AutoCloner

Multiple sequence alignment - TraesCS2D01G581300

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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	TraesCS2D01G581300	chr2D	100.000	2869	0	0	1	2869	642988465	642991333	0.000000e+00	5299.0
1	TraesCS2D01G581300	chrUn	91.702	1639	66	24	694	2301	31599664	31601263	0.000000e+00	2209.0
2	TraesCS2D01G581300	chrUn	86.926	719	42	18	1	690	31598871	31599566	0.000000e+00	760.0
3	TraesCS2D01G581300	chrUn	88.762	614	48	12	2213	2815	31601261	31601864	0.000000e+00	732.0
4	TraesCS2D01G581300	chr2A	92.727	1375	64	15	1513	2869	767944032	767945388	0.000000e+00	1953.0
5	TraesCS2D01G581300	chr2A	92.140	827	40	9	695	1499	767943108	767943931	0.000000e+00	1144.0
6	TraesCS2D01G581300	chr2A	91.819	709	31	12	1	692	767942229	767942927	0.000000e+00	963.0
7	TraesCS2D01G581300	chr6D	87.542	1485	107	29	1004	2461	467048830	467050263	0.000000e+00	1646.0
8	TraesCS2D01G581300	chr6D	76.350	778	114	35	118	855	467047856	467048603	1.260000e-93	353.0
9	TraesCS2D01G581300	chr6D	91.781	73	2	1	2665	2733	467050272	467050344	6.540000e-17	99.0
10	TraesCS2D01G581300	chr6B	86.907	1497	121	24	1007	2487	712251575	712253012	0.000000e+00	1609.0
11	TraesCS2D01G581300	chr6B	77.820	798	99	36	92	855	712250590	712251343	3.420000e-114	422.0
12	TraesCS2D01G581300	chr6B	83.673	98	3	1	2665	2762	712253028	712253112	2.370000e-11	80.5
13	TraesCS2D01G581300	chr6A	90.080	998	70	10	1014	1997	613342683	613343665	0.000000e+00	1267.0
14	TraesCS2D01G581300	chr6A	77.835	776	85	36	118	855	613341748	613342474	1.600000e-107	399.0
15	TraesCS2D01G581300	chr6A	87.907	215	14	5	2029	2239	613343665	613343871	2.860000e-60	243.0
16	TraesCS2D01G581300	chr6A	88.430	121	3	2	2285	2401	613343882	613343995	4.990000e-28	135.0
17	TraesCS2D01G581300	chr6A	77.184	206	12	14	2665	2869	613344065	613344236	1.420000e-13	87.9
18	TraesCS2D01G581300	chr4B	81.982	444	76	4	1019	1460	22991600	22991159	9.710000e-100	374.0
19	TraesCS2D01G581300	chr4A	81.208	447	84	0	1014	1460	589878976	589879422	7.560000e-96	361.0
20	TraesCS2D01G581300	chr4D	81.264	443	81	2	1019	1460	12599711	12599270	9.780000e-95	357.0

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	TraesCS2D01G581300	chr2D	642988465	642991333	2868	False	5299.000000	5299	100.000000	1	2869	1	chr2D.!!$F1	2868
1	TraesCS2D01G581300	chrUn	31598871	31601864	2993	False	1233.666667	2209	89.130000	1	2815	3	chrUn.!!$F1	2814
2	TraesCS2D01G581300	chr2A	767942229	767945388	3159	False	1353.333333	1953	92.228667	1	2869	3	chr2A.!!$F1	2868
3	TraesCS2D01G581300	chr6D	467047856	467050344	2488	False	699.333333	1646	85.224333	118	2733	3	chr6D.!!$F1	2615
4	TraesCS2D01G581300	chr6B	712250590	712253112	2522	False	703.833333	1609	82.800000	92	2762	3	chr6B.!!$F1	2670
5	TraesCS2D01G581300	chr6A	613341748	613344236	2488	False	426.380000	1267	84.287200	118	2869	5	chr6A.!!$F1	2751

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
456	499	0.035439	TTTCCCTCCCGATGCTTGAC	60.035	55.0	0.00	0.00	0.0	3.18	F
920	1261	0.104855	TTTCGAGTGACTGCTGCTGT	59.895	50.0	12.15	12.15	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1295	1663	0.171903	CATCTCGGGCTTTGCAAAGG	59.828	55.0	34.02	20.88	36.53	3.11	R
2403	2982	0.598065	GGAACATGGCACTTGTGACC	59.402	55.0	3.97	5.83	0.00	4.02	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
86	88	4.715523	CCCAATCACACGCCCCGT	62.716	66.667	0.00	0.00	42.36	5.28
233	243	1.287739	GGTTTCCCCATCTTCATCCCA	59.712	52.381	0.00	0.00	0.00	4.37
318	328	2.203394	CCCCTGCAGTTGCTGTGT	60.203	61.111	13.81	0.00	42.66	3.72
320	330	1.228063	CCCTGCAGTTGCTGTGTCT	60.228	57.895	13.81	0.00	42.66	3.41
456	499	0.035439	TTTCCCTCCCGATGCTTGAC	60.035	55.000	0.00	0.00	0.00	3.18
535	597	4.725790	ACTAATGGAATTTTGGCAGCTC	57.274	40.909	0.00	0.00	37.87	4.09
603	667	3.224007	ATGCCGGCCCCTGTTTCTT	62.224	57.895	26.77	0.00	0.00	2.52
692	782	5.338056	CCCTCCACTGCTGTTAGTTAATACA	60.338	44.000	0.00	0.00	0.00	2.29
759	1027	0.248621	AGACGCTTTTGCTGCACAAC	60.249	50.000	0.00	0.00	44.80	3.32
772	1040	3.482786	CTGCACAACGCTTGTTCTTATC	58.517	45.455	1.37	0.00	43.23	1.75
850	1122	1.405105	TGTTGTTTGCCAGCTCTGTTC	59.595	47.619	0.00	0.00	0.00	3.18
867	1198	4.887071	TCTGTTCATAACCTTTTGCAGTGT	59.113	37.500	0.00	0.00	0.00	3.55
869	1200	5.587289	TGTTCATAACCTTTTGCAGTGTTC	58.413	37.500	0.00	0.00	0.00	3.18
920	1261	0.104855	TTTCGAGTGACTGCTGCTGT	59.895	50.000	12.15	12.15	0.00	4.40
941	1282	6.676456	GCTGTGTATTGTTATTTCCAGCAGAG	60.676	42.308	0.00	0.00	42.63	3.35
946	1287	2.301870	TGTTATTTCCAGCAGAGGTCGT	59.698	45.455	0.00	0.00	0.00	4.34
994	1335	2.393271	AATGGCTCAGAAGGACGAAG	57.607	50.000	0.00	0.00	0.00	3.79
1371	1739	2.079925	GAGTTCAGCTGGGTAAAGCAG	58.920	52.381	15.13	0.00	46.08	4.24
1531	1989	3.136626	AGTTGCCCACTACTGAGAAAAGT	59.863	43.478	0.00	0.00	31.97	2.66
1599	2082	4.517285	GGAACAGGAGATGTCAAGCATAA	58.483	43.478	0.00	0.00	43.00	1.90
1700	2183	9.860898	GAGCCATAATTTCATTAAACTCTGTTT	57.139	29.630	1.33	1.33	0.00	2.83
1859	2342	1.474077	CATTACAAGGTCAAGCTGGGC	59.526	52.381	0.00	0.00	0.00	5.36
1939	2422	2.555757	AGTGCAAGCAGATTCTTGTTCC	59.444	45.455	0.00	0.00	43.92	3.62
1972	2455	1.434622	CCACTCACAGATGCGATGGC	61.435	60.000	0.00	0.00	40.52	4.40
2011	2494	2.977914	TGGCTAGTTCTCATCTTGTGC	58.022	47.619	0.00	0.00	0.00	4.57
2021	2504	3.969312	TCTCATCTTGTGCTGGGATGATA	59.031	43.478	0.00	0.00	42.91	2.15
2049	2532	2.406130	AGCATTGATTTGTTTGGTGCG	58.594	42.857	0.00	0.00	36.32	5.34
2050	2533	2.134346	GCATTGATTTGTTTGGTGCGT	58.866	42.857	0.00	0.00	0.00	5.24
2126	2610	6.151144	ACTGTCGATACATTATGATCCGATCA	59.849	38.462	13.46	13.46	38.18	2.92
2241	2729	2.867368	TGCATTGCTTGAAACTTGCTTG	59.133	40.909	10.49	0.00	0.00	4.01
2242	2730	3.125316	GCATTGCTTGAAACTTGCTTGA	58.875	40.909	0.16	0.00	0.00	3.02
2243	2731	3.744426	GCATTGCTTGAAACTTGCTTGAT	59.256	39.130	0.16	0.00	0.00	2.57
2261	2752	3.089284	TGATATCGGATATGTCGGTGCT	58.911	45.455	14.96	0.00	0.00	4.40
2506	3085	1.172175	GCAAGAGGAAGCAAGGAAGG	58.828	55.000	0.00	0.00	0.00	3.46
2507	3086	1.271597	GCAAGAGGAAGCAAGGAAGGA	60.272	52.381	0.00	0.00	0.00	3.36
2508	3087	2.709213	CAAGAGGAAGCAAGGAAGGAG	58.291	52.381	0.00	0.00	0.00	3.69
2509	3088	1.284313	AGAGGAAGCAAGGAAGGAGG	58.716	55.000	0.00	0.00	0.00	4.30
2536	3115	2.224018	GCAAGCAAGGTTTGTCCATTCA	60.224	45.455	0.00	0.00	39.02	2.57
2577	3156	3.434453	CCTCCCTCTCACGTATTCTCTCT	60.434	52.174	0.00	0.00	0.00	3.10
2587	3170	7.594015	TCTCACGTATTCTCTCTTTGTGTTTAC	59.406	37.037	0.00	0.00	0.00	2.01
2590	3173	8.004344	CACGTATTCTCTCTTTGTGTTTACTTG	58.996	37.037	0.00	0.00	0.00	3.16
2595	3178	6.349300	TCTCTCTTTGTGTTTACTTGCTCTT	58.651	36.000	0.00	0.00	0.00	2.85
2598	3181	8.500753	TCTCTTTGTGTTTACTTGCTCTTAAA	57.499	30.769	0.00	0.00	0.00	1.52
2611	3194	8.870075	ACTTGCTCTTAAAAATTATCTCACCT	57.130	30.769	0.00	0.00	0.00	4.00
2621	3204	3.769739	TTATCTCACCTGCTGTGTTGT	57.230	42.857	6.80	0.00	45.61	3.32
2653	3238	9.111613	GCAGTATATCTACCTACCTGTATACAG	57.888	40.741	23.58	23.58	43.40	2.74
2764	3353	1.803555	GCTTCTGCCTCTGTTTCTCAC	59.196	52.381	0.00	0.00	0.00	3.51
2783	3372	2.682155	CCTGCTTCTTCTCAGGTACC	57.318	55.000	2.73	2.73	43.66	3.34
2799	3388	5.063204	CAGGTACCACTCTTCACAATCAAA	58.937	41.667	15.94	0.00	0.00	2.69
2801	3390	6.207417	CAGGTACCACTCTTCACAATCAAATT	59.793	38.462	15.94	0.00	0.00	1.82
2827	3425	4.829968	TCATCTTCTCCTCTTGCTTTCTG	58.170	43.478	0.00	0.00	0.00	3.02
2828	3426	3.051081	TCTTCTCCTCTTGCTTTCTGC	57.949	47.619	0.00	0.00	43.25	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
233	243	6.018180	GCGGGATTTCTATTGAACTTAATCGT	60.018	38.462	0.00	0.00	31.02	3.73
318	328	0.468226	AACAAGCCGTTCCTCACAGA	59.532	50.000	0.00	0.00	29.27	3.41
320	330	1.876416	GCTAACAAGCCGTTCCTCACA	60.876	52.381	0.00	0.00	39.14	3.58
429	468	3.128764	GCATCGGGAGGGAAAGTTAAAAG	59.871	47.826	0.00	0.00	0.00	2.27
456	499	3.016736	CACCCCAAATGCAACTACCTAG	58.983	50.000	0.00	0.00	0.00	3.02
551	613	1.630878	AGGATTTCCTCGAACAAGCCT	59.369	47.619	2.61	2.61	44.77	4.58
737	1005	0.110192	GTGCAGCAAAAGCGTCTACC	60.110	55.000	0.00	0.00	33.85	3.18
759	1027	4.319333	GCATCATCTGGATAAGAACAAGCG	60.319	45.833	0.00	0.00	38.79	4.68
772	1040	4.096190	ACATCTTAAGGGCATCATCTGG	57.904	45.455	1.85	0.00	0.00	3.86
850	1122	6.449698	AGAATGAACACTGCAAAAGGTTATG	58.550	36.000	0.00	0.00	0.00	1.90
920	1261	5.815581	ACCTCTGCTGGAAATAACAATACA	58.184	37.500	0.00	0.00	0.00	2.29
994	1335	6.719365	CCTGTTTTTCGTCCTTCATATCATC	58.281	40.000	0.00	0.00	0.00	2.92
1295	1663	0.171903	CATCTCGGGCTTTGCAAAGG	59.828	55.000	34.02	20.88	36.53	3.11
1371	1739	0.905357	CATCATACCCCGGATCTCCC	59.095	60.000	0.73	0.00	0.00	4.30
1492	1863	2.945008	CAACTGGGCATACAGGTACATG	59.055	50.000	5.87	5.87	42.75	3.21
1499	1870	1.001020	TGGGCAACTGGGCATACAG	60.001	57.895	1.32	1.32	45.66	2.74
1531	1989	4.924305	AGACAAGCAGAAAGATTTGCAA	57.076	36.364	0.00	0.00	42.67	4.08
1599	2082	8.258007	ACAGCATCATCATCAAAATTCTCAAAT	58.742	29.630	0.00	0.00	0.00	2.32
1700	2183	9.664332	TCCAATTGATTCTGAAACAAAAAGAAA	57.336	25.926	15.55	0.17	33.86	2.52
1859	2342	4.496670	GGAACCCATCAGTCGTCG	57.503	61.111	0.00	0.00	0.00	5.12
1972	2455	5.240891	AGCCAATGGATTATCACTATCACG	58.759	41.667	2.05	0.00	0.00	4.35
2011	2494	8.853077	TCAATGCTTTATTACTATCATCCCAG	57.147	34.615	0.00	0.00	0.00	4.45
2021	2504	9.206870	CACCAAACAAATCAATGCTTTATTACT	57.793	29.630	0.00	0.00	0.00	2.24
2049	2532	1.014564	GCCACAACTAGAGCACGGAC	61.015	60.000	0.00	0.00	0.00	4.79
2050	2533	1.292223	GCCACAACTAGAGCACGGA	59.708	57.895	0.00	0.00	0.00	4.69
2126	2610	1.071699	ACACCAAGCGTACCATCAACT	59.928	47.619	0.00	0.00	0.00	3.16
2241	2729	3.696898	GAGCACCGACATATCCGATATC	58.303	50.000	0.00	0.00	0.00	1.63
2242	2730	2.097629	CGAGCACCGACATATCCGATAT	59.902	50.000	0.00	0.00	41.76	1.63
2243	2731	1.467342	CGAGCACCGACATATCCGATA	59.533	52.381	0.00	0.00	41.76	2.92
2261	2752	1.901948	AGACAGGACTGAACCGCGA	60.902	57.895	8.23	0.00	34.73	5.87
2403	2982	0.598065	GGAACATGGCACTTGTGACC	59.402	55.000	3.97	5.83	0.00	4.02
2506	3085	2.718073	CCTTGCTTGCCATGGCCTC	61.718	63.158	33.44	21.40	41.09	4.70
2507	3086	2.682494	CCTTGCTTGCCATGGCCT	60.682	61.111	33.44	0.00	41.09	5.19
2508	3087	2.115734	AAACCTTGCTTGCCATGGCC	62.116	55.000	33.44	18.85	41.31	5.36
2509	3088	0.952010	CAAACCTTGCTTGCCATGGC	60.952	55.000	30.54	30.54	41.31	4.40
2536	3115	1.212935	GGTTCAGGTGAGGCATACCAT	59.787	52.381	11.93	0.00	40.74	3.55
2540	3119	1.204146	GGAGGTTCAGGTGAGGCATA	58.796	55.000	0.00	0.00	0.00	3.14
2587	3170	7.699812	GCAGGTGAGATAATTTTTAAGAGCAAG	59.300	37.037	0.00	0.00	0.00	4.01
2590	3173	7.148171	ACAGCAGGTGAGATAATTTTTAAGAGC	60.148	37.037	6.61	0.00	0.00	4.09
2621	3204	8.391699	ACAGGTAGGTAGATATACTGCTGATAA	58.608	37.037	0.00	0.00	0.00	1.75
2628	3211	9.111613	GCTGTATACAGGTAGGTAGATATACTG	57.888	40.741	29.45	3.77	43.94	2.74
2653	3238	1.210478	ACCTCTGGTGATGTGTATGGC	59.790	52.381	0.00	0.00	32.98	4.40
2783	3372	9.125906	GATGAAGAAATTTGATTGTGAAGAGTG	57.874	33.333	0.00	0.00	0.00	3.51
2799	3388	6.064735	AGCAAGAGGAGAAGATGAAGAAAT	57.935	37.500	0.00	0.00	0.00	2.17
2801	3390	5.495926	AAGCAAGAGGAGAAGATGAAGAA	57.504	39.130	0.00	0.00	0.00	2.52
2827	3425	4.342862	TCTTATCCCAGCAAGAGTATGC	57.657	45.455	0.00	0.00	46.78	3.14
2828	3426	6.204301	CACAATCTTATCCCAGCAAGAGTATG	59.796	42.308	0.00	0.00	34.43	2.39
2829	3427	6.126652	ACACAATCTTATCCCAGCAAGAGTAT	60.127	38.462	0.00	0.00	34.43	2.12
2830	3428	5.189736	ACACAATCTTATCCCAGCAAGAGTA	59.810	40.000	0.00	0.00	34.43	2.59
2834	3432	4.264253	TGACACAATCTTATCCCAGCAAG	58.736	43.478	0.00	0.00	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.