AutoCloner

Multiple sequence alignment - TraesCS2B01G539800

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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	TraesCS2B01G539800	chr2B	100.000	5696	0	0	1	5696	734915499	734921194	0.000000e+00	10519.0
1	TraesCS2B01G539800	chr2B	96.393	3327	92	7	867	4168	734943707	734947030	0.000000e+00	5454.0
2	TraesCS2B01G539800	chr2B	96.947	1179	33	3	4166	5343	734951008	734952184	0.000000e+00	1975.0
3	TraesCS2B01G539800	chr2B	93.445	778	33	13	1	777	734940321	734941081	0.000000e+00	1138.0
4	TraesCS2B01G539800	chr2B	74.139	1771	380	56	3002	4740	759440639	759442363	0.000000e+00	662.0
5	TraesCS2B01G539800	chr2B	95.810	358	13	2	5340	5696	734952333	734952689	1.380000e-160	577.0
6	TraesCS2B01G539800	chr2B	78.989	752	140	14	3862	4606	759347236	759347976	1.100000e-136	497.0
7	TraesCS2B01G539800	chr2B	73.151	987	215	33	3618	4580	707240188	707239228	5.540000e-80	309.0
8	TraesCS2B01G539800	chr2B	92.308	104	6	1	768	871	734942308	734942409	4.600000e-31	147.0
9	TraesCS2B01G539800	chr2D	94.363	4524	199	25	864	5343	604287419	604291930	0.000000e+00	6890.0
10	TraesCS2B01G539800	chr2D	90.900	2066	165	16	2774	4827	604052920	604050866	0.000000e+00	2752.0
11	TraesCS2B01G539800	chr2D	85.901	1227	129	27	867	2064	604056490	604055279	0.000000e+00	1267.0
12	TraesCS2B01G539800	chr2D	95.238	357	16	1	5340	5696	604292079	604292434	1.070000e-156	564.0
13	TraesCS2B01G539800	chr2D	87.841	403	25	16	2295	2687	604055283	604054895	8.700000e-123	451.0
14	TraesCS2B01G539800	chr2D	86.872	358	41	3	5340	5696	604025202	604024850	4.140000e-106	396.0
15	TraesCS2B01G539800	chr2D	90.511	274	19	4	5074	5343	604025623	604025353	7.020000e-94	355.0
16	TraesCS2B01G539800	chr2D	90.517	232	19	3	4841	5070	604026222	604025992	2.580000e-78	303.0
17	TraesCS2B01G539800	chr2D	94.301	193	9	1	472	664	604287018	604287208	1.550000e-75	294.0
18	TraesCS2B01G539800	chr2D	91.623	191	13	1	681	871	604056728	604056541	1.570000e-65	261.0
19	TraesCS2B01G539800	chr2D	91.758	182	12	1	690	871	604287193	604287371	3.410000e-62	250.0
20	TraesCS2B01G539800	chr2D	86.441	118	15	1	4959	5075	604025994	604025877	1.670000e-25	128.0
21	TraesCS2B01G539800	chr2D	81.203	133	22	3	3618	3748	585750029	585749898	2.810000e-18	104.0
22	TraesCS2B01G539800	chr2A	95.941	2365	92	3	2980	5343	736036962	736039323	0.000000e+00	3832.0
23	TraesCS2B01G539800	chr2A	90.815	2123	119	31	864	2946	736034875	736036961	0.000000e+00	2771.0
24	TraesCS2B01G539800	chr2A	75.515	1650	338	51	3009	4634	751233178	751234785	0.000000e+00	749.0
25	TraesCS2B01G539800	chr2A	74.584	1621	335	59	3012	4606	751208989	751210558	1.730000e-179	640.0
26	TraesCS2B01G539800	chr2A	93.557	357	21	2	5340	5696	736039472	736039826	1.090000e-146	531.0
27	TraesCS2B01G539800	chr3B	80.183	328	58	6	5372	5696	429529953	429529630	7.380000e-59	239.0
28	TraesCS2B01G539800	chrUn	78.505	321	64	5	5340	5657	132092063	132092381	7.480000e-49	206.0
29	TraesCS2B01G539800	chrUn	78.683	319	57	10	5340	5652	132098407	132098720	9.680000e-48	202.0
30	TraesCS2B01G539800	chr6D	77.429	350	72	7	5340	5685	338415538	338415192	9.680000e-48	202.0
31	TraesCS2B01G539800	chr6D	88.406	138	8	3	2571	2706	83104826	83104695	5.910000e-35	159.0
32	TraesCS2B01G539800	chr6D	85.714	140	12	4	2571	2706	84028570	84028705	2.140000e-29	141.0
33	TraesCS2B01G539800	chr4B	78.261	322	63	7	5340	5657	213502387	213502069	3.480000e-47	200.0
34	TraesCS2B01G539800	chr6B	86.957	138	12	3	2571	2706	158147212	158147079	3.560000e-32	150.0
35	TraesCS2B01G539800	chr6A	86.232	138	13	3	2571	2706	100182529	100182396	1.650000e-30	145.0
36	TraesCS2B01G539800	chr6A	83.784	74	12	0	3664	3737	593437429	593437356	2.850000e-08	71.3

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	TraesCS2B01G539800	chr2B	734915499	734921194	5695	False	10519.00	10519	100.000000	1	5696	1	chr2B.!!$F1	5695
1	TraesCS2B01G539800	chr2B	734940321	734952689	12368	False	1858.20	5454	94.980600	1	5696	5	chr2B.!!$F4	5695
2	TraesCS2B01G539800	chr2B	759440639	759442363	1724	False	662.00	662	74.139000	3002	4740	1	chr2B.!!$F3	1738
3	TraesCS2B01G539800	chr2B	759347236	759347976	740	False	497.00	497	78.989000	3862	4606	1	chr2B.!!$F2	744
4	TraesCS2B01G539800	chr2B	707239228	707240188	960	True	309.00	309	73.151000	3618	4580	1	chr2B.!!$R1	962
5	TraesCS2B01G539800	chr2D	604287018	604292434	5416	False	1999.50	6890	93.915000	472	5696	4	chr2D.!!$F1	5224
6	TraesCS2B01G539800	chr2D	604050866	604056728	5862	True	1182.75	2752	89.066250	681	4827	4	chr2D.!!$R3	4146
7	TraesCS2B01G539800	chr2D	604024850	604026222	1372	True	295.50	396	88.585250	4841	5696	4	chr2D.!!$R2	855
8	TraesCS2B01G539800	chr2A	736034875	736039826	4951	False	2378.00	3832	93.437667	864	5696	3	chr2A.!!$F3	4832
9	TraesCS2B01G539800	chr2A	751233178	751234785	1607	False	749.00	749	75.515000	3009	4634	1	chr2A.!!$F2	1625
10	TraesCS2B01G539800	chr2A	751208989	751210558	1569	False	640.00	640	74.584000	3012	4606	1	chr2A.!!$F1	1594

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	End Stability	Orientation
747	749	0.255033	GGTGCCCCTAATTCGGTTCT	59.745	55.000	3.01	F
1494	4059	0.974010	TTGGCGACTTCCTCCCGTAT	60.974	55.000	3.06	F
2111	4713	0.461961	TTTTTGCGAACACCCCCTTG	59.538	50.000	3.61	F
3420	7936	2.359975	GGCAGAGGTGGTTTCGGG	60.360	66.667	5.14	F
4189	12702	3.181489	CGGTTACATGTCTCCTGAGTACC	60.181	52.174	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1914	4514	0.454600	GCCAAGATGATGCACCAGTG	59.545	55.000	0.00	0.00	0.00	3.66	R
2448	5055	3.813166	CGCTGAGGTTAACAAGAAAAGGA	59.187	43.478	8.10	0.00	0.00	3.36	R
3818	8338	4.566759	TCTTCGAAGACCAATGCGAAATAG	59.433	41.667	23.74	0.00	41.46	1.73	R
4273	12786	1.854743	CGCTATGACATGGACTGAACG	59.145	52.381	2.48	0.00	0.00	3.95	R
5421	14481	5.930405	TCAAAGATGTTCATGTCGACAATG	58.070	37.500	24.13	19.65	0.00	2.82	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
26	27	2.924290	GCTAAGCTACAGAAACTGGTCG	59.076	50.000	0.00	0.00	35.51	4.79
58	59	2.600731	CACTAGTGAAGCACTTCCTCG	58.399	52.381	18.45	4.11	42.59	4.63
67	68	5.408604	GTGAAGCACTTCCTCGATAGAAAAA	59.591	40.000	7.88	0.00	40.27	1.94
434	436	9.936759	TTTACAAATTTGAAAGAAAACTCACCT	57.063	25.926	24.64	0.00	0.00	4.00
580	582	3.330267	GTTACTGCTGTCTTCTCTTGGG	58.670	50.000	0.00	0.00	0.00	4.12
670	672	3.839432	CGAGACCGGGCTTCCCTC	61.839	72.222	13.62	0.00	42.67	4.30
673	675	2.046217	GACCGGGCTTCCCTCAAC	60.046	66.667	6.32	0.00	42.67	3.18
676	678	1.971695	CCGGGCTTCCCTCAACAAC	60.972	63.158	0.00	0.00	42.67	3.32
679	681	0.673985	GGGCTTCCCTCAACAACAAC	59.326	55.000	0.00	0.00	41.34	3.32
747	749	0.255033	GGTGCCCCTAATTCGGTTCT	59.745	55.000	0.00	0.00	0.00	3.01
756	758	3.197116	CCTAATTCGGTTCTGGGTAGTGT	59.803	47.826	0.00	0.00	0.00	3.55
797	2035	1.404986	CCGTTCAGGATTCGCTAACCA	60.405	52.381	0.00	0.00	45.00	3.67
965	3527	3.719268	AGCTCTGTCTCTCTCTCTCAA	57.281	47.619	0.00	0.00	0.00	3.02
1049	3614	3.555324	TGTGCTGGCCTCCGACAA	61.555	61.111	3.32	0.00	0.00	3.18
1118	3683	4.838152	CTGGGTCGACATGGGCGG	62.838	72.222	18.91	0.00	0.00	6.13
1152	3717	4.598894	CATCCGAGCCTCCGCCTG	62.599	72.222	0.00	0.00	34.57	4.85
1182	3747	2.253758	CCGCACACCTGTTCTGTGG	61.254	63.158	1.03	0.00	39.62	4.17
1494	4059	0.974010	TTGGCGACTTCCTCCCGTAT	60.974	55.000	0.00	0.00	0.00	3.06
1525	4090	2.290260	ACCCAATGCGAGAAAGTCATCA	60.290	45.455	0.00	0.00	0.00	3.07
1652	4217	2.125912	GGCGATGAGTGAGTGCGT	60.126	61.111	0.00	0.00	0.00	5.24
1722	4287	3.454375	GAAGAAGTCTTGGACGTTCACA	58.546	45.455	0.00	0.00	37.67	3.58
1799	4382	5.320549	ACGTACGACAGTTATTCCTTCAT	57.679	39.130	24.41	0.00	0.00	2.57
1838	4421	5.699001	TCACTATTGCTTGCTTTACTTTCGA	59.301	36.000	0.00	0.00	0.00	3.71
1882	4482	1.671328	TGACGCAAACGGTCAATTTGA	59.329	42.857	0.00	0.00	46.04	2.69
1901	4501	4.901197	TGATGGTTGGTGCTAGAACTTA	57.099	40.909	0.00	0.00	0.00	2.24
1914	4514	5.239306	TGCTAGAACTTATGGTATGCATTGC	59.761	40.000	3.54	0.46	0.00	3.56
1937	4537	3.018856	CTGGTGCATCATCTTGGCTTTA	58.981	45.455	0.00	0.00	0.00	1.85
1962	4562	5.617308	GCGTGTAAATACGGTGAAAATTCCA	60.617	40.000	1.48	0.00	43.87	3.53
2110	4712	2.903404	TTTTTGCGAACACCCCCTT	58.097	47.368	0.00	0.00	0.00	3.95
2111	4713	0.461961	TTTTTGCGAACACCCCCTTG	59.538	50.000	0.00	0.00	0.00	3.61
2164	4770	8.766492	ACATATAACCCCTAAATCCCAATCTA	57.234	34.615	0.00	0.00	0.00	1.98
2190	4796	5.981315	GTGTATGACCGGATTCGAATCTTAA	59.019	40.000	31.32	16.58	39.00	1.85
2542	5156	3.132925	GTTTCCTGCGTAACAGTACCAA	58.867	45.455	0.00	0.00	45.68	3.67
2676	5292	2.766263	TGATTCTCCCACGAGCTAACAT	59.234	45.455	0.00	0.00	35.94	2.71
2786	7291	3.311322	CGCCGCTCCTAAACAAATCAATA	59.689	43.478	0.00	0.00	0.00	1.90
2919	7425	8.485578	TTTGGTATTTTTGGATGGTAAAGTCT	57.514	30.769	0.00	0.00	0.00	3.24
3174	7684	8.456471	ACAAGTTAACAGGTAGAACAACTTTTC	58.544	33.333	8.61	0.00	34.82	2.29
3420	7936	2.359975	GGCAGAGGTGGTTTCGGG	60.360	66.667	0.00	0.00	0.00	5.14
3818	8338	7.009265	GCAAAACTTTCTTTGGTTTACTGAGTC	59.991	37.037	0.00	0.00	36.89	3.36
4189	12702	3.181489	CGGTTACATGTCTCCTGAGTACC	60.181	52.174	0.00	0.00	0.00	3.34
4190	12703	4.024670	GGTTACATGTCTCCTGAGTACCT	58.975	47.826	0.00	0.00	0.00	3.08
4273	12786	9.436957	TGGAGATTATAAGCGGATTAAAGATTC	57.563	33.333	0.00	0.00	0.00	2.52
4440	12966	0.461961	CGAGAGGATTGGTGGACTCC	59.538	60.000	0.00	0.00	0.00	3.85
4688	13214	5.163120	ACATTACTATCACCGAGGTAGAGGA	60.163	44.000	0.00	0.00	0.00	3.71
4943	13479	7.939782	TCTTCTATGAAATTTGTGCTTGTGAA	58.060	30.769	0.00	0.00	0.00	3.18
5212	14113	7.060421	TGCCCCCACAAAAATTAAAAATAACA	58.940	30.769	0.00	0.00	0.00	2.41
5260	14165	1.247567	CGGCCATCCTTGTTTTCACT	58.752	50.000	2.24	0.00	0.00	3.41
5324	14229	1.255882	CACTGCTTAATTGGGTGCCA	58.744	50.000	0.00	0.00	0.00	4.92
5329	14234	2.703007	TGCTTAATTGGGTGCCAACTTT	59.297	40.909	0.00	0.00	46.95	2.66
5361	14420	3.890756	TGTTGACATCAGATTTTGGCACT	59.109	39.130	0.00	0.00	28.39	4.40
5401	14461	2.933906	GTGACCTCAAACAAAGACGTGA	59.066	45.455	0.00	0.00	0.00	4.35
5421	14481	6.017933	CGTGATCTACATGAAGAAGTTTTGC	58.982	40.000	0.00	0.00	37.69	3.68
5593	14654	2.162681	ACATGGTTGTCTTAGCCTTGC	58.837	47.619	0.00	0.00	38.05	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	1.002315	TCACTAGTGGTTAAACGGGCC	59.998	52.381	22.48	0.00	0.00	5.80
67	68	5.124776	TCAACTGTTGATCAACGAACCTTTT	59.875	36.000	28.55	13.31	43.94	2.27
68	69	4.638421	TCAACTGTTGATCAACGAACCTTT	59.362	37.500	28.55	14.47	43.94	3.11
407	409	9.967245	GGTGAGTTTTCTTTCAAATTTGTAAAC	57.033	29.630	17.47	17.44	0.00	2.01
428	430	7.078228	GCGCATAGGATTTTTAAATAGGTGAG	58.922	38.462	0.30	0.00	0.00	3.51
434	436	6.016610	GGAGGTGCGCATAGGATTTTTAAATA	60.017	38.462	15.91	0.00	0.00	1.40
468	470	4.495690	AGCCCTTGGTTTTAAAAAGCAA	57.504	36.364	1.31	11.28	36.39	3.91
469	471	4.495690	AAGCCCTTGGTTTTAAAAAGCA	57.504	36.364	1.31	4.43	0.00	3.91
539	541	1.014352	CACTAGGCCATGTTAACGCC	58.986	55.000	5.01	13.39	43.35	5.68
617	619	1.588082	GGCACCACATTCCTTGCTG	59.412	57.895	0.00	0.00	35.24	4.41
732	734	0.916809	ACCCAGAACCGAATTAGGGG	59.083	55.000	9.59	2.71	39.19	4.79
733	735	2.770232	ACTACCCAGAACCGAATTAGGG	59.230	50.000	9.59	1.48	40.23	3.53
736	738	3.119388	CGACACTACCCAGAACCGAATTA	60.119	47.826	0.00	0.00	0.00	1.40
756	758	2.589442	GGTTTCGTGTGTGCCCGA	60.589	61.111	0.00	0.00	0.00	5.14
831	2069	3.689649	CCGGTTTCCTGAACTGAATTAGG	59.310	47.826	0.00	0.00	45.70	2.69
832	2070	3.689649	CCCGGTTTCCTGAACTGAATTAG	59.310	47.826	0.00	0.00	45.70	1.73
833	2071	3.681593	CCCGGTTTCCTGAACTGAATTA	58.318	45.455	0.00	0.00	45.70	1.40
1182	3747	1.591863	GTATTCTCCCGACGGCAGC	60.592	63.158	8.86	0.00	0.00	5.25
1254	3819	0.322277	AGACGCCTAGGTCGAACAGA	60.322	55.000	25.67	0.00	41.81	3.41
1475	4040	0.974010	ATACGGGAGGAAGTCGCCAA	60.974	55.000	0.00	0.00	37.03	4.52
1494	4059	0.321210	CGCATTGGGTGGTGTAGTCA	60.321	55.000	0.00	0.00	0.00	3.41
1525	4090	0.249911	GTTCTCAGAACCGGCACTGT	60.250	55.000	22.05	0.00	35.84	3.55
1722	4287	2.489329	GGCACTAGCATTTGTCACACAT	59.511	45.455	0.00	0.00	44.61	3.21
1799	4382	2.264005	AGTGACAACATGCGGGTTTA	57.736	45.000	0.00	0.00	0.00	2.01
1838	4421	9.545105	TCAAGTTCAAGCATCAATTTTAAATGT	57.455	25.926	0.00	0.00	0.00	2.71
1882	4482	4.018415	ACCATAAGTTCTAGCACCAACCAT	60.018	41.667	0.00	0.00	0.00	3.55
1901	4501	1.752498	CACCAGTGCAATGCATACCAT	59.248	47.619	12.38	0.00	41.91	3.55
1914	4514	0.454600	GCCAAGATGATGCACCAGTG	59.545	55.000	0.00	0.00	0.00	3.66
1937	4537	5.391203	GGAATTTTCACCGTATTTACACGCT	60.391	40.000	0.00	0.00	40.59	5.07
2022	4623	1.565390	CCCTCTTGGCCATCCAGTCA	61.565	60.000	6.09	0.00	44.53	3.41
2164	4770	3.812156	TTCGAATCCGGTCATACACAT	57.188	42.857	0.00	0.00	36.24	3.21
2190	4796	6.017687	GGTTATTTCTTCCGTGTTGTACAGTT	60.018	38.462	0.00	0.00	0.00	3.16
2264	4870	1.068610	GTCATAAGCTGCCAACGCAAA	60.069	47.619	0.00	0.00	46.66	3.68
2447	5054	4.274950	CGCTGAGGTTAACAAGAAAAGGAA	59.725	41.667	8.10	0.00	0.00	3.36
2448	5055	3.813166	CGCTGAGGTTAACAAGAAAAGGA	59.187	43.478	8.10	0.00	0.00	3.36
2512	5126	4.930405	TGTTACGCAGGAAACGATATTTCA	59.070	37.500	0.00	0.00	31.48	2.69
2542	5156	9.624373	AGCATCTAAAAACAAGATATCATGAGT	57.376	29.630	14.59	0.00	32.40	3.41
3420	7936	8.919777	AATGGCATCTTACCTTATAAACTACC	57.080	34.615	0.00	0.00	0.00	3.18
3591	8108	6.494491	TGACCAAGATCACCTCATTTTTGAAT	59.506	34.615	0.00	0.00	0.00	2.57
3818	8338	4.566759	TCTTCGAAGACCAATGCGAAATAG	59.433	41.667	23.74	0.00	41.46	1.73
4189	12702	4.770795	ACGGAATAGAAACCTTCCATCAG	58.229	43.478	2.58	0.00	40.85	2.90
4190	12703	4.224147	TGACGGAATAGAAACCTTCCATCA	59.776	41.667	0.00	0.00	40.37	3.07
4273	12786	1.854743	CGCTATGACATGGACTGAACG	59.145	52.381	2.48	0.00	0.00	3.95
4607	13133	2.294233	CCTGTTCCATGGTTCTGTTGTG	59.706	50.000	12.58	0.00	0.00	3.33
4688	13214	7.050970	TCAATGGAAGTACATATCTAGCGTT	57.949	36.000	0.00	0.00	0.00	4.84
4943	13479	5.934402	ACCGAATGACTAACATAGGAAGT	57.066	39.130	0.00	0.00	38.97	3.01
4999	13535	9.965902	ACTCTGAAAAATATGAACTTCTACCAT	57.034	29.630	0.00	0.00	0.00	3.55
5324	14229	6.998074	TGATGTCAACATTGGAGACTAAAGTT	59.002	34.615	10.69	0.00	36.57	2.66
5329	14234	6.550938	ATCTGATGTCAACATTGGAGACTA	57.449	37.500	10.69	1.16	36.57	2.59
5401	14461	7.889469	ACAATGCAAAACTTCTTCATGTAGAT	58.111	30.769	2.58	0.00	0.00	1.98
5421	14481	5.930405	TCAAAGATGTTCATGTCGACAATG	58.070	37.500	24.13	19.65	0.00	2.82
5593	14654	8.676454	TTTTATATCAAAATCGACCGTTTTGG	57.324	30.769	17.99	10.27	43.36	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.