.00	3.67
2167	2878	1.476488	GCTGTTCTGGTGTGTTTTGGT	59.524	47.619	0.00	0.00	0.00	3.67
2168	2879	1.476085	TGCTGTTCTGGTGTGTTTTGG	59.524	47.619	0.00	0.00	0.00	3.28
2169	2880	2.923020	GTTGCTGTTCTGGTGTGTTTTG	59.077	45.455	0.00	0.00	0.00	2.44
2170	2881	2.825532	AGTTGCTGTTCTGGTGTGTTTT	59.174	40.909	0.00	0.00	0.00	2.43
2171	2882	2.164219	CAGTTGCTGTTCTGGTGTGTTT	59.836	45.455	0.00	0.00	0.00	2.83
2215	2929	0.744771	GCGGGTTGGATCCTTCTGAC	60.745	60.000	14.23	4.01	0.00	3.51
2232	2946	2.254459	GTCTACATCAGTGTGTCTGCG	58.746	52.381	2.24	0.00	43.32	5.18
2345	3060	1.960417	TGGTGATGTTTCAAGCGTCA	58.040	45.000	0.00	0.00	32.48	4.35
2368	3083	1.160289	TTCTCCCCACCTAGTCCCCT	61.160	60.000	0.00	0.00	0.00	4.79
2415	3130	2.202676	CTCAGGAAGACGAGCCGC	60.203	66.667	0.00	0.00	0.00	6.53
2477	3197	3.267597	CTTGCCGGCGAAAGGGTTG	62.268	63.158	23.90	1.62	0.00	3.77
2534	3262	3.989838	ATCGGTCCGCCTCGTCTCA	62.990	63.158	6.34	0.00	0.00	3.27
2560	3294	1.306141	ATTCCCTGCCTCTCACCGA	60.306	57.895	0.00	0.00	0.00	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.