AutoCloner

Multiple sequence alignment - TraesCS3B01G462500

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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	TraesCS3B01G462500	chr3B	100.000	4299	0	0	1	4299	705545170	705549468	0.000000e+00	7939.0
1	TraesCS3B01G462500	chr3B	90.608	905	75	7	2211	3110	705564240	705565139	0.000000e+00	1192.0
2	TraesCS3B01G462500	chr3B	81.711	935	145	16	1560	2478	705566540	705567464	0.000000e+00	756.0
3	TraesCS3B01G462500	chr3B	82.258	620	94	10	1560	2167	705563625	705564240	4.930000e-144	521.0
4	TraesCS3B01G462500	chr3B	79.245	477	80	13	2649	3110	705154490	705154962	8.970000e-82	315.0
5	TraesCS3B01G462500	chr3B	78.664	464	81	13	2642	3092	705005447	705005905	4.200000e-75	292.0
6	TraesCS3B01G462500	chr3B	87.879	231	27	1	2587	2817	705567519	705567748	1.970000e-68	270.0
7	TraesCS3B01G462500	chr3B	93.750	48	3	0	3358	3405	74456325	74456278	5.960000e-09	73.1
8	TraesCS3B01G462500	chr3B	88.333	60	4	2	2483	2542	399974488	399974544	7.710000e-08	69.4
9	TraesCS3B01G462500	chr3A	94.031	3535	182	17	776	4299	669523662	669527178	0.000000e+00	5332.0
10	TraesCS3B01G462500	chr3A	81.537	937	144	19	1560	2478	669566315	669567240	0.000000e+00	745.0
11	TraesCS3B01G462500	chr3A	86.067	689	72	7	1	685	669522852	669523520	0.000000e+00	719.0
12	TraesCS3B01G462500	chr3A	89.180	573	57	4	2541	3110	669564339	669564909	0.000000e+00	710.0
13	TraesCS3B01G462500	chr3A	83.110	746	103	10	1553	2282	669563485	669564223	0.000000e+00	658.0
14	TraesCS3B01G462500	chr3A	86.580	231	30	1	2587	2817	669567295	669567524	1.980000e-63	254.0
15	TraesCS3B01G462500	chr3D	94.333	1394	60	9	776	2156	533668255	533669642	0.000000e+00	2119.0
16	TraesCS3B01G462500	chr3D	93.913	1150	59	8	2217	3362	533669641	533670783	0.000000e+00	1725.0
17	TraesCS3B01G462500	chr3D	94.463	596	20	4	3394	3988	533671046	533671629	0.000000e+00	905.0
18	TraesCS3B01G462500	chr3D	82.963	945	123	23	1560	2478	533673609	533674541	0.000000e+00	819.0
19	TraesCS3B01G462500	chr3D	90.925	573	46	3	2541	3110	533674538	533675107	0.000000e+00	765.0
20	TraesCS3B01G462500	chr3D	81.838	936	140	21	1560	2478	533676509	533677431	0.000000e+00	760.0
21	TraesCS3B01G462500	chr3D	90.717	474	35	6	1	467	533667432	533667903	1.310000e-174	623.0
22	TraesCS3B01G462500	chr3D	92.661	327	21	3	3975	4299	533671644	533671969	6.510000e-128	468.0
23	TraesCS3B01G462500	chr3D	79.192	495	83	14	2632	3110	532956683	532957173	4.150000e-85	326.0
24	TraesCS3B01G462500	chr3D	78.119	521	91	16	2586	3092	532776989	532777500	4.180000e-80	309.0
25	TraesCS3B01G462500	chr3D	75.929	565	102	28	1652	2201	532955830	532956375	4.260000e-65	259.0
26	TraesCS3B01G462500	chr2A	87.379	206	22	3	486	688	42185562	42185358	2.580000e-57	233.0
27	TraesCS3B01G462500	chr2D	86.772	189	22	2	479	665	384256062	384256249	1.570000e-49	207.0
28	TraesCS3B01G462500	chr7D	85.149	202	28	1	486	685	191547124	191547325	5.640000e-49	206.0
29	TraesCS3B01G462500	chr7D	92.308	52	1	2	3196	3247	351576980	351577028	2.140000e-08	71.3
30	TraesCS3B01G462500	chr6A	85.149	202	27	2	486	685	262056494	262056694	2.030000e-48	204.0
31	TraesCS3B01G462500	chr6A	84.080	201	31	1	488	687	462228071	462227871	4.390000e-45	193.0
32	TraesCS3B01G462500	chr6A	77.812	320	52	15	3198	3510	535177667	535177360	3.420000e-41	180.0
33	TraesCS3B01G462500	chr6A	82.812	64	8	3	713	773	162441764	162441827	2.000000e-03	54.7
34	TraesCS3B01G462500	chr4A	83.902	205	32	1	485	688	110088263	110088059	1.220000e-45	195.0
35	TraesCS3B01G462500	chr4A	83.495	206	32	2	485	688	110087735	110087530	1.580000e-44	191.0
36	TraesCS3B01G462500	chr2B	83.654	208	28	4	485	688	672525572	672525777	1.580000e-44	191.0
37	TraesCS3B01G462500	chr5A	83.415	205	32	1	486	688	484562458	484562662	5.680000e-44	189.0
38	TraesCS3B01G462500	chr6B	76.418	335	65	11	3198	3527	581287953	581287628	7.390000e-38	169.0
39	TraesCS3B01G462500	chr5B	76.214	206	33	9	3202	3403	489507248	489507441	1.270000e-15	95.3

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	TraesCS3B01G462500	chr3B	705545170	705549468	4298	False	7939.00	7939	100.000000	1	4299	1	chr3B.!!$F4	4298
1	TraesCS3B01G462500	chr3B	705563625	705567748	4123	False	684.75	1192	85.614000	1560	3110	4	chr3B.!!$F5	1550
2	TraesCS3B01G462500	chr3A	669522852	669527178	4326	False	3025.50	5332	90.049000	1	4299	2	chr3A.!!$F1	4298
3	TraesCS3B01G462500	chr3A	669563485	669567524	4039	False	591.75	745	85.101750	1553	3110	4	chr3A.!!$F2	1557
4	TraesCS3B01G462500	chr3D	533667432	533677431	9999	False	1023.00	2119	90.226625	1	4299	8	chr3D.!!$F3	4298
5	TraesCS3B01G462500	chr3D	532776989	532777500	511	False	309.00	309	78.119000	2586	3092	1	chr3D.!!$F1	506
6	TraesCS3B01G462500	chr3D	532955830	532957173	1343	False	292.50	326	77.560500	1652	3110	2	chr3D.!!$F2	1458

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	Hairpin	End Stability	Orientation
145	147	0.032403	CATTGTATGCCATTGCCGGG	59.968	55.000	2.18	36.33	5.73	F
509	517	0.890683	GCATGGCCAATGTATAGCCC	59.109	55.000	10.96	46.55	5.19	F
803	939	1.067071	ACGCTTCCCTCGTCTAAAAGG	60.067	52.381	0.00	34.84	3.11	F
2666	7424	0.620556	CTTTCCAGGGCAAGCTCCTA	59.379	55.000	0.00	32.49	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1821	1985	0.318955	GCAAGTGCGGCTCAATTTGT	60.319	50.000	0.00	29.43	2.83	R
2413	2595	3.444703	ACTGAGACTCAACAGTGTGAC	57.555	47.619	6.61	44.18	3.67	R
2705	7463	0.464036	GGGCGATCATGGTGTGTAGA	59.536	55.000	0.00	0.00	2.59	R
3979	8802	0.240945	CCATCCGCAGTTTCCACAAC	59.759	55.000	0.00	0.00	3.32	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
126	128	4.409187	ACTATATTCTCCGTCCTCCTTCC	58.591	47.826	0.00	0.00	0.00	3.46
133	135	2.700897	CTCCGTCCTCCTTCCATTGTAT	59.299	50.000	0.00	0.00	0.00	2.29
139	141	3.205056	TCCTCCTTCCATTGTATGCCATT	59.795	43.478	0.00	0.00	0.00	3.16
145	147	0.032403	CATTGTATGCCATTGCCGGG	59.968	55.000	2.18	0.00	36.33	5.73
157	159	2.758736	TTGCCGGGGATTGAAAAATG	57.241	45.000	2.18	0.00	0.00	2.32
162	164	2.462889	CGGGGATTGAAAAATGCATCG	58.537	47.619	0.00	0.00	0.00	3.84
165	167	4.696455	GGGGATTGAAAAATGCATCGAAT	58.304	39.130	0.00	0.00	0.00	3.34
168	170	5.461078	GGGATTGAAAAATGCATCGAATCAG	59.539	40.000	0.00	0.00	0.00	2.90
172	174	4.622313	TGAAAAATGCATCGAATCAGCAAC	59.378	37.500	0.00	1.90	42.15	4.17
194	196	2.514458	AGGAAATGGCCACCTACAAG	57.486	50.000	8.16	0.00	31.78	3.16
207	209	1.679944	CCTACAAGTGCCCTCACCATG	60.680	57.143	0.00	0.00	44.16	3.66
230	232	5.935206	TGTCAGTCTTTGAATACCGCAATAA	59.065	36.000	0.00	0.00	37.61	1.40
238	240	6.603237	TTGAATACCGCAATAATCACTCAG	57.397	37.500	0.00	0.00	0.00	3.35
263	269	3.710326	TGAGACGAGATCCATAAACCG	57.290	47.619	0.00	0.00	0.00	4.44
309	316	4.724399	TCACCCACACATAACAATCTTGT	58.276	39.130	0.00	0.00	44.72	3.16
321	328	7.491372	ACATAACAATCTTGTAGTACATCACCG	59.509	37.037	3.28	0.00	41.31	4.94
333	340	2.729479	ATCACCGCCAGCTCAGAGG	61.729	63.158	0.00	1.86	0.00	3.69
373	381	3.428725	GCCACACAACACTGTTGAAATCA	60.429	43.478	25.50	0.00	31.64	2.57
395	403	3.255831	TCATACCAATAGCCAGCCCATA	58.744	45.455	0.00	0.00	0.00	2.74
418	426	5.048846	ACTCTCTTTAAAAGACTTGCCCA	57.951	39.130	0.00	0.00	33.12	5.36
457	465	9.191479	TCTTTAAAAGACATACCAGGAAACAAA	57.809	29.630	0.00	0.00	31.20	2.83
462	470	7.418337	AAGACATACCAGGAAACAAACTTTT	57.582	32.000	0.00	0.00	0.00	2.27
463	471	8.528044	AAGACATACCAGGAAACAAACTTTTA	57.472	30.769	0.00	0.00	0.00	1.52
466	474	6.041182	ACATACCAGGAAACAAACTTTTACCC	59.959	38.462	0.00	0.00	0.00	3.69
467	475	4.616553	ACCAGGAAACAAACTTTTACCCT	58.383	39.130	0.00	0.00	0.00	4.34

Showing 1 to 25 of 126 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	7.648142	TCTGTTTCCAGTTGTCAATTCATTAC	58.352	34.615	0.00	0.00	39.82	1.89
117	119	2.204463	TGGCATACAATGGAAGGAGGA	58.796	47.619	0.00	0.00	0.00	3.71
126	128	0.032403	CCCGGCAATGGCATACAATG	59.968	55.000	7.75	0.00	43.71	2.82
133	135	2.759149	CAATCCCCGGCAATGGCA	60.759	61.111	7.75	0.00	43.71	4.92
139	141	0.248843	GCATTTTTCAATCCCCGGCA	59.751	50.000	0.00	0.00	0.00	5.69
145	147	5.051240	GCTGATTCGATGCATTTTTCAATCC	60.051	40.000	0.00	0.00	0.00	3.01
157	159	2.162208	TCCTTTGTTGCTGATTCGATGC	59.838	45.455	0.00	0.00	0.00	3.91
162	164	3.681417	GCCATTTCCTTTGTTGCTGATTC	59.319	43.478	0.00	0.00	0.00	2.52
165	167	1.344114	GGCCATTTCCTTTGTTGCTGA	59.656	47.619	0.00	0.00	0.00	4.26
168	170	1.511850	GTGGCCATTTCCTTTGTTGC	58.488	50.000	9.72	0.00	0.00	4.17
172	174	2.524306	TGTAGGTGGCCATTTCCTTTG	58.476	47.619	17.93	0.00	33.34	2.77
194	196	0.674895	GACTGACATGGTGAGGGCAC	60.675	60.000	0.00	0.00	44.39	5.01
207	209	4.946784	ATTGCGGTATTCAAAGACTGAC	57.053	40.909	0.65	0.00	32.21	3.51
238	240	0.755686	ATGGATCTCGTCTCAAGGGC	59.244	55.000	0.00	0.00	0.00	5.19
263	269	8.988934	TGATACTTTAACCGATAATGCTTCATC	58.011	33.333	0.00	0.00	0.00	2.92
309	316	0.744874	GAGCTGGCGGTGATGTACTA	59.255	55.000	0.00	0.00	0.00	1.82
321	328	0.829333	TCTTCATCCTCTGAGCTGGC	59.171	55.000	0.00	0.00	34.68	4.85
333	340	2.557924	TGGCATGGTGTGTTTCTTCATC	59.442	45.455	0.00	0.00	0.00	2.92
373	381	2.065007	TGGGCTGGCTATTGGTATGAT	58.935	47.619	0.00	0.00	0.00	2.45
395	403	5.445964	TGGGCAAGTCTTTTAAAGAGAGTT	58.554	37.500	7.74	11.51	38.41	3.01
444	452	5.768752	AGGGTAAAAGTTTGTTTCCTGGTA	58.231	37.500	0.00	0.00	0.00	3.25
457	465	6.051074	CGTCCCGATTAATAAGGGTAAAAGT	58.949	40.000	21.44	0.00	45.27	2.66
462	470	3.253188	CGACGTCCCGATTAATAAGGGTA	59.747	47.826	21.44	10.53	45.27	3.69
463	471	2.035066	CGACGTCCCGATTAATAAGGGT	59.965	50.000	21.44	8.43	45.27	4.34
466	474	4.913924	CCTTACGACGTCCCGATTAATAAG	59.086	45.833	10.58	3.91	0.00	1.73

Showing 1 to 25 of 142 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.