AutoCloner

Multiple sequence alignment - TraesCS2D01G425300

Loading Multiple Alignment...

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	TraesCS2D01G425300	chr2D	100.000	2812	0	0	1	2812	537706359	537703548	0.000000e+00	5193.0
1	TraesCS2D01G425300	chr2B	94.037	1459	68	11	345	1801	640491307	640489866	0.000000e+00	2194.0
2	TraesCS2D01G425300	chr2B	85.496	262	23	4	1	251	640491627	640491370	2.780000e-65	259.0
3	TraesCS2D01G425300	chr2B	87.500	80	10	0	362	441	732835703	732835782	2.980000e-15	93.5
4	TraesCS2D01G425300	chr2A	92.706	1042	53	7	774	1801	680097835	680096803	0.000000e+00	1482.0
5	TraesCS2D01G425300	chr2A	85.098	765	78	11	1	753	680098568	680097828	0.000000e+00	749.0
6	TraesCS2D01G425300	chr2A	94.845	194	10	0	2619	2812	680096810	680096617	1.270000e-78	303.0
7	TraesCS2D01G425300	chr3D	94.022	803	37	9	1802	2600	607326566	607327361	0.000000e+00	1206.0
8	TraesCS2D01G425300	chr3D	93.696	809	40	7	1796	2600	115642973	115643774	0.000000e+00	1201.0
9	TraesCS2D01G425300	chr3D	93.649	803	39	6	1801	2600	374392362	374393155	0.000000e+00	1190.0
10	TraesCS2D01G425300	chr7D	93.201	809	43	10	1796	2600	561874240	561873440	0.000000e+00	1179.0
11	TraesCS2D01G425300	chr4D	93.392	802	44	8	1802	2600	359204304	359203509	0.000000e+00	1179.0
12	TraesCS2D01G425300	chr5D	92.998	814	46	9	1793	2600	213033069	213033877	0.000000e+00	1177.0
13	TraesCS2D01G425300	chr5D	92.875	814	46	10	1793	2600	212952135	212952942	0.000000e+00	1171.0
14	TraesCS2D01G425300	chr5D	92.875	814	46	10	1793	2600	213006458	213007265	0.000000e+00	1171.0
15	TraesCS2D01G425300	chrUn	92.972	811	43	11	1796	2600	320693002	320692200	0.000000e+00	1170.0
16	TraesCS2D01G425300	chrUn	81.553	103	19	0	360	462	27862619	27862721	4.990000e-13	86.1
17	TraesCS2D01G425300	chr1B	87.967	856	75	20	1793	2627	65585924	65585076	0.000000e+00	985.0
18	TraesCS2D01G425300	chr7A	86.408	103	14	0	360	462	19909740	19909638	2.290000e-21	113.0
19	TraesCS2D01G425300	chr7A	77.419	124	19	8	244	366	63081549	63081434	6.500000e-07	65.8
20	TraesCS2D01G425300	chr6D	83.495	103	17	0	360	462	427170214	427170112	2.310000e-16	97.1
21	TraesCS2D01G425300	chr6D	81.553	103	19	0	360	462	137249356	137249254	4.990000e-13	86.1
22	TraesCS2D01G425300	chr6D	80.172	116	22	1	360	474	260364466	260364351	4.990000e-13	86.1
23	TraesCS2D01G425300	chr6A	83.333	102	17	0	360	461	560541207	560541106	8.290000e-16	95.3
24	TraesCS2D01G425300	chr1D	82.524	103	18	0	360	462	66824185	66824083	1.070000e-14	91.6

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	TraesCS2D01G425300	chr2D	537703548	537706359	2811	True	5193.000000	5193	100.0000	1	2812	1	chr2D.!!$R1	2811
1	TraesCS2D01G425300	chr2B	640489866	640491627	1761	True	1226.500000	2194	89.7665	1	1801	2	chr2B.!!$R1	1800
2	TraesCS2D01G425300	chr2A	680096617	680098568	1951	True	844.666667	1482	90.8830	1	2812	3	chr2A.!!$R1	2811
3	TraesCS2D01G425300	chr3D	607326566	607327361	795	False	1206.000000	1206	94.0220	1802	2600	1	chr3D.!!$F3	798
4	TraesCS2D01G425300	chr3D	115642973	115643774	801	False	1201.000000	1201	93.6960	1796	2600	1	chr3D.!!$F1	804
5	TraesCS2D01G425300	chr3D	374392362	374393155	793	False	1190.000000	1190	93.6490	1801	2600	1	chr3D.!!$F2	799
6	TraesCS2D01G425300	chr7D	561873440	561874240	800	True	1179.000000	1179	93.2010	1796	2600	1	chr7D.!!$R1	804
7	TraesCS2D01G425300	chr4D	359203509	359204304	795	True	1179.000000	1179	93.3920	1802	2600	1	chr4D.!!$R1	798
8	TraesCS2D01G425300	chr5D	213033069	213033877	808	False	1177.000000	1177	92.9980	1793	2600	1	chr5D.!!$F3	807
9	TraesCS2D01G425300	chr5D	212952135	212952942	807	False	1171.000000	1171	92.8750	1793	2600	1	chr5D.!!$F1	807
10	TraesCS2D01G425300	chr5D	213006458	213007265	807	False	1171.000000	1171	92.8750	1793	2600	1	chr5D.!!$F2	807
11	TraesCS2D01G425300	chrUn	320692200	320693002	802	True	1170.000000	1170	92.9720	1796	2600	1	chrUn.!!$R1	804
12	TraesCS2D01G425300	chr1B	65585076	65585924	848	True	985.000000	985	87.9670	1793	2627	1	chr1B.!!$R1	834

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
483	510	0.874607	GTGGACCATGTATCGGCGAC	60.875	60.0	13.76	0.58	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1844	1885	0.108329	GTGTGCTATAGGCCGTGTGT	60.108	55.0	0.0	0.0	40.92	3.72	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
21	22	3.287867	AAAGACGATGCATTGGGAGAT	57.712	42.857	18.31	0.00	0.00	2.75
36	37	1.506025	GAGATGCCCCCTTCTCTCTT	58.494	55.000	0.00	0.00	38.54	2.85
45	46	4.487804	CCCCCTTCTCTCTTCATCATAGA	58.512	47.826	0.00	0.00	0.00	1.98
55	56	7.069702	TCTCTCTTCATCATAGAAGCTGACATT	59.930	37.037	0.00	0.00	43.64	2.71
137	149	5.505173	TTTTTGCTGAGTTGAAGAAGAGG	57.495	39.130	0.00	0.00	0.00	3.69
170	182	4.340950	AGAGAATAGAAGCAGGCTACAGAC	59.659	45.833	0.00	0.00	0.00	3.51
225	237	4.487714	TTGTGAAAGAGTGAGGTGAGTT	57.512	40.909	0.00	0.00	0.00	3.01
252	264	9.975218	ATGTATCAACAAAGTAATACTCCCTTT	57.025	29.630	0.00	0.00	39.58	3.11
254	266	6.569179	TCAACAAAGTAATACTCCCTTTGC	57.431	37.500	10.37	0.00	45.58	3.68
259	271	6.214819	ACAAAGTAATACTCCCTTTGCCTAGA	59.785	38.462	10.37	0.00	45.58	2.43
269	281	5.887754	TCCCTTTGCCTAGAAATACTTGTT	58.112	37.500	0.00	0.00	0.00	2.83
273	285	6.208599	CCTTTGCCTAGAAATACTTGTTGGAA	59.791	38.462	0.00	0.00	0.00	3.53
277	289	8.189119	TGCCTAGAAATACTTGTTGGAAAAAT	57.811	30.769	0.00	0.00	0.00	1.82
278	290	9.303116	TGCCTAGAAATACTTGTTGGAAAAATA	57.697	29.630	0.00	0.00	0.00	1.40
328	340	9.691362	GAATTAAAATACGCCCAAATACATCAT	57.309	29.630	0.00	0.00	0.00	2.45
457	484	2.151202	GCAGCCGGCTATGCTATTAAA	58.849	47.619	32.30	0.00	39.38	1.52
462	489	3.502211	GCCGGCTATGCTATTAAACATGT	59.498	43.478	22.15	0.00	0.00	3.21
464	491	5.451908	CCGGCTATGCTATTAAACATGTTG	58.548	41.667	12.82	0.00	0.00	3.33
466	493	5.909054	CGGCTATGCTATTAAACATGTTGTG	59.091	40.000	12.82	2.37	0.00	3.33
480	507	1.014352	GTTGTGGACCATGTATCGGC	58.986	55.000	0.00	0.00	0.00	5.54
483	510	0.874607	GTGGACCATGTATCGGCGAC	60.875	60.000	13.76	0.58	0.00	5.19
513	540	9.865321	ATTATTGTTCATTCAATCACTTTCCAG	57.135	29.630	0.00	0.00	38.68	3.86
550	577	8.708378	TCTACAGATGGGATATAAATATGGCTG	58.292	37.037	0.00	0.00	0.00	4.85
591	618	3.251571	GACGGCCGGTATCAAATATCTC	58.748	50.000	31.76	9.08	0.00	2.75
617	644	8.341173	CCTGTTATCATAAGTTGAAGCATCTTC	58.659	37.037	0.00	0.00	38.03	2.87
736	763	2.915659	TGTTCCCGTGAGAGGCGT	60.916	61.111	0.00	0.00	0.00	5.68
806	833	9.942850	ACCCATTTCTTTTCTTTTATTGGTATG	57.057	29.630	0.00	0.00	0.00	2.39
846	874	3.040147	ACCACATAACCTTGTCGACAG	57.960	47.619	19.11	10.82	0.00	3.51
847	875	2.367567	ACCACATAACCTTGTCGACAGT	59.632	45.455	19.11	11.52	0.00	3.55
1002	1030	2.196925	CCTCTCGTCCTCCCATCGG	61.197	68.421	0.00	0.00	0.00	4.18
1029	1057	1.983972	GTGAAGCTCACACGACCTAG	58.016	55.000	10.30	0.00	46.22	3.02
1069	1097	4.191544	TCCATCAGCAGTTTTTCTATCGG	58.808	43.478	0.00	0.00	0.00	4.18
1322	1351	7.876068	TGGTTAATCAATCGTTCTATGGGATAC	59.124	37.037	0.00	0.00	0.00	2.24
1395	1424	1.811266	CACCGACAAGGCCATCGAG	60.811	63.158	21.59	14.89	46.52	4.04
1698	1739	9.912634	TCTCAATTCATTTTCCATTGTAAGAAC	57.087	29.630	0.00	0.00	31.08	3.01
1815	1856	6.293244	GCAATAAAGAAGGACAACACTAACGT	60.293	38.462	0.00	0.00	0.00	3.99
1917	1958	9.709495	CATGTGGAAATCTTTTTGGATTTTCTA	57.291	29.630	8.92	1.27	43.36	2.10
2016	2057	7.222000	AGATCTTCGAAACTAGATCCCATAC	57.778	40.000	17.33	0.00	45.05	2.39
2082	2126	4.437794	CGTGTCTATTGCACATGAATTGCT	60.438	41.667	0.00	0.00	40.86	3.91
2392	2440	7.257397	GTGAAACATCATGGCAACTTTTGGC	62.257	44.000	5.56	5.56	46.81	4.52
2488	2538	8.126074	GGTGAAAACGGATTTTTAATTTGCTTT	58.874	29.630	0.00	0.00	38.17	3.51
2537	2589	7.851387	TTAAGCCGAAAACCAAAAAGATTTT	57.149	28.000	0.00	0.00	0.00	1.82
2563	2615	5.520288	GCTGATGTCATCTGTTTATACGTGT	59.480	40.000	17.91	0.00	0.00	4.49
2576	2628	6.072948	TGTTTATACGTGTCAAAATGAGTGGG	60.073	38.462	0.00	0.00	0.00	4.61
2655	2722	9.884465	GATGCTAAAAGGTTTACATAATAGCTG	57.116	33.333	0.00	0.00	36.40	4.24
2666	2733	4.253685	ACATAATAGCTGTGCGTGAGTTT	58.746	39.130	0.00	0.00	0.00	2.66
2667	2734	5.416083	ACATAATAGCTGTGCGTGAGTTTA	58.584	37.500	0.00	0.00	0.00	2.01
2672	2739	3.338249	AGCTGTGCGTGAGTTTATTGAT	58.662	40.909	0.00	0.00	0.00	2.57
2701	2768	1.226603	GAGTCGGTCGATTCGTGGG	60.227	63.158	5.89	0.00	0.00	4.61
2725	2792	1.513622	GAAGGAGGAGACGAGGTGC	59.486	63.158	0.00	0.00	0.00	5.01
2802	2869	2.677875	CAAGGCCTTGGCTGGGAC	60.678	66.667	34.08	0.00	38.81	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	1.207791	GATGAAGAGAGAAGGGGGCA	58.792	55.000	0.00	0.00	0.00	5.36
27	28	6.919662	GTCAGCTTCTATGATGAAGAGAGAAG	59.080	42.308	8.25	5.74	44.40	2.85
74	75	9.982651	TCTTACATCACTTATTATACTTGCTCC	57.017	33.333	0.00	0.00	0.00	4.70
132	144	6.507568	TCTATTCTCTTTTCTCTCCCCTCTT	58.492	40.000	0.00	0.00	0.00	2.85
137	149	5.983540	TGCTTCTATTCTCTTTTCTCTCCC	58.016	41.667	0.00	0.00	0.00	4.30
170	182	5.220854	GGCACATGCTACAACTGGTTATTAG	60.221	44.000	3.48	0.00	41.70	1.73
210	222	7.039011	TGTTGATACATAACTCACCTCACTCTT	60.039	37.037	0.00	0.00	0.00	2.85
251	263	7.589958	TTTTCCAACAAGTATTTCTAGGCAA	57.410	32.000	0.00	0.00	0.00	4.52
252	264	7.589958	TTTTTCCAACAAGTATTTCTAGGCA	57.410	32.000	0.00	0.00	0.00	4.75
298	310	9.616156	TGTATTTGGGCGTATTTTAATTCTAGA	57.384	29.630	0.00	0.00	0.00	2.43
305	317	9.877178	AAAATGATGTATTTGGGCGTATTTTAA	57.123	25.926	0.00	0.00	38.93	1.52
335	347	8.210946	ACTCCATCCGTCTGAAAATATTTATCA	58.789	33.333	0.01	6.94	0.00	2.15
338	350	8.479689	TGTACTCCATCCGTCTGAAAATATTTA	58.520	33.333	0.01	0.00	0.00	1.40
401	428	7.851387	TGTTGGCACGTCATCTATAATTAAA	57.149	32.000	0.00	0.00	0.00	1.52
420	447	2.486982	GCTGCTGGCTATATGATGTTGG	59.513	50.000	0.00	0.00	38.06	3.77
462	489	0.461163	CGCCGATACATGGTCCACAA	60.461	55.000	0.00	0.00	0.00	3.33
464	491	0.874607	GTCGCCGATACATGGTCCAC	60.875	60.000	0.00	0.00	0.00	4.02
466	493	1.660575	CGTCGCCGATACATGGTCC	60.661	63.158	0.00	0.00	35.63	4.46
480	507	7.162546	GTGATTGAATGAACAATAATGACGTCG	59.837	37.037	11.62	0.00	40.03	5.12
483	510	8.900511	AAGTGATTGAATGAACAATAATGACG	57.099	30.769	0.00	0.00	40.03	4.35
550	577	5.233689	CCGTCGATTAATCAAGGGTAAGTTC	59.766	44.000	15.57	0.00	0.00	3.01
591	618	7.798596	AGATGCTTCAACTTATGATAACAGG	57.201	36.000	2.07	0.00	38.03	4.00
617	644	3.217626	AGGTTTTGTCAGGAGCTCTTTG	58.782	45.455	14.64	12.57	0.00	2.77
736	763	2.108168	CTACTAGCTGCTTACCCCACA	58.892	52.381	7.79	0.00	0.00	4.17
806	833	5.005107	GTGGTAATGTACGGTCGAATTTCTC	59.995	44.000	0.00	0.00	0.00	2.87
807	834	4.866486	GTGGTAATGTACGGTCGAATTTCT	59.134	41.667	0.00	0.00	0.00	2.52
870	898	1.008194	CGACGGTCGACAAGGTTGA	60.008	57.895	25.29	0.00	43.74	3.18
871	899	1.008194	TCGACGGTCGACAAGGTTG	60.008	57.895	27.66	14.89	44.82	3.77
929	957	3.927481	GAAGGGTGAGGTGGCTGGC	62.927	68.421	0.00	0.00	0.00	4.85
932	960	4.021925	GCGAAGGGTGAGGTGGCT	62.022	66.667	0.00	0.00	0.00	4.75
1023	1051	0.559699	TGGGTAGGGTAGGCTAGGTC	59.440	60.000	0.00	0.00	0.00	3.85
1029	1057	1.385489	ATGGGTGGGTAGGGTAGGC	60.385	63.158	0.00	0.00	0.00	3.93
1087	1115	4.074526	GAGGCTCCGAGCAGCACA	62.075	66.667	21.76	0.00	44.75	4.57
1243	1271	0.591741	GATCGAACGGTACTGCTCGG	60.592	60.000	23.39	8.61	32.25	4.63
1322	1351	1.539341	CGCATATATCTCGGTCAGCG	58.461	55.000	0.00	0.00	37.91	5.18
1420	1449	3.121030	CGCCACGCCCTTCTTCAG	61.121	66.667	0.00	0.00	0.00	3.02
1515	1544	2.335712	GCCGAAGTCCTTGGCCTTG	61.336	63.158	3.32	0.00	43.06	3.61
1718	1759	9.732130	ACAGCTATCTTATCTCTTTTCTTTTGT	57.268	29.630	0.00	0.00	0.00	2.83
1764	1805	4.570930	TGACATTAACAGTGCGGTAATCA	58.429	39.130	0.00	0.00	0.00	2.57
1844	1885	0.108329	GTGTGCTATAGGCCGTGTGT	60.108	55.000	0.00	0.00	40.92	3.72
1851	1892	2.859032	GCGTAGTCTGTGTGCTATAGGC	60.859	54.545	1.04	0.00	42.22	3.93
2036	2079	9.036671	CACGTCAACTTTTAACCCAAAAATAAT	57.963	29.630	0.00	0.00	35.71	1.28
2038	2081	7.545489	ACACGTCAACTTTTAACCCAAAAATA	58.455	30.769	0.00	0.00	35.71	1.40
2039	2082	6.399743	ACACGTCAACTTTTAACCCAAAAAT	58.600	32.000	0.00	0.00	35.71	1.82
2045	2089	6.368213	CAATAGACACGTCAACTTTTAACCC	58.632	40.000	0.00	0.00	0.00	4.11
2058	2102	4.672542	GCAATTCATGTGCAATAGACACGT	60.673	41.667	2.12	0.00	41.80	4.49
2082	2126	6.000840	TGGCAACTTCAGTGTAAACATCATA	58.999	36.000	0.00	0.00	37.61	2.15
2257	2302	8.623903	GCATCCAGTACTTTGATCATGAAAATA	58.376	33.333	0.00	0.00	0.00	1.40
2405	2454	6.015918	AGACCCCATGTTGATATGTTTCAAA	58.984	36.000	0.00	0.00	37.36	2.69
2406	2455	5.579047	AGACCCCATGTTGATATGTTTCAA	58.421	37.500	0.00	0.00	33.32	2.69
2452	2502	6.597832	AATCCGTTTTCACCATTAAATCCA	57.402	33.333	0.00	0.00	0.00	3.41
2537	2589	6.035975	CACGTATAAACAGATGACATCAGCAA	59.964	38.462	17.57	0.00	34.14	3.91
2563	2615	2.025037	CCTCCATCCCCACTCATTTTGA	60.025	50.000	0.00	0.00	0.00	2.69
2655	2722	5.379003	TCGAAAATCAATAAACTCACGCAC	58.621	37.500	0.00	0.00	0.00	5.34
2701	2768	2.021457	CTCGTCTCCTCCTTCCTTCTC	58.979	57.143	0.00	0.00	0.00	2.87
2725	2792	1.662044	GTCTTTGGCCTTGGTGCTG	59.338	57.895	3.32	0.00	0.00	4.41
2737	2804	2.809601	CCGGCTCCGTCGTCTTTG	60.810	66.667	7.59	0.00	37.81	2.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.