AutoCloner

Multiple sequence alignment - TraesCS5D01G106300

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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	TraesCS5D01G106300	chr5D	100.000	6269	0	0	1	6269	119761251	119767519	0.000000e+00	11577.0
1	TraesCS5D01G106300	chr5D	100.000	43	0	0	1825	1867	122198430	122198472	5.210000e-11	80.5
2	TraesCS5D01G106300	chr5D	100.000	43	0	0	1823	1865	122198517	122198475	5.210000e-11	80.5
3	TraesCS5D01G106300	chr5B	95.074	2558	79	23	3258	5806	133008471	133010990	0.000000e+00	3982.0
4	TraesCS5D01G106300	chr5B	95.984	2316	55	10	963	3256	133005984	133008283	0.000000e+00	3727.0
5	TraesCS5D01G106300	chr5B	96.753	924	13	3	1	907	132615239	132616162	0.000000e+00	1524.0
6	TraesCS5D01G106300	chr5B	95.522	469	18	3	5802	6269	133010690	133011156	0.000000e+00	747.0
7	TraesCS5D01G106300	chr5A	96.103	2130	60	2	3300	5407	130132767	130134895	0.000000e+00	3452.0
8	TraesCS5D01G106300	chr5A	95.371	1037	25	6	2292	3313	130128623	130129651	0.000000e+00	1628.0
9	TraesCS5D01G106300	chr5A	95.411	937	23	5	1	917	130122708	130123644	0.000000e+00	1474.0
10	TraesCS5D01G106300	chr5A	91.141	903	31	18	963	1825	130127140	130128033	0.000000e+00	1179.0
11	TraesCS5D01G106300	chr5A	96.756	524	16	1	5747	6269	130136594	130137117	0.000000e+00	872.0
12	TraesCS5D01G106300	chr5A	96.056	431	17	0	1863	2293	130128035	130128465	0.000000e+00	702.0
13	TraesCS5D01G106300	chr5A	96.857	350	6	2	5404	5748	130136162	130136511	1.170000e-161	580.0
14	TraesCS5D01G106300	chr5A	100.000	43	0	0	1825	1867	688764046	688764004	5.210000e-11	80.5
15	TraesCS5D01G106300	chr7B	82.536	418	48	15	1149	1560	211797187	211796789	1.670000e-90	344.0
16	TraesCS5D01G106300	chr7B	85.366	246	34	2	2461	2704	211795389	211795144	2.900000e-63	254.0
17	TraesCS5D01G106300	chr7B	79.231	260	41	8	2863	3116	211794897	211794645	1.080000e-37	169.0
18	TraesCS5D01G106300	chr7B	88.000	100	10	2	3616	3714	211792878	211792780	3.970000e-22	117.0
19	TraesCS5D01G106300	chr2B	83.117	385	42	13	3846	4212	375172936	375172557	4.690000e-86	329.0
20	TraesCS5D01G106300	chr7D	81.818	418	51	11	1149	1560	235578956	235578558	1.690000e-85	327.0
21	TraesCS5D01G106300	chr7D	86.547	223	29	1	2461	2682	235576895	235576673	1.750000e-60	244.0
22	TraesCS5D01G106300	chr7D	81.154	260	40	8	2863	3116	235576417	235576161	3.830000e-47	200.0
23	TraesCS5D01G106300	chr7D	75.661	378	65	21	4648	5004	235573163	235572792	5.030000e-36	163.0
24	TraesCS5D01G106300	chr7D	89.535	86	9	0	3618	3703	235574226	235574141	6.640000e-20	110.0
25	TraesCS5D01G106300	chr2A	86.667	285	33	5	3793	4073	218140906	218140623	1.700000e-80	311.0
26	TraesCS5D01G106300	chr2A	100.000	42	0	0	1826	1867	745094743	745094702	1.870000e-10	78.7
27	TraesCS5D01G106300	chr2D	89.700	233	16	6	3846	4073	199134276	199134047	2.210000e-74	291.0
28	TraesCS5D01G106300	chr2D	84.896	192	18	10	3846	4030	565470848	565471035	3.860000e-42	183.0
29	TraesCS5D01G106300	chr7A	84.959	246	35	2	2461	2704	250688989	250688744	1.350000e-61	248.0
30	TraesCS5D01G106300	chr7A	76.455	378	64	20	4648	5004	250681053	250680680	1.390000e-41	182.0
31	TraesCS5D01G106300	chr7A	92.647	68	5	0	3618	3685	250681956	250681889	1.440000e-16	99.0
32	TraesCS5D01G106300	chr6D	85.106	94	9	3	3886	3976	407918352	407918443	2.410000e-14	91.6
33	TraesCS5D01G106300	chr6D	97.778	45	1	0	1823	1867	39676412	39676456	1.870000e-10	78.7
34	TraesCS5D01G106300	chr6A	98.039	51	1	0	1816	1866	105053230	105053280	8.660000e-14	89.8
35	TraesCS5D01G106300	chr6A	94.000	50	3	0	1818	1867	540610175	540610224	6.740000e-10	76.8
36	TraesCS5D01G106300	chr4D	100.000	43	0	0	1825	1867	504090795	504090753	5.210000e-11	80.5
37	TraesCS5D01G106300	chr1D	100.000	29	0	0	1140	1168	28831828	28831800	3.000000e-03	54.7

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	TraesCS5D01G106300	chr5D	119761251	119767519	6268	False	11577.000000	11577	100.000000	1	6269	1	chr5D.!!$F1	6268
1	TraesCS5D01G106300	chr5B	133005984	133011156	5172	False	2818.666667	3982	95.526667	963	6269	3	chr5B.!!$F2	5306
2	TraesCS5D01G106300	chr5B	132615239	132616162	923	False	1524.000000	1524	96.753000	1	907	1	chr5B.!!$F1	906
3	TraesCS5D01G106300	chr5A	130122708	130137117	14409	False	1412.428571	3452	95.385000	1	6269	7	chr5A.!!$F1	6268
4	TraesCS5D01G106300	chr7B	211792780	211797187	4407	True	221.000000	344	83.783250	1149	3714	4	chr7B.!!$R1	2565
5	TraesCS5D01G106300	chr7D	235572792	235578956	6164	True	208.800000	327	82.943000	1149	5004	5	chr7D.!!$R1	3855

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
917	938	0.034896	ATGGCCGTCTCGTTTCTGTT	59.965	50.000	0.00	0.00	0.00	3.16	F
924	945	0.034896	TCTCGTTTCTGTTGGAGGGC	59.965	55.000	0.00	0.00	0.00	5.19	F
928	949	0.609406	GTTTCTGTTGGAGGGCCCTC	60.609	60.000	39.86	39.86	42.04	4.30	F
929	950	0.772124	TTTCTGTTGGAGGGCCCTCT	60.772	55.000	43.34	18.43	42.38	3.69	F
1618	5168	0.906756	TGAGCAGCAAGGGAGTAGCT	60.907	55.000	0.00	0.00	39.63	3.32	F
2018	6231	1.745087	AGTAACCATTGGCAATGCTCG	59.255	47.619	30.21	20.52	37.57	5.03	F
3906	13342	0.712380	ACCATGCCCCTCATTTTCCT	59.288	50.000	0.00	0.00	31.79	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2489	6948	2.227388	CACAACCTGTCATTCAAGAGCC	59.773	50.000	0.00	0.00	4.70	R
2911	7546	6.149474	AGGAACTGAAGATATGAAACAAACCG	59.851	38.462	0.00	37.18	4.44	R
3297	8425	6.575162	ATGGTACTTAGGAACAAGCTTTTG	57.425	37.500	0.00	0.00	2.44	R
3298	8426	8.879427	ATTATGGTACTTAGGAACAAGCTTTT	57.121	30.769	0.00	0.00	2.27	R
3517	12491	0.539986	ACACGGGCTCCATAAACGAT	59.460	50.000	0.00	0.00	3.73	R
4071	13507	1.373497	GTCCTCATATGCTCGGGCG	60.373	63.158	1.14	42.25	6.13	R
5859	17155	0.031449	ATTTCCCGGCGTTGTTTGTG	59.969	50.000	6.01	0.00	3.33	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
89	90	3.222354	GACGACGGTGAGGCTGGTT	62.222	63.158	0.00	0.00	0.00	3.67
917	938	0.034896	ATGGCCGTCTCGTTTCTGTT	59.965	50.000	0.00	0.00	0.00	3.16
918	939	0.878523	TGGCCGTCTCGTTTCTGTTG	60.879	55.000	0.00	0.00	0.00	3.33
920	941	0.599204	GCCGTCTCGTTTCTGTTGGA	60.599	55.000	0.00	0.00	0.00	3.53
922	943	1.419374	CGTCTCGTTTCTGTTGGAGG	58.581	55.000	0.00	0.00	0.00	4.30
923	944	1.797025	GTCTCGTTTCTGTTGGAGGG	58.203	55.000	0.00	0.00	0.00	4.30
924	945	0.034896	TCTCGTTTCTGTTGGAGGGC	59.965	55.000	0.00	0.00	0.00	5.19
925	946	0.955919	CTCGTTTCTGTTGGAGGGCC	60.956	60.000	0.00	0.00	0.00	5.80
926	947	1.971695	CGTTTCTGTTGGAGGGCCC	60.972	63.158	16.46	16.46	0.00	5.80
928	949	0.609406	GTTTCTGTTGGAGGGCCCTC	60.609	60.000	39.86	39.86	42.04	4.30
929	950	0.772124	TTTCTGTTGGAGGGCCCTCT	60.772	55.000	43.34	18.43	42.38	3.69
930	951	1.492133	TTCTGTTGGAGGGCCCTCTG	61.492	60.000	43.34	28.64	42.38	3.35
932	953	2.190488	CTGTTGGAGGGCCCTCTGAC	62.190	65.000	43.34	37.57	42.38	3.51
933	954	3.003173	TTGGAGGGCCCTCTGACG	61.003	66.667	43.34	0.00	42.38	4.35
1104	4574	4.168291	GAGCAGGGCGGAGAAGGG	62.168	72.222	0.00	0.00	0.00	3.95
1326	4841	4.803426	CGCGGCCTCTTCTTCGCT	62.803	66.667	0.00	0.00	45.11	4.93
1573	5116	4.590850	AAGAAGGCTTTGTTGATTCACC	57.409	40.909	0.00	0.00	0.00	4.02
1618	5168	0.906756	TGAGCAGCAAGGGAGTAGCT	60.907	55.000	0.00	0.00	39.63	3.32
1834	6008	7.040409	CCAATTAGCATGTTTAATACTCCCTCC	60.040	40.741	0.00	0.00	0.00	4.30
1921	6095	5.490472	GCACATAAATATGCTGCATTTCG	57.510	39.130	21.56	8.20	38.91	3.46
1935	6109	9.831737	ATGCTGCATTTCGTAATCTTATTTATC	57.168	29.630	9.81	0.00	0.00	1.75
2018	6231	1.745087	AGTAACCATTGGCAATGCTCG	59.255	47.619	30.21	20.52	37.57	5.03
2029	6242	2.358898	GGCAATGCTCGTTGACCATAAT	59.641	45.455	4.82	0.00	30.67	1.28
2489	6948	6.365247	AGCATTAACGTTGGCTAATATAGTCG	59.635	38.462	18.39	0.00	34.25	4.18
2841	7318	8.226819	TCCTTCACTATAGATATGCTTATCCG	57.773	38.462	14.30	5.52	35.74	4.18
2846	7323	9.847224	TCACTATAGATATGCTTATCCGTATGA	57.153	33.333	14.30	10.06	35.74	2.15
2911	7546	5.057149	ACTGAACTGTTGGTAGATGTTCAC	58.943	41.667	0.00	0.00	41.02	3.18
3185	8119	6.053005	TGCCCAGGACGTTTATTATCTAAAG	58.947	40.000	0.00	0.00	0.00	1.85
3365	11623	6.970043	GTGCCATATTTAGATTTGCGTTAACA	59.030	34.615	6.39	0.00	0.00	2.41
3564	12824	7.478044	CCATTTGTTTTGCATTTATTTGCTACG	59.522	33.333	0.00	0.00	43.18	3.51
3728	13164	8.500773	ACAAAGGTATGTACTTAACATCGTTTG	58.499	33.333	19.61	19.61	46.15	2.93
3906	13342	0.712380	ACCATGCCCCTCATTTTCCT	59.288	50.000	0.00	0.00	31.79	3.36
4035	13471	4.742201	CCTGCCCTGACACGACCG	62.742	72.222	0.00	0.00	0.00	4.79
4071	13507	1.620323	GGCTTGGATATGGGGATTTGC	59.380	52.381	0.00	0.00	0.00	3.68
4158	13594	2.746359	GCAGTGACCAGGCTGTCT	59.254	61.111	14.43	3.52	36.21	3.41
4422	13867	8.184304	ACTAACAATAAATTGGCACAGGTAAA	57.816	30.769	7.56	0.00	42.39	2.01
4766	14664	5.574970	ACCTGAACTTCTTCCTTGAAGAT	57.425	39.130	7.32	0.00	46.20	2.40
4778	14676	5.369409	TCCTTGAAGATGATGATGAGCTT	57.631	39.130	0.00	0.00	0.00	3.74
4844	14742	9.433153	ACACTTTATAGCTACTTAGTTTCCAAC	57.567	33.333	0.00	0.00	0.00	3.77
5285	15222	3.898482	ACTATTAATGTGAACCTGGCCC	58.102	45.455	0.00	0.00	0.00	5.80
5351	15288	9.409312	CATGTGATATGTTTGTTTTCAAGCTTA	57.591	29.630	0.00	0.00	40.75	3.09
5480	16687	8.275040	AGCTTCCTTCTGTATTATGGTTATGTT	58.725	33.333	0.00	0.00	0.00	2.71
5518	16725	4.039124	ACGAATTTGAAAAATCTGCAGGGT	59.961	37.500	15.13	0.00	0.00	4.34
5525	16732	5.826643	TGAAAAATCTGCAGGGTAATACCT	58.173	37.500	15.13	0.00	43.08	3.08
5538	16745	7.280044	AGGGTAATACCTGAAGTTACCAATT	57.720	36.000	9.58	0.00	45.80	2.32
5776	17072	5.741982	AGAAACGACCAAAAATGAAAGAACG	59.258	36.000	0.00	0.00	0.00	3.95
5777	17073	3.368495	ACGACCAAAAATGAAAGAACGC	58.632	40.909	0.00	0.00	0.00	4.84
5859	17155	3.052036	GTGATGCCATGTTCAAACACAC	58.948	45.455	0.00	0.00	42.51	3.82
5871	17167	1.388431	CAAACACACACAAACAACGCC	59.612	47.619	0.00	0.00	0.00	5.68
5881	17177	2.559231	ACAAACAACGCCGGGAAATATT	59.441	40.909	2.18	0.00	0.00	1.28
5887	17183	3.107642	ACGCCGGGAAATATTACTCAG	57.892	47.619	2.18	0.00	0.00	3.35
5888	17184	2.696707	ACGCCGGGAAATATTACTCAGA	59.303	45.455	2.18	0.00	0.00	3.27
6186	17483	0.327924	TGATTTGTCAGACCCGCCAT	59.672	50.000	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
113	114	2.047465	CTCAGCTTGCTCGTGCCT	60.047	61.111	7.05	0.00	38.71	4.75
764	774	0.755686	ATCCAGGCGACAAGGATCTC	59.244	55.000	9.30	0.00	41.88	2.75
790	800	5.622180	GAGAACTAACCCCATCCTAAATCC	58.378	45.833	0.00	0.00	0.00	3.01
830	840	2.363788	TCGTGTAGTTTGGCTAGCTG	57.636	50.000	15.72	0.00	0.00	4.24
834	844	4.096833	ACGTATCATCGTGTAGTTTGGCTA	59.903	41.667	0.00	0.00	42.56	3.93
895	916	0.608640	AGAAACGAGACGGCCATTCT	59.391	50.000	2.24	2.93	0.00	2.40
966	4414	1.173913	GGAATCGACAAGGGGGTTTG	58.826	55.000	0.00	0.00	0.00	2.93
967	4415	0.039180	GGGAATCGACAAGGGGGTTT	59.961	55.000	0.00	0.00	0.00	3.27
970	4440	1.984288	GAGGGGAATCGACAAGGGGG	61.984	65.000	0.00	0.00	0.00	5.40
1104	4574	1.227674	CGAGGCCATGGCTAGTTCC	60.228	63.158	34.70	17.88	38.98	3.62
1383	4901	1.325640	CCGAGATTGTGTCAGCGATTG	59.674	52.381	0.00	0.00	0.00	2.67
1573	5116	2.664424	CGTTGCCCAGATAAACAACACG	60.664	50.000	0.00	0.00	41.90	4.49
1608	5158	2.356535	CCAAGAATGCAAGCTACTCCCT	60.357	50.000	0.00	0.00	0.00	4.20
1618	5168	3.052455	TCGTTCTAGCCAAGAATGCAA	57.948	42.857	11.90	0.00	46.67	4.08
1834	6008	7.095397	TGCAAAACGATCTTATATTATGGGACG	60.095	37.037	0.00	0.00	0.00	4.79
2018	6231	8.498054	TCTGAAGAAAGATCATTATGGTCAAC	57.502	34.615	8.28	0.00	27.47	3.18
2029	6242	7.341030	TCCTGCAAATATCTGAAGAAAGATCA	58.659	34.615	0.00	0.00	37.98	2.92
2489	6948	2.227388	CACAACCTGTCATTCAAGAGCC	59.773	50.000	0.00	0.00	0.00	4.70
2841	7318	8.457238	AGATGGCCTCTTAAAAATTCTCATAC	57.543	34.615	3.32	0.00	0.00	2.39
2911	7546	6.149474	AGGAACTGAAGATATGAAACAAACCG	59.851	38.462	0.00	0.00	37.18	4.44
3297	8425	6.575162	ATGGTACTTAGGAACAAGCTTTTG	57.425	37.500	0.00	0.00	0.00	2.44
3298	8426	8.879427	ATTATGGTACTTAGGAACAAGCTTTT	57.121	30.769	0.00	0.00	0.00	2.27
3465	12438	6.202570	GCTAGATGGAGAAATAGCAAGTTCAG	59.797	42.308	0.00	0.00	40.27	3.02
3517	12491	0.539986	ACACGGGCTCCATAAACGAT	59.460	50.000	0.00	0.00	0.00	3.73
3564	12824	2.717639	AGTGCCATCCATAACAGGAC	57.282	50.000	0.00	0.00	41.30	3.85
3764	13200	6.096705	TCACACAAACAAGGATCAACTGAAAT	59.903	34.615	0.00	0.00	0.00	2.17
3906	13342	2.299013	GCATGTGACCGGACATATAGGA	59.701	50.000	15.00	0.00	34.69	2.94
4035	13471	3.560025	CCAAGCCATATACAGGGATGTCC	60.560	52.174	0.00	0.00	0.00	4.02
4071	13507	1.373497	GTCCTCATATGCTCGGGCG	60.373	63.158	1.14	0.00	42.25	6.13
4766	14664	0.108041	TGCGCTCAAGCTCATCATCA	60.108	50.000	9.73	0.00	39.32	3.07
4778	14676	6.293407	GCAATATTACCTTCTTTATGCGCTCA	60.293	38.462	9.73	0.00	0.00	4.26
4844	14742	0.960364	ACAACATTAGCACGGCCCAG	60.960	55.000	0.00	0.00	0.00	4.45
5285	15222	0.886490	GCCGCCATACAGGATTGAGG	60.886	60.000	0.00	0.00	41.22	3.86
5351	15288	4.573900	AGAAATCTTTGCAGTGATCGAGT	58.426	39.130	0.00	0.00	0.00	4.18
5647	16859	4.339872	AGCAAATCACAATCCAGCAAAA	57.660	36.364	0.00	0.00	0.00	2.44
5776	17072	4.618693	GCAGGTATTCTTCTATAGGGTCGC	60.619	50.000	0.00	0.00	0.00	5.19
5777	17073	4.767928	AGCAGGTATTCTTCTATAGGGTCG	59.232	45.833	0.00	0.00	0.00	4.79
5815	17111	9.575868	TCACAAAAACATATTGGTAACTTAGGA	57.424	29.630	0.00	0.00	37.61	2.94
5833	17129	5.064452	GTGTTTGAACATGGCATCACAAAAA	59.936	36.000	18.14	13.39	41.59	1.94
5859	17155	0.031449	ATTTCCCGGCGTTGTTTGTG	59.969	50.000	6.01	0.00	0.00	3.33
5914	17210	6.055588	CCAGAACCTCAGAAACTTGAAAGTA	58.944	40.000	0.00	0.00	38.57	2.24
6186	17483	0.762418	TTGCTTCGGAGTGAAAGGGA	59.238	50.000	0.00	0.00	35.79	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.