AutoCloner

Multiple sequence alignment - TraesCS2B01G191300

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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	TraesCS2B01G191300	chr2B	100.000	3535	0	0	1	3535	166613414	166609880	0.000000e+00	6529.0
1	TraesCS2B01G191300	chr2A	94.423	2851	87	15	721	3533	117404184	117401368	0.000000e+00	4318.0
2	TraesCS2B01G191300	chr2D	95.381	2165	76	9	721	2867	115959552	115957394	0.000000e+00	3422.0
3	TraesCS2B01G191300	chr2D	92.340	718	33	6	1	718	56586056	56586751	0.000000e+00	1002.0
4	TraesCS2B01G191300	chr2D	85.069	288	16	8	3270	3535	115957401	115957119	5.820000e-68	268.0
5	TraesCS2B01G191300	chr4A	93.793	725	36	6	1	725	618557830	618558545	0.000000e+00	1081.0
6	TraesCS2B01G191300	chr3A	93.305	717	42	4	1	717	646858234	646858944	0.000000e+00	1053.0
7	TraesCS2B01G191300	chr6B	92.758	718	41	5	1	718	685975702	685974996	0.000000e+00	1027.0
8	TraesCS2B01G191300	chr6B	91.586	618	46	5	1	618	618326962	618327573	0.000000e+00	848.0
9	TraesCS2B01G191300	chr6B	90.675	622	49	7	1	621	618138977	618139590	0.000000e+00	819.0
10	TraesCS2B01G191300	chr6B	83.668	398	60	4	1185	1581	679365055	679365448	1.550000e-98	370.0
11	TraesCS2B01G191300	chr5D	92.094	721	52	4	1	721	487947553	487948268	0.000000e+00	1011.0
12	TraesCS2B01G191300	chr5A	93.209	589	35	3	132	720	582914704	582915287	0.000000e+00	861.0
13	TraesCS2B01G191300	chr4B	90.758	422	33	5	298	719	4553843	4553428	3.080000e-155	558.0
14	TraesCS2B01G191300	chr5B	78.099	726	139	16	1	720	710682822	710682111	3.240000e-120	442.0
15	TraesCS2B01G191300	chr5B	84.404	109	15	2	1187	1294	607272799	607272906	4.830000e-19	106.0
16	TraesCS2B01G191300	chr3B	84.383	397	59	3	1185	1581	467068558	467068165	1.540000e-103	387.0
17	TraesCS2B01G191300	chr7A	86.707	331	42	2	1185	1515	64595519	64595191	2.010000e-97	366.0
18	TraesCS2B01G191300	chr6A	86.707	331	42	2	1185	1515	580187120	580187448	2.010000e-97	366.0
19	TraesCS2B01G191300	chr1B	83.123	397	64	3	1185	1581	15690218	15690611	3.360000e-95	359.0
20	TraesCS2B01G191300	chr7B	94.231	52	1	2	666	716	703708314	703708364	1.050000e-10	78.7

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	TraesCS2B01G191300	chr2B	166609880	166613414	3534	True	6529	6529	100.000	1	3535	1	chr2B.!!$R1	3534
1	TraesCS2B01G191300	chr2A	117401368	117404184	2816	True	4318	4318	94.423	721	3533	1	chr2A.!!$R1	2812
2	TraesCS2B01G191300	chr2D	115957119	115959552	2433	True	1845	3422	90.225	721	3535	2	chr2D.!!$R1	2814
3	TraesCS2B01G191300	chr2D	56586056	56586751	695	False	1002	1002	92.340	1	718	1	chr2D.!!$F1	717
4	TraesCS2B01G191300	chr4A	618557830	618558545	715	False	1081	1081	93.793	1	725	1	chr4A.!!$F1	724
5	TraesCS2B01G191300	chr3A	646858234	646858944	710	False	1053	1053	93.305	1	717	1	chr3A.!!$F1	716
6	TraesCS2B01G191300	chr6B	685974996	685975702	706	True	1027	1027	92.758	1	718	1	chr6B.!!$R1	717
7	TraesCS2B01G191300	chr6B	618326962	618327573	611	False	848	848	91.586	1	618	1	chr6B.!!$F2	617
8	TraesCS2B01G191300	chr6B	618138977	618139590	613	False	819	819	90.675	1	621	1	chr6B.!!$F1	620
9	TraesCS2B01G191300	chr5D	487947553	487948268	715	False	1011	1011	92.094	1	721	1	chr5D.!!$F1	720
10	TraesCS2B01G191300	chr5A	582914704	582915287	583	False	861	861	93.209	132	720	1	chr5A.!!$F1	588
11	TraesCS2B01G191300	chr5B	710682111	710682822	711	True	442	442	78.099	1	720	1	chr5B.!!$R1	719

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
638	640	0.044244	CCCCACCCTCCCTTTCTCTA	59.956	60.0	0.0	0.0	0.0	2.43	F
1682	1694	1.166531	GCACTGACTGGAAGCCGTTT	61.167	55.0	0.0	0.0	37.6	3.60	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1859	1871	0.619543	TTTTACCTCTAGGCGGCCCT	60.620	55.0	17.02	5.78	45.61	5.19	R
3322	3353	0.317938	GCCAGTAGATAGTCCACGCG	60.318	60.0	3.53	3.53	0.00	6.01	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
23	24	3.449737	CCTTGAATTTGCAGGTGATGGAT	59.550	43.478	0.00	0.00	0.00	3.41
33	34	3.438781	GCAGGTGATGGATAAACGAACAA	59.561	43.478	0.00	0.00	0.00	2.83
69	70	4.978083	CAAGCCTATGACTTGCAAATCT	57.022	40.909	9.58	0.00	38.23	2.40
71	72	3.960571	AGCCTATGACTTGCAAATCTGT	58.039	40.909	9.58	0.00	0.00	3.41
115	116	1.937546	GCCAATTGACCCCTTCGCAG	61.938	60.000	7.12	0.00	0.00	5.18
118	119	2.463589	AATTGACCCCTTCGCAGCGA	62.464	55.000	15.11	15.11	0.00	4.93
299	300	3.196207	AATGCCACCACCTGCGTCT	62.196	57.895	0.00	0.00	0.00	4.18
393	394	1.515521	CCAACAAACCTCGCTCCACC	61.516	60.000	0.00	0.00	0.00	4.61
573	574	4.695455	CGAGATTGGAGTACCATGTTGTTT	59.305	41.667	0.00	0.00	46.34	2.83
638	640	0.044244	CCCCACCCTCCCTTTCTCTA	59.956	60.000	0.00	0.00	0.00	2.43
654	656	8.755977	CCCTTTCTCTACCTTGTAAATGTACTA	58.244	37.037	0.00	0.00	0.00	1.82
712	714	3.849953	GCCGTAGCGCCGTCAAAG	61.850	66.667	2.29	0.00	0.00	2.77
800	807	8.434392	AGTAAATAAATCGCTGTAAATAGGGGA	58.566	33.333	0.00	0.00	0.00	4.81
804	811	4.543590	ATCGCTGTAAATAGGGGAGATG	57.456	45.455	0.00	0.00	0.00	2.90
996	1008	2.203788	TCGCTGACTTCCCCCACT	60.204	61.111	0.00	0.00	0.00	4.00
1073	1085	4.933064	CGGTCGCTGGAGATCGCC	62.933	72.222	8.81	8.81	37.96	5.54
1682	1694	1.166531	GCACTGACTGGAAGCCGTTT	61.167	55.000	0.00	0.00	37.60	3.60
2376	2388	3.268023	AGCTGGTAATCTGTTGTAGCC	57.732	47.619	0.00	0.00	0.00	3.93
2444	2458	6.488006	CCAGATTAGTTTGGGGATTCATAGTG	59.512	42.308	0.00	0.00	0.00	2.74
2562	2576	2.996249	TTTGCAAGGCCATTGTTTGA	57.004	40.000	5.01	0.00	41.29	2.69
2604	2618	6.822667	TGATTCTGTTTGCACTGTTCATAT	57.177	33.333	0.00	0.00	0.00	1.78
2619	2633	9.546909	CACTGTTCATATTACACAAAGTTGATC	57.453	33.333	0.00	0.00	0.00	2.92
2713	2727	6.183360	CCAGCCTTATTGTTGTCATGATCATT	60.183	38.462	5.16	0.00	0.00	2.57
2869	2892	7.901874	TTTTTGTAAAACTGTGAAGCGTATC	57.098	32.000	0.00	0.00	0.00	2.24
2876	2899	3.937814	ACTGTGAAGCGTATCCAAATGA	58.062	40.909	0.00	0.00	0.00	2.57
2898	2921	1.647084	GTTGGTCACGTGGAACAGC	59.353	57.895	17.00	9.67	45.79	4.40
2941	2964	1.068194	GCTCGTAGGTGGCTATAGCAG	60.068	57.143	25.53	12.70	44.36	4.24
2955	2981	6.371548	TGGCTATAGCAGAAAAAGTAACAGTG	59.628	38.462	25.53	0.00	44.36	3.66
2964	2990	7.113544	GCAGAAAAAGTAACAGTGACTAAATGC	59.886	37.037	0.00	0.00	0.00	3.56
2974	3000	3.503748	AGTGACTAAATGCCAGTTTGCTC	59.496	43.478	0.00	0.00	0.00	4.26
3020	3046	3.799432	ACACTTGGTGGGCTTACAATA	57.201	42.857	2.75	0.00	37.94	1.90
3021	3047	4.316025	ACACTTGGTGGGCTTACAATAT	57.684	40.909	2.75	0.00	37.94	1.28
3022	3048	4.016444	ACACTTGGTGGGCTTACAATATG	58.984	43.478	2.75	0.00	37.94	1.78
3023	3049	3.023832	ACTTGGTGGGCTTACAATATGC	58.976	45.455	0.00	0.00	0.00	3.14
3024	3050	3.290710	CTTGGTGGGCTTACAATATGCT	58.709	45.455	0.00	0.00	0.00	3.79
3025	3051	3.380471	TGGTGGGCTTACAATATGCTT	57.620	42.857	0.00	0.00	0.00	3.91
3026	3052	3.707316	TGGTGGGCTTACAATATGCTTT	58.293	40.909	0.00	0.00	0.00	3.51
3027	3053	3.699038	TGGTGGGCTTACAATATGCTTTC	59.301	43.478	0.00	0.00	0.00	2.62
3028	3054	3.954258	GGTGGGCTTACAATATGCTTTCT	59.046	43.478	0.00	0.00	0.00	2.52
3029	3055	5.130350	GGTGGGCTTACAATATGCTTTCTA	58.870	41.667	0.00	0.00	0.00	2.10
3030	3056	5.008712	GGTGGGCTTACAATATGCTTTCTAC	59.991	44.000	0.00	0.00	0.00	2.59
3031	3057	5.588648	GTGGGCTTACAATATGCTTTCTACA	59.411	40.000	0.00	0.00	0.00	2.74
3032	3058	6.094881	GTGGGCTTACAATATGCTTTCTACAA	59.905	38.462	0.00	0.00	0.00	2.41
3033	3059	6.661377	TGGGCTTACAATATGCTTTCTACAAA	59.339	34.615	0.00	0.00	0.00	2.83
3086	3112	8.132995	CAGTCAATGAGCTGCATTTTATAATCA	58.867	33.333	1.02	0.00	44.68	2.57
3121	3147	6.347079	GCTGTAAGTTGTGTTTTCGTATGCTA	60.347	38.462	0.00	0.00	35.30	3.49
3250	3276	7.392953	TGGTAATTTGCAGAGATGTATTGAACA	59.607	33.333	0.00	0.00	43.86	3.18
3251	3277	7.698130	GGTAATTTGCAGAGATGTATTGAACAC	59.302	37.037	0.00	0.00	42.09	3.32
3252	3278	6.822667	ATTTGCAGAGATGTATTGAACACA	57.177	33.333	0.00	0.00	42.09	3.72
3258	3289	6.365839	CAGAGATGTATTGAACACACAACAC	58.634	40.000	0.00	0.00	42.09	3.32
3261	3292	6.671190	AGATGTATTGAACACACAACACATG	58.329	36.000	9.48	0.00	44.37	3.21
3262	3293	5.826601	TGTATTGAACACACAACACATGT	57.173	34.783	0.00	0.00	36.36	3.21
3279	3310	3.181487	ACATGTTTGTCCTGAAACTGTGC	60.181	43.478	0.00	0.00	36.86	4.57
3322	3353	5.406780	GTGTGGTTCATCATATCCTCGAATC	59.593	44.000	0.00	0.00	0.00	2.52
3410	3441	5.358160	CCCTTTTGTTTCAGATATCTGGACC	59.642	44.000	28.30	16.26	43.91	4.46
3440	3471	2.462456	TTCTCTGGTGACATCAGTGC	57.538	50.000	15.31	0.00	41.51	4.40
3442	3473	1.693606	TCTCTGGTGACATCAGTGCAA	59.306	47.619	15.31	0.00	41.51	4.08
3461	3514	3.308323	GCAACTGAATAAGAAGAGCGAGG	59.692	47.826	0.00	0.00	0.00	4.63
3482	3535	3.244457	GGGGATTGGTTTAGGGACTATCG	60.244	52.174	0.00	0.00	42.38	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	1.067635	GGCTTGCCATCAAAACGTCAT	60.068	47.619	6.79	0.00	0.00	3.06
69	70	3.072330	TGATCCAAACAGCCTTGTAGACA	59.928	43.478	0.00	0.00	36.23	3.41
71	72	4.072131	GTTGATCCAAACAGCCTTGTAGA	58.928	43.478	0.00	0.00	36.23	2.59
115	116	3.487544	GCATAGTTCTTCCAAATGGTCGC	60.488	47.826	0.00	0.00	36.34	5.19
118	119	3.763897	GGTGCATAGTTCTTCCAAATGGT	59.236	43.478	0.00	0.00	36.34	3.55
193	194	4.142381	CCCCCTTTTGAATCGTCTTTCATC	60.142	45.833	0.00	0.00	35.64	2.92
195	196	3.153919	CCCCCTTTTGAATCGTCTTTCA	58.846	45.455	0.00	0.00	33.89	2.69
254	255	4.651503	GGAGGAGGTGAGTGATTGATTCTA	59.348	45.833	0.00	0.00	0.00	2.10
299	300	6.723298	TTGAATTTAGCTCTTCCCAAAACA	57.277	33.333	0.00	0.00	0.00	2.83
573	574	9.588096	TTAAGCTACCATCTCATAGATAAGTGA	57.412	33.333	0.00	0.00	32.12	3.41
590	591	8.718102	TGAGAGTACAAATCAATTAAGCTACC	57.282	34.615	0.00	0.00	0.00	3.18
623	625	2.157989	ACAAGGTAGAGAAAGGGAGGGT	60.158	50.000	0.00	0.00	0.00	4.34
624	626	2.552367	ACAAGGTAGAGAAAGGGAGGG	58.448	52.381	0.00	0.00	0.00	4.30
625	627	5.757099	TTTACAAGGTAGAGAAAGGGAGG	57.243	43.478	0.00	0.00	0.00	4.30
626	628	6.712276	ACATTTACAAGGTAGAGAAAGGGAG	58.288	40.000	0.00	0.00	0.00	4.30
664	666	3.429410	GCCAGCCTGAACCATTTCATTAC	60.429	47.826	0.00	0.00	41.05	1.89
746	748	9.961266	CGATTTACAAAGATTACATTCGTAACA	57.039	29.630	0.00	0.00	40.35	2.41
832	842	5.246429	CCCTCTCTGTTTATATAGACCACCC	59.754	48.000	1.24	0.00	0.00	4.61
1226	1238	1.838846	GAGGATGGCGAGGGGATCA	60.839	63.158	0.00	0.00	0.00	2.92
1606	1618	0.981277	ACCCCAGGCGCAGTAGTAAT	60.981	55.000	10.83	0.00	0.00	1.89
1857	1869	2.525284	TTACCTCTAGGCGGCCCTGT	62.525	60.000	17.02	8.45	42.90	4.00
1858	1870	1.335132	TTTACCTCTAGGCGGCCCTG	61.335	60.000	17.02	9.05	42.90	4.45
1859	1871	0.619543	TTTTACCTCTAGGCGGCCCT	60.620	55.000	17.02	5.78	45.61	5.19
1964	1976	0.899717	TCCAATCAGGCCCAAGCAAC	60.900	55.000	0.00	0.00	42.56	4.17
2547	2561	6.147656	GGAGTTAATTTCAAACAATGGCCTTG	59.852	38.462	3.32	8.86	40.90	3.61
2562	2576	8.195436	CAGAATCATGCAATCAGGAGTTAATTT	58.805	33.333	0.00	0.00	36.37	1.82
2604	2618	6.207221	AGCATCACATGATCAACTTTGTGTAA	59.793	34.615	20.92	8.42	31.21	2.41
2619	2633	3.061563	CCGCAAATCAAAAGCATCACATG	59.938	43.478	0.00	0.00	0.00	3.21
2654	2668	6.878923	TGAATAGGGATCACCATTTAATAGCG	59.121	38.462	0.00	0.00	43.89	4.26
2881	2904	0.753867	TAGCTGTTCCACGTGACCAA	59.246	50.000	19.30	3.64	0.00	3.67
2941	2964	7.422399	TGGCATTTAGTCACTGTTACTTTTTC	58.578	34.615	0.00	0.00	0.00	2.29
2955	2981	3.084786	AGGAGCAAACTGGCATTTAGTC	58.915	45.455	0.00	0.00	35.83	2.59
2964	2990	3.826157	TCCACATAAAAGGAGCAAACTGG	59.174	43.478	0.00	0.00	0.00	4.00
2974	3000	6.238648	ACAGAACCTAAGTCCACATAAAAGG	58.761	40.000	0.00	0.00	0.00	3.11
3020	3046	7.605449	AGCACAATACATTTTGTAGAAAGCAT	58.395	30.769	0.00	0.00	37.73	3.79
3021	3047	6.980593	AGCACAATACATTTTGTAGAAAGCA	58.019	32.000	0.00	0.00	37.73	3.91
3022	3048	8.964420	TTAGCACAATACATTTTGTAGAAAGC	57.036	30.769	0.00	0.00	37.73	3.51
3086	3112	7.568199	AACACAACTTACAGCTAACTTGAAT	57.432	32.000	0.00	0.00	0.00	2.57
3142	3168	9.490379	CTATGGACCCTTTTTATGATGTACTAC	57.510	37.037	0.00	0.00	0.00	2.73
3145	3171	8.837389	GTTCTATGGACCCTTTTTATGATGTAC	58.163	37.037	0.00	0.00	0.00	2.90
3149	3175	6.062095	CGGTTCTATGGACCCTTTTTATGAT	58.938	40.000	0.00	0.00	0.00	2.45
3159	3185	5.796424	TTATTAGACGGTTCTATGGACCC	57.204	43.478	0.00	0.00	34.15	4.46
3233	3259	5.049474	TGTTGTGTGTTCAATACATCTCTGC	60.049	40.000	0.00	0.00	39.39	4.26
3250	3276	3.351740	TCAGGACAAACATGTGTTGTGT	58.648	40.909	22.58	14.68	38.99	3.72
3251	3277	4.368874	TTCAGGACAAACATGTGTTGTG	57.631	40.909	22.58	12.20	38.99	3.33
3252	3278	4.462483	AGTTTCAGGACAAACATGTGTTGT	59.538	37.500	19.56	19.56	41.53	3.32
3258	3289	3.374745	GCACAGTTTCAGGACAAACATG	58.625	45.455	0.00	0.00	38.53	3.21
3261	3292	1.748493	TGGCACAGTTTCAGGACAAAC	59.252	47.619	0.00	0.00	36.64	2.93
3262	3293	1.748493	GTGGCACAGTTTCAGGACAAA	59.252	47.619	13.86	0.00	41.80	2.83
3279	3310	1.912043	ACAGAGAAAGGGATCCAGTGG	59.088	52.381	15.23	1.40	0.00	4.00
3322	3353	0.317938	GCCAGTAGATAGTCCACGCG	60.318	60.000	3.53	3.53	0.00	6.01
3440	3471	3.868077	CCCTCGCTCTTCTTATTCAGTTG	59.132	47.826	0.00	0.00	0.00	3.16
3442	3473	2.432510	CCCCTCGCTCTTCTTATTCAGT	59.567	50.000	0.00	0.00	0.00	3.41
3461	3514	3.244457	CCGATAGTCCCTAAACCAATCCC	60.244	52.174	0.00	0.00	0.00	3.85
3482	3535	3.253188	TGTTTTGCAAGCTACTGATGTCC	59.747	43.478	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.