AutoCloner

Multiple sequence alignment - TraesCS7B01G322900

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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	TraesCS7B01G322900	chr7B	100.000	3709	0	0	1	3709	573264406	573260698	0.000000e+00	6850.0
1	TraesCS7B01G322900	chr7B	88.148	135	11	5	2885	3018	573261390	573261260	4.960000e-34	156.0
2	TraesCS7B01G322900	chr7B	88.148	135	11	5	3017	3147	573261522	573261389	4.960000e-34	156.0
3	TraesCS7B01G322900	chr7D	91.711	3740	190	37	18	3709	532902509	532898842	0.000000e+00	5079.0
4	TraesCS7B01G322900	chr7D	95.262	2596	78	14	849	3438	533434687	533432131	0.000000e+00	4071.0
5	TraesCS7B01G322900	chr7D	94.035	285	8	6	3433	3709	533430855	533430572	1.230000e-114	424.0
6	TraesCS7B01G322900	chr7D	91.353	266	10	5	1	257	533434948	533434687	5.890000e-93	351.0
7	TraesCS7B01G322900	chr7D	88.235	136	11	4	2885	3019	532899505	532899374	1.380000e-34	158.0
8	TraesCS7B01G322900	chr7D	87.500	136	12	4	2885	3019	533432536	533432405	6.420000e-33	152.0
9	TraesCS7B01G322900	chr7D	85.821	134	15	3	3017	3147	532899636	532899504	4.990000e-29	139.0
10	TraesCS7B01G322900	chr7D	85.714	91	10	3	3060	3147	533432625	533432535	3.940000e-15	93.5
11	TraesCS7B01G322900	chr7D	80.172	116	10	9	686	795	532901668	532901560	1.430000e-09	75.0
12	TraesCS7B01G322900	chr7D	92.683	41	3	0	3013	3053	533432656	533432616	4.000000e-05	60.2
13	TraesCS7B01G322900	chr7A	87.618	3804	237	100	1	3709	612994217	612990553	0.000000e+00	4200.0
14	TraesCS7B01G322900	chr7A	86.517	89	9	2	3060	3147	612991326	612991240	1.100000e-15	95.3
15	TraesCS7B01G322900	chr7A	97.500	40	1	0	756	795	612993302	612993263	6.650000e-08	69.4
16	TraesCS7B01G322900	chr5B	86.659	847	95	14	1962	2798	479203707	479202869	0.000000e+00	922.0
17	TraesCS7B01G322900	chr5B	82.109	531	86	5	1022	1544	479204944	479204415	2.630000e-121	446.0
18	TraesCS7B01G322900	chr5D	82.358	1094	121	39	1961	3020	398908888	398907833	0.000000e+00	885.0
19	TraesCS7B01G322900	chr5D	82.707	532	82	7	1022	1544	398910111	398909581	7.260000e-127	464.0
20	TraesCS7B01G322900	chr5A	85.919	838	99	12	1962	2798	503952276	503953095	0.000000e+00	876.0
21	TraesCS7B01G322900	chr5A	83.051	531	83	5	1019	1544	503950724	503951252	3.350000e-130	475.0
22	TraesCS7B01G322900	chr6D	83.947	679	107	2	2013	2690	72229911	72229234	0.000000e+00	649.0
23	TraesCS7B01G322900	chr6B	83.847	681	108	2	2013	2692	146838513	146837834	0.000000e+00	647.0
24	TraesCS7B01G322900	chr6A	82.627	708	114	7	2007	2710	88855997	88855295	5.260000e-173	617.0

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	TraesCS7B01G322900	chr7B	573260698	573264406	3708	True	2387.333333	6850	92.098667	1	3709	3	chr7B.!!$R1	3708
1	TraesCS7B01G322900	chr7D	532898842	532902509	3667	True	1362.750000	5079	86.484750	18	3709	4	chr7D.!!$R1	3691
2	TraesCS7B01G322900	chr7D	533430572	533434948	4376	True	858.616667	4071	91.091167	1	3709	6	chr7D.!!$R2	3708
3	TraesCS7B01G322900	chr7A	612990553	612994217	3664	True	1454.900000	4200	90.545000	1	3709	3	chr7A.!!$R1	3708
4	TraesCS7B01G322900	chr5B	479202869	479204944	2075	True	684.000000	922	84.384000	1022	2798	2	chr5B.!!$R1	1776
5	TraesCS7B01G322900	chr5D	398907833	398910111	2278	True	674.500000	885	82.532500	1022	3020	2	chr5D.!!$R1	1998
6	TraesCS7B01G322900	chr5A	503950724	503953095	2371	False	675.500000	876	84.485000	1019	2798	2	chr5A.!!$F1	1779
7	TraesCS7B01G322900	chr6D	72229234	72229911	677	True	649.000000	649	83.947000	2013	2690	1	chr6D.!!$R1	677
8	TraesCS7B01G322900	chr6B	146837834	146838513	679	True	647.000000	647	83.847000	2013	2692	1	chr6B.!!$R1	679
9	TraesCS7B01G322900	chr6A	88855295	88855997	702	True	617.000000	617	82.627000	2007	2710	1	chr6A.!!$R1	703

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
123	132	0.036577	CCATCCATCGCCATCTCCTC	60.037	60.0	0.00	3.71	F
124	133	0.389556	CATCCATCGCCATCTCCTCG	60.390	60.0	0.00	4.63	F
477	585	0.389817	GAATTGGGTTTGCTTCCGGC	60.390	55.0	42.22	6.13	F
1467	1601	1.075542	TATGCGTCGGCTCTGTTTTG	58.924	50.0	40.82	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1191	1318	2.859165	TCTTCTTGATGGCGACCTTT	57.141	45.000	0.00	3.11	R
1467	1601	3.791353	GCGTTATGCAAAGGTAAGAATGC	59.209	43.478	45.45	3.56	R
2171	3025	0.734942	AGCGGGTGACAACGTATTCG	60.735	55.000	43.34	3.34	R
3273	4164	2.409570	GGGGAGGGCAGAGTTTATACT	58.590	52.381	37.31	2.12	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
109	118	4.864334	CCTGAGCGGCACCCATCC	62.864	72.222	1.45	0.00	0.00	3.51
110	119	4.100084	CTGAGCGGCACCCATCCA	62.100	66.667	1.45	0.00	0.00	3.41
111	120	3.410628	TGAGCGGCACCCATCCAT	61.411	61.111	1.45	0.00	0.00	3.41
112	121	2.592861	GAGCGGCACCCATCCATC	60.593	66.667	1.45	0.00	0.00	3.51
113	122	4.552365	AGCGGCACCCATCCATCG	62.552	66.667	1.45	0.00	0.00	3.84
116	125	4.504596	GGCACCCATCCATCGCCA	62.505	66.667	0.00	0.00	42.50	5.69
117	126	2.203394	GCACCCATCCATCGCCAT	60.203	61.111	0.00	0.00	0.00	4.40
121	130	1.002868	CCCATCCATCGCCATCTCC	60.003	63.158	0.00	0.00	0.00	3.71
122	131	1.486997	CCCATCCATCGCCATCTCCT	61.487	60.000	0.00	0.00	0.00	3.69
123	132	0.036577	CCATCCATCGCCATCTCCTC	60.037	60.000	0.00	0.00	0.00	3.71
124	133	0.389556	CATCCATCGCCATCTCCTCG	60.390	60.000	0.00	0.00	0.00	4.63
136	156	1.606601	CTCCTCGTCACCACTCCCA	60.607	63.158	0.00	0.00	0.00	4.37
418	526	3.073946	TCCTCCATTTTCGTTCCCTTTCT	59.926	43.478	0.00	0.00	0.00	2.52
477	585	0.389817	GAATTGGGTTTGCTTCCGGC	60.390	55.000	0.00	0.00	42.22	6.13
745	858	4.003648	GGAAACACATGCTGCTAGTAGTT	58.996	43.478	9.73	4.59	0.00	2.24
802	916	2.689553	AATTAAATTGGCCAAGGCGG	57.310	45.000	24.94	0.00	43.06	6.13
824	938	2.429571	GCGTCGCTCACCGTGTTA	60.430	61.111	10.68	0.00	38.35	2.41
825	939	2.434134	GCGTCGCTCACCGTGTTAG	61.434	63.158	10.68	0.00	38.35	2.34
826	940	2.434134	CGTCGCTCACCGTGTTAGC	61.434	63.158	0.00	0.27	38.35	3.09
858	972	4.393062	CACTTGTGTTAGGGTGATGATGAC	59.607	45.833	0.00	0.00	32.12	3.06
970	1096	6.731292	AACTTTTTCCTTGTTATGCTTCCT	57.269	33.333	0.00	0.00	0.00	3.36
990	1116	8.951243	GCTTCCTTTGTTCTCAATTAATAGACT	58.049	33.333	0.00	0.00	33.32	3.24
992	1118	8.792830	TCCTTTGTTCTCAATTAATAGACTGG	57.207	34.615	0.00	0.00	33.32	4.00
1191	1318	1.124780	TCAACCAGGAGACCAACGAA	58.875	50.000	0.00	0.00	0.00	3.85
1467	1601	1.075542	TATGCGTCGGCTCTGTTTTG	58.924	50.000	0.00	0.00	40.82	2.44
1585	1997	7.148983	CCAGTATAATGTTGTTTTTGCAGTTCG	60.149	37.037	0.00	0.00	0.00	3.95
1605	2017	9.607285	CAGTTCGTACTAATTTGCATTAAGTTT	57.393	29.630	0.00	0.00	31.96	2.66
1933	2778	7.023575	CAGATTAGTCTTGTTTGTTACCATGC	58.976	38.462	0.00	0.00	30.42	4.06
2002	2855	7.016170	TCGATCAATCAATAATCTAAGACCCCA	59.984	37.037	0.00	0.00	0.00	4.96
2003	2856	7.118390	CGATCAATCAATAATCTAAGACCCCAC	59.882	40.741	0.00	0.00	0.00	4.61
2004	2857	7.451731	TCAATCAATAATCTAAGACCCCACT	57.548	36.000	0.00	0.00	0.00	4.00
2363	3217	0.250684	TTCTTGGCACCATGAGCGAA	60.251	50.000	0.00	0.65	32.87	4.70
2364	3218	0.250684	TCTTGGCACCATGAGCGAAA	60.251	50.000	0.00	0.00	0.00	3.46
2462	3316	1.068417	TATCATGTACCCGCACGCC	59.932	57.895	0.00	0.00	0.00	5.68
2867	3755	4.038042	CGTATGGATTTCTCTAGCTGTGGA	59.962	45.833	0.00	0.00	0.00	4.02
2878	3766	2.393271	AGCTGTGGATCAGTACTTGC	57.607	50.000	0.00	0.70	45.23	4.01
2967	3857	7.659652	AGCTTGTGTAAGTTGTAATCTTCTC	57.340	36.000	0.00	0.00	36.27	2.87
3095	3985	8.896320	TGAAGAAGCTTGTGTAAGTTGTAATA	57.104	30.769	2.10	0.00	36.27	0.98
3099	3989	8.947115	AGAAGCTTGTGTAAGTTGTAATATTCC	58.053	33.333	2.10	0.00	36.27	3.01
3103	3993	8.520351	GCTTGTGTAAGTTGTAATATTCCCTTT	58.480	33.333	0.00	0.00	36.27	3.11
3147	4037	9.884636	TGTAATTTTAGAAGCTGCTCTATGTAA	57.115	29.630	0.00	0.00	0.00	2.41
3247	4138	4.400884	TGCAGTTTGTATGGTGTTTTCTGT	59.599	37.500	0.00	0.00	0.00	3.41
3248	4139	5.105554	TGCAGTTTGTATGGTGTTTTCTGTT	60.106	36.000	0.00	0.00	0.00	3.16
3249	4140	5.810074	GCAGTTTGTATGGTGTTTTCTGTTT	59.190	36.000	0.00	0.00	0.00	2.83
3250	4141	6.312672	GCAGTTTGTATGGTGTTTTCTGTTTT	59.687	34.615	0.00	0.00	0.00	2.43
3286	4177	8.912658	GTTTGGCTTAAAAAGTATAAACTCTGC	58.087	33.333	0.00	0.00	33.75	4.26
3287	4178	7.153217	TGGCTTAAAAAGTATAAACTCTGCC	57.847	36.000	0.00	0.00	33.75	4.85
3288	4179	6.152154	TGGCTTAAAAAGTATAAACTCTGCCC	59.848	38.462	0.00	0.00	33.75	5.36
3289	4180	6.377429	GGCTTAAAAAGTATAAACTCTGCCCT	59.623	38.462	0.00	0.00	33.75	5.19
3294	4185	1.420514	GTATAAACTCTGCCCTCCCCC	59.579	57.143	0.00	0.00	0.00	5.40
3328	4219	1.640670	ACTCCCCAACCTGCAATGTAT	59.359	47.619	0.00	0.00	0.00	2.29
3460	5655	5.641636	GTGGTTGGATTGTTTTCACTTTGTT	59.358	36.000	0.00	0.00	0.00	2.83
3464	5659	8.722394	GGTTGGATTGTTTTCACTTTGTTTTTA	58.278	29.630	0.00	0.00	0.00	1.52
3513	5713	5.179045	AGAACTTGCATTCTGTTGACTTG	57.821	39.130	1.73	0.00	37.54	3.16
3523	5723	4.818534	TCTGTTGACTTGAAATCACAGC	57.181	40.909	0.00	0.00	31.17	4.40
3542	5745	5.689514	CACAGCACTAGTACTTCAGATATGC	59.310	44.000	0.00	0.00	0.00	3.14
3693	5896	0.608856	CACATTGTACCCCTGCAGCA	60.609	55.000	8.66	0.00	0.00	4.41
3705	5908	1.153066	TGCAGCACCAAAACGAGGA	60.153	52.632	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	118	0.596083	GTGACGAGGAGATGGCGATG	60.596	60.000	0.00	0.00	0.00	3.84
110	119	1.736586	GTGACGAGGAGATGGCGAT	59.263	57.895	0.00	0.00	0.00	4.58
111	120	2.415608	GGTGACGAGGAGATGGCGA	61.416	63.158	0.00	0.00	0.00	5.54
112	121	2.105128	GGTGACGAGGAGATGGCG	59.895	66.667	0.00	0.00	0.00	5.69
113	122	1.153549	GTGGTGACGAGGAGATGGC	60.154	63.158	0.00	0.00	0.00	4.40
115	124	0.457851	GGAGTGGTGACGAGGAGATG	59.542	60.000	0.00	0.00	0.00	2.90
116	125	0.684805	GGGAGTGGTGACGAGGAGAT	60.685	60.000	0.00	0.00	0.00	2.75
117	126	1.304217	GGGAGTGGTGACGAGGAGA	60.304	63.158	0.00	0.00	0.00	3.71
121	130	0.319900	CTTGTGGGAGTGGTGACGAG	60.320	60.000	0.00	0.00	0.00	4.18
122	131	1.046472	ACTTGTGGGAGTGGTGACGA	61.046	55.000	0.00	0.00	0.00	4.20
123	132	0.600255	GACTTGTGGGAGTGGTGACG	60.600	60.000	0.00	0.00	0.00	4.35
124	133	0.250338	GGACTTGTGGGAGTGGTGAC	60.250	60.000	0.00	0.00	0.00	3.67
136	156	0.603569	CGTAGCTCCACTGGACTTGT	59.396	55.000	0.00	0.00	0.00	3.16
386	474	4.888325	ATGGAGGAGGAGGGGGCG	62.888	72.222	0.00	0.00	0.00	6.13
418	526	0.311790	CTTGCTTTGCTTCGCCTCAA	59.688	50.000	0.00	0.00	0.00	3.02
489	597	1.068741	CCCCTAACACGAGCATCCTAC	59.931	57.143	0.00	0.00	0.00	3.18
683	793	1.873591	CAACCTAACACCAGTGTCTGC	59.126	52.381	3.49	0.00	44.13	4.26
820	934	4.141801	ACACAAGTGTCTAACAGGCTAACA	60.142	41.667	0.00	0.00	40.24	2.41
824	938	3.560636	AACACAAGTGTCTAACAGGCT	57.439	42.857	6.28	0.00	44.13	4.58
825	939	3.746492	CCTAACACAAGTGTCTAACAGGC	59.254	47.826	6.28	0.00	44.13	4.85
826	940	4.202326	ACCCTAACACAAGTGTCTAACAGG	60.202	45.833	6.28	8.18	44.13	4.00
858	972	0.744281	GTTTCCACCCCACACACAAG	59.256	55.000	0.00	0.00	0.00	3.16
990	1116	7.310485	GGAGAAGAAGGAAACATAGAGTTACCA	60.310	40.741	0.00	0.00	40.26	3.25
992	1118	6.752815	CGGAGAAGAAGGAAACATAGAGTTAC	59.247	42.308	0.00	0.00	40.26	2.50
1191	1318	2.859165	TCTTCTTGATGGCGACCTTT	57.141	45.000	0.00	0.00	0.00	3.11
1467	1601	3.791353	GCGTTATGCAAAGGTAAGAATGC	59.209	43.478	0.00	0.00	45.45	3.56
1605	2017	7.618019	ACCCAACAGCTTTAGATAGATCATA	57.382	36.000	0.00	0.00	0.00	2.15
1933	2778	4.330250	TCAGCAGAAAAAGGAGAAGATGG	58.670	43.478	0.00	0.00	0.00	3.51
2002	2855	4.938226	GCAGCTACAGTCAAGGAAAATAGT	59.062	41.667	0.00	0.00	0.00	2.12
2003	2856	5.181748	AGCAGCTACAGTCAAGGAAAATAG	58.818	41.667	0.00	0.00	0.00	1.73
2004	2857	5.165961	AGCAGCTACAGTCAAGGAAAATA	57.834	39.130	0.00	0.00	0.00	1.40
2171	3025	0.734942	AGCGGGTGACAACGTATTCG	60.735	55.000	0.00	0.00	43.34	3.34
2213	3067	1.284657	CATAGTTGTCGCAGCAGAGG	58.715	55.000	0.00	0.00	0.00	3.69
2462	3316	2.885266	CAGATCAATGGCAAGAGGATGG	59.115	50.000	0.00	0.00	0.00	3.51
2908	3798	5.523916	CAGATTCTTGATAACCGAATTCCGT	59.476	40.000	0.00	0.00	36.31	4.69
2976	3866	7.703058	AAGATTACAAACTTACAATCAGGGG	57.297	36.000	0.00	0.00	31.25	4.79
3095	3985	4.078932	ACAATCATGGGGAAAAGGGAAT	57.921	40.909	0.00	0.00	0.00	3.01
3099	3989	5.245977	ACAACTTACAATCATGGGGAAAAGG	59.754	40.000	0.00	0.00	0.00	3.11
3103	3993	8.429237	AAATTACAACTTACAATCATGGGGAA	57.571	30.769	0.00	0.00	0.00	3.97
3147	4037	5.454897	GGTCACTTGAAAGTTTAGACCTCCT	60.455	44.000	17.62	0.00	42.17	3.69
3273	4164	2.409570	GGGGAGGGCAGAGTTTATACT	58.590	52.381	0.00	0.00	37.31	2.12
3310	4201	2.917713	AATACATTGCAGGTTGGGGA	57.082	45.000	0.00	0.00	0.00	4.81
3464	5659	8.764287	GCTTTTGTTTGCTTATTTGTTCAGTAT	58.236	29.630	0.00	0.00	0.00	2.12
3503	5703	4.036027	AGTGCTGTGATTTCAAGTCAACAG	59.964	41.667	7.62	7.62	32.67	3.16
3513	5713	6.390721	TCTGAAGTACTAGTGCTGTGATTTC	58.609	40.000	14.67	7.60	0.00	2.17
3523	5723	6.546972	TCTCGCATATCTGAAGTACTAGTG	57.453	41.667	5.39	0.00	0.00	2.74
3542	5745	8.600625	TGGATTTTCGTCAGTTAATATTTCTCG	58.399	33.333	0.00	0.00	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.