AutoCloner

Multiple sequence alignment - TraesCS1D01G014500

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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	TraesCS1D01G014500	chr1D	100.000	2051	0	0	1	2051	7040607	7038557	0.000000e+00	3788.0
1	TraesCS1D01G014500	chr1D	90.836	1986	128	29	1	1965	7693108	7695060	0.000000e+00	2610.0
2	TraesCS1D01G014500	chr1D	100.000	563	0	0	2221	2783	7038387	7037825	0.000000e+00	1040.0
3	TraesCS1D01G014500	chr1D	84.553	984	129	15	991	1962	7707013	7707985	0.000000e+00	953.0
4	TraesCS1D01G014500	chr1D	87.069	116	6	4	11	125	7472981	7472874	3.760000e-24	122.0
5	TraesCS1D01G014500	chr1B	94.956	2042	85	11	11	2041	9716724	9714690	0.000000e+00	3184.0
6	TraesCS1D01G014500	chr1B	92.771	830	54	4	1149	1973	9673023	9672195	0.000000e+00	1195.0
7	TraesCS1D01G014500	chr1B	94.858	564	26	3	2223	2783	9714367	9713804	0.000000e+00	878.0
8	TraesCS1D01G014500	chr1B	87.156	763	88	8	995	1750	9845459	9846218	0.000000e+00	857.0
9	TraesCS1D01G014500	chr1B	84.757	597	74	9	176	759	9673618	9673026	1.440000e-162	582.0
10	TraesCS1D01G014500	chr1B	81.429	70	11	2	2708	2777	9712917	9712984	3.870000e-04	56.5
11	TraesCS1D01G014500	chr1A	91.895	1974	139	12	7	1965	9155357	9157324	0.000000e+00	2739.0
12	TraesCS1D01G014500	chr1A	93.310	1166	73	3	804	1965	9194294	9195458	0.000000e+00	1716.0
13	TraesCS1D01G014500	chr1A	85.802	162	20	3	8	166	9131231	9131392	4.770000e-38	169.0
14	TraesCS1D01G014500	chr1A	93.684	95	4	2	33	125	9105089	9104995	1.040000e-29	141.0
15	TraesCS1D01G014500	chrUn	91.473	1548	110	11	432	1965	276780873	276779334	0.000000e+00	2108.0
16	TraesCS1D01G014500	chrUn	93.352	1068	66	3	902	1965	278893720	278892654	0.000000e+00	1574.0
17	TraesCS1D01G014500	chrUn	90.559	286	20	4	517	796	76770494	76770778	3.390000e-99	372.0

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	TraesCS1D01G014500	chr1D	7037825	7040607	2782	True	2414.0	3788	100.000	1	2783	2	chr1D.!!$R2	2782
1	TraesCS1D01G014500	chr1D	7693108	7695060	1952	False	2610.0	2610	90.836	1	1965	1	chr1D.!!$F1	1964
2	TraesCS1D01G014500	chr1D	7707013	7707985	972	False	953.0	953	84.553	991	1962	1	chr1D.!!$F2	971
3	TraesCS1D01G014500	chr1B	9713804	9716724	2920	True	2031.0	3184	94.907	11	2783	2	chr1B.!!$R2	2772
4	TraesCS1D01G014500	chr1B	9672195	9673618	1423	True	888.5	1195	88.764	176	1973	2	chr1B.!!$R1	1797
5	TraesCS1D01G014500	chr1B	9845459	9846218	759	False	857.0	857	87.156	995	1750	1	chr1B.!!$F2	755
6	TraesCS1D01G014500	chr1A	9155357	9157324	1967	False	2739.0	2739	91.895	7	1965	1	chr1A.!!$F2	1958
7	TraesCS1D01G014500	chr1A	9194294	9195458	1164	False	1716.0	1716	93.310	804	1965	1	chr1A.!!$F3	1161
8	TraesCS1D01G014500	chrUn	276779334	276780873	1539	True	2108.0	2108	91.473	432	1965	1	chrUn.!!$R1	1533
9	TraesCS1D01G014500	chrUn	278892654	278893720	1066	True	1574.0	1574	93.352	902	1965	1	chrUn.!!$R2	1063

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
31	32	0.613777	CCCCTGTACCCTTGTGAGTC	59.386	60.0	0.0	0.0	0.00	3.36	F
328	335	0.905357	ATGCCTCTCATATACCCGGC	59.095	55.0	0.0	0.0	38.01	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1158	1189	1.055849	TGAGCACTGGCACCTTCTTA	58.944	50.000	0.0	0.0	44.61	2.1	R
1973	2018	2.105821	AGGTTTTCACCCTGATTGTCGA	59.894	45.455	0.0	0.0	45.63	4.2	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
31	32	0.613777	CCCCTGTACCCTTGTGAGTC	59.386	60.000	0.00	0.00	0.00	3.36
67	68	3.042887	GTGTCCTTGTCGAAAACATTGC	58.957	45.455	0.00	0.00	37.82	3.56
136	142	2.749441	GCTTGACTCCCCTGCTGC	60.749	66.667	0.00	0.00	0.00	5.25
244	251	8.320396	AGAATGCACATGATATCAGTAATCAC	57.680	34.615	11.78	0.19	36.24	3.06
248	255	5.180117	GCACATGATATCAGTAATCACCACC	59.820	44.000	11.78	0.00	36.24	4.61
324	331	9.973450	CATATGTAGTTATGCCTCTCATATACC	57.027	37.037	0.00	0.00	37.49	2.73
325	332	6.852420	TGTAGTTATGCCTCTCATATACCC	57.148	41.667	0.00	0.00	37.49	3.69
326	333	5.417894	TGTAGTTATGCCTCTCATATACCCG	59.582	44.000	0.00	0.00	37.49	5.28
327	334	3.769844	AGTTATGCCTCTCATATACCCGG	59.230	47.826	0.00	0.00	37.49	5.73
328	335	0.905357	ATGCCTCTCATATACCCGGC	59.095	55.000	0.00	0.00	38.01	6.13
348	365	1.695242	CCCATACATGGCATGGCAAAT	59.305	47.619	29.49	18.74	46.70	2.32
394	412	7.698130	GTGCATGTCCTAGATTCACAAAAATAC	59.302	37.037	0.00	0.00	0.00	1.89
577	600	7.373493	TCTTAAAGTTAGTTAACGAGGACTGG	58.627	38.462	0.00	0.00	40.96	4.00
580	603	1.927487	TAGTTAACGAGGACTGGCCA	58.073	50.000	4.71	4.71	40.02	5.36
647	677	6.648192	CCTTCTTCTCCAAGACAATGACTAT	58.352	40.000	0.00	0.00	38.44	2.12
724	755	4.697352	ACTAATGTTGCTAAGCACTGAAGG	59.303	41.667	0.00	0.00	38.71	3.46
817	848	5.690464	AGCAGGAAGTCTATTCAATGTCT	57.310	39.130	0.00	0.00	0.00	3.41
863	894	1.687123	AGTGTCCTTGACGTTAGCACT	59.313	47.619	0.00	0.00	34.95	4.40
1158	1189	2.112297	ACGTCAAACCCGGTGCAT	59.888	55.556	0.00	0.00	0.00	3.96
1342	1377	8.705048	CCAGAAGGTTTACTCTTATAGTGTTC	57.295	38.462	0.00	0.00	39.39	3.18
1786	1822	6.348050	GGCTTTGTCTATCAAGAAGTGAACTG	60.348	42.308	0.00	0.00	40.50	3.16
2005	2050	3.196901	GGGTGAAAACCTTTGTCCACTTT	59.803	43.478	0.00	0.00	0.00	2.66
2043	2088	0.946528	GGTGTTTACCGTTGTGTCCC	59.053	55.000	0.00	0.00	37.19	4.46
2044	2089	1.475571	GGTGTTTACCGTTGTGTCCCT	60.476	52.381	0.00	0.00	37.19	4.20
2045	2090	1.869132	GTGTTTACCGTTGTGTCCCTC	59.131	52.381	0.00	0.00	0.00	4.30
2046	2091	1.764134	TGTTTACCGTTGTGTCCCTCT	59.236	47.619	0.00	0.00	0.00	3.69
2047	2092	2.171027	TGTTTACCGTTGTGTCCCTCTT	59.829	45.455	0.00	0.00	0.00	2.85
2048	2093	2.536761	TTACCGTTGTGTCCCTCTTG	57.463	50.000	0.00	0.00	0.00	3.02
2049	2094	1.416243	TACCGTTGTGTCCCTCTTGT	58.584	50.000	0.00	0.00	0.00	3.16
2050	2095	0.179056	ACCGTTGTGTCCCTCTTGTG	60.179	55.000	0.00	0.00	0.00	3.33
2327	2513	3.335579	GGAGAAAGCGTGTTACAAGGAT	58.664	45.455	0.00	0.00	0.00	3.24
2336	2522	4.006989	CGTGTTACAAGGATGGAATTGGA	58.993	43.478	0.00	0.00	30.36	3.53
2360	2546	2.471815	TCCTCCGTGATTCCAGGTAT	57.528	50.000	0.00	0.00	0.00	2.73
2396	2582	7.806690	TGACTGAATTGGTCTCTAATTTTTCG	58.193	34.615	8.86	0.00	35.04	3.46
2402	2588	9.331106	GAATTGGTCTCTAATTTTTCGTTCTTC	57.669	33.333	0.00	0.00	0.00	2.87
2421	2607	7.549488	CGTTCTTCAGTGACCCTTATCTTAAAT	59.451	37.037	0.00	0.00	0.00	1.40
2477	2663	3.783082	CCTGGAAGATCCCTCCTTAGTTT	59.217	47.826	11.69	0.00	35.03	2.66
2478	2664	4.384647	CCTGGAAGATCCCTCCTTAGTTTG	60.385	50.000	11.69	0.00	35.03	2.93
2488	2674	9.114952	GATCCCTCCTTAGTTTGATTTTTCTAG	57.885	37.037	0.00	0.00	0.00	2.43
2574	2763	4.505324	AGAAATGGTTTAGGGGACTAGC	57.495	45.455	0.00	0.00	45.45	3.42
2590	2779	4.417506	GACTAGCGTTTTCTCTCTCCTTC	58.582	47.826	0.00	0.00	0.00	3.46
2603	2792	3.055094	TCTCTCCTTCCCACAATGTTAGC	60.055	47.826	0.00	0.00	0.00	3.09
2604	2793	2.912956	TCTCCTTCCCACAATGTTAGCT	59.087	45.455	0.00	0.00	0.00	3.32
2760	2949	1.967319	AGACGGTTTTGTGCTGATGT	58.033	45.000	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.155167	GGGTACAGGGGAGAGCCG	61.155	72.222	0.00	0.00	33.83	5.52
31	32	1.645034	GACACCATCACTCCATCACG	58.355	55.000	0.00	0.00	0.00	4.35
67	68	6.767423	TCCACAGTCCATACATTCATTATGTG	59.233	38.462	0.00	0.00	46.81	3.21
136	142	9.064706	AGTGCAGAGGATAAATAAATCAATCAG	57.935	33.333	0.00	0.00	0.00	2.90
206	212	8.920509	TCATGTGCATTCTCAAAATATTTGAG	57.079	30.769	21.22	21.22	45.38	3.02
244	251	0.606401	AACCGACAGATGCAAGGTGG	60.606	55.000	0.00	0.00	35.08	4.61
248	255	3.044986	CAAACAAACCGACAGATGCAAG	58.955	45.455	0.00	0.00	0.00	4.01
320	327	2.074967	CCATGTATGGGCCGGGTAT	58.925	57.895	2.18	0.00	44.31	2.73
321	328	3.569849	CCATGTATGGGCCGGGTA	58.430	61.111	2.18	0.00	44.31	3.69
348	365	5.819379	TGCACAAAGGCAAACATCAAATAAA	59.181	32.000	0.00	0.00	41.65	1.40
363	380	4.095483	GTGAATCTAGGACATGCACAAAGG	59.905	45.833	0.00	0.00	0.00	3.11
394	412	3.474600	CATCCTTCCCAGATACTTGCAG	58.525	50.000	0.00	0.00	0.00	4.41
577	600	1.751927	CTTGACATCCCCAGCTGGC	60.752	63.158	28.39	13.03	0.00	4.85
580	603	0.548682	AGTCCTTGACATCCCCAGCT	60.549	55.000	0.00	0.00	34.60	4.24
647	677	4.944048	TCATGTCAAGTTTCTCGAGACAA	58.056	39.130	16.36	10.07	41.86	3.18
817	848	7.701539	ATTTTGCACAATCACTTAGTATCCA	57.298	32.000	0.00	0.00	0.00	3.41
1158	1189	1.055849	TGAGCACTGGCACCTTCTTA	58.944	50.000	0.00	0.00	44.61	2.10
1269	1300	2.643232	GGCACGTTCGTAGGGGTCT	61.643	63.158	0.00	0.00	0.00	3.85
1342	1377	8.578308	ACATAAATGTGAAATCAACAACACAG	57.422	30.769	0.00	0.00	44.39	3.66
1786	1822	4.208632	CCATTCGGGTGACAGCTC	57.791	61.111	4.38	0.00	0.00	4.09
1973	2018	2.105821	AGGTTTTCACCCTGATTGTCGA	59.894	45.455	0.00	0.00	45.63	4.20
2005	2050	2.830827	CCACCGTGGTGTTTGCCA	60.831	61.111	17.31	0.00	44.02	4.92
2220	2265	7.148639	GCTAATCAAACATAAAGACACGACAGA	60.149	37.037	0.00	0.00	0.00	3.41
2221	2266	6.955963	GCTAATCAAACATAAAGACACGACAG	59.044	38.462	0.00	0.00	0.00	3.51
2315	2501	5.010282	AGTCCAATTCCATCCTTGTAACAC	58.990	41.667	0.00	0.00	0.00	3.32
2336	2522	1.827969	CTGGAATCACGGAGGAAGAGT	59.172	52.381	0.00	0.00	0.00	3.24
2360	2546	9.528018	GAGACCAATTCAGTCATTTTACAAAAA	57.472	29.630	7.66	0.00	36.68	1.94
2375	2561	8.391075	AGAACGAAAAATTAGAGACCAATTCA	57.609	30.769	0.00	0.00	0.00	2.57
2396	2582	8.669243	CATTTAAGATAAGGGTCACTGAAGAAC	58.331	37.037	0.00	0.00	0.00	3.01
2402	2588	9.838339	AGAATACATTTAAGATAAGGGTCACTG	57.162	33.333	0.00	0.00	0.00	3.66
2421	2607	7.145985	GTCCATTAGATAAGCACGAGAATACA	58.854	38.462	0.00	0.00	0.00	2.29
2457	2643	4.435137	TCAAACTAAGGAGGGATCTTCCA	58.565	43.478	15.96	0.14	38.64	3.53
2458	2644	5.638530	ATCAAACTAAGGAGGGATCTTCC	57.361	43.478	8.28	8.28	35.23	3.46
2574	2763	2.037251	TGTGGGAAGGAGAGAGAAAACG	59.963	50.000	0.00	0.00	0.00	3.60
2590	2779	7.759433	CCTTAAATAAACAGCTAACATTGTGGG	59.241	37.037	0.00	0.00	0.00	4.61
2628	2817	7.175104	ACTATTGCTAAGTTGAGGGATGAAAA	58.825	34.615	0.00	0.00	0.00	2.29
2677	2866	3.552875	GGGGACTAGCCTTATTTGGTTC	58.447	50.000	0.00	0.00	36.66	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.