AutoCloner

Multiple sequence alignment - TraesCS5B01G312100

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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	TraesCS5B01G312100	chr5B	100.000	2720	0	0	1	2720	493673057	493675776	0.000000e+00	5024.0
1	TraesCS5B01G312100	chr5B	79.506	932	140	27	798	1718	493931210	493932101	1.380000e-172	616.0
2	TraesCS5B01G312100	chr5B	84.110	365	52	6	1066	1427	492619520	492619881	5.570000e-92	348.0
3	TraesCS5B01G312100	chr5D	92.660	2643	126	22	56	2674	411195793	411198391	0.000000e+00	3744.0
4	TraesCS5B01G312100	chr5D	80.216	925	136	28	804	1718	411627439	411628326	0.000000e+00	651.0
5	TraesCS5B01G312100	chr5D	84.932	365	48	7	1066	1427	410444225	410444585	1.990000e-96	363.0
6	TraesCS5B01G312100	chr5D	83.429	350	54	4	1067	1414	411785487	411785140	3.380000e-84	322.0
7	TraesCS5B01G312100	chr5D	88.506	87	8	2	283	367	446741151	446741237	1.330000e-18	104.0
8	TraesCS5B01G312100	chr5D	97.826	46	0	1	2676	2720	411198419	411198464	8.070000e-11	78.7
9	TraesCS5B01G312100	chr5A	92.013	2554	152	21	2	2522	523135702	523138236	0.000000e+00	3539.0
10	TraesCS5B01G312100	chr5A	76.282	1501	229	77	804	2237	523449896	523451336	0.000000e+00	682.0
11	TraesCS5B01G312100	chr5A	84.097	371	47	12	1066	1427	522066673	522067040	5.570000e-92	348.0
12	TraesCS5B01G312100	chr2D	96.825	63	1	1	285	346	2724957	2725019	1.330000e-18	104.0
13	TraesCS5B01G312100	chr7D	90.909	77	5	2	291	366	613891350	613891275	4.790000e-18	102.0
14	TraesCS5B01G312100	chr2B	92.958	71	4	1	299	368	355383378	355383308	4.790000e-18	102.0
15	TraesCS5B01G312100	chr2B	83.333	102	15	2	284	383	24126681	24126580	2.880000e-15	93.5
16	TraesCS5B01G312100	chr7A	89.610	77	6	1	283	357	40531657	40531581	2.230000e-16	97.1
17	TraesCS5B01G312100	chr2A	86.022	93	9	4	285	374	360872945	360873036	2.230000e-16	97.1

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	TraesCS5B01G312100	chr5B	493673057	493675776	2719	False	5024.00	5024	100.000	1	2720	1	chr5B.!!$F2	2719
1	TraesCS5B01G312100	chr5B	493931210	493932101	891	False	616.00	616	79.506	798	1718	1	chr5B.!!$F3	920
2	TraesCS5B01G312100	chr5D	411195793	411198464	2671	False	1911.35	3744	95.243	56	2720	2	chr5D.!!$F4	2664
3	TraesCS5B01G312100	chr5D	411627439	411628326	887	False	651.00	651	80.216	804	1718	1	chr5D.!!$F2	914
4	TraesCS5B01G312100	chr5A	523135702	523138236	2534	False	3539.00	3539	92.013	2	2522	1	chr5A.!!$F2	2520
5	TraesCS5B01G312100	chr5A	523449896	523451336	1440	False	682.00	682	76.282	804	2237	1	chr5A.!!$F3	1433

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
345	347	0.951040	CGAGCACCAGGACTTGAACC	60.951	60.000	0.00	0.0	0.0	3.62	F
955	975	1.967066	CTCCATAGATCGACCTTGGCT	59.033	52.381	3.77	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1446	1471	0.251916	CGGATTGGCTACAGGTTCCA	59.748	55.0	0.0	0.0	0.0	3.53	R
2496	2604	0.807667	GCTCCGTCACTATGCACCAG	60.808	60.0	0.0	0.0	0.0	4.00	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
27	28	4.498513	CCCGTGTCACTAATACTTCGCATA	60.499	45.833	0.65	0.00	0.00	3.14
29	30	5.051907	CCGTGTCACTAATACTTCGCATAAC	60.052	44.000	0.65	0.00	0.00	1.89
46	47	2.060050	AACGATTGTGGTTGTGGGAA	57.940	45.000	0.00	0.00	0.00	3.97
69	70	2.749466	CGCCTCCAATACCATGGACAAT	60.749	50.000	21.47	5.94	44.52	2.71
76	77	5.065914	CCAATACCATGGACAATGTAGGAG	58.934	45.833	21.47	0.00	43.54	3.69
85	86	4.019681	TGGACAATGTAGGAGTTTCCGAAT	60.020	41.667	0.00	0.00	42.75	3.34
86	87	5.188163	TGGACAATGTAGGAGTTTCCGAATA	59.812	40.000	0.00	0.00	42.75	1.75
87	88	6.110707	GGACAATGTAGGAGTTTCCGAATAA	58.889	40.000	0.00	0.00	42.75	1.40
88	89	6.596497	GGACAATGTAGGAGTTTCCGAATAAA	59.404	38.462	0.00	0.00	42.75	1.40
89	90	7.282450	GGACAATGTAGGAGTTTCCGAATAAAT	59.718	37.037	0.00	0.00	42.75	1.40
178	179	6.875726	TGATAGTCAGATGAAACACTCTTTGG	59.124	38.462	0.00	0.00	0.00	3.28
182	183	7.054124	AGTCAGATGAAACACTCTTTGGTTTA	58.946	34.615	0.00	0.00	34.18	2.01
183	184	7.721399	AGTCAGATGAAACACTCTTTGGTTTAT	59.279	33.333	0.00	0.00	34.18	1.40
190	191	9.349713	TGAAACACTCTTTGGTTTATGTATTCT	57.650	29.630	0.00	0.00	34.18	2.40
191	192	9.612620	GAAACACTCTTTGGTTTATGTATTCTG	57.387	33.333	0.00	0.00	34.18	3.02
193	194	8.099364	ACACTCTTTGGTTTATGTATTCTGTG	57.901	34.615	0.00	0.00	0.00	3.66
219	220	3.978217	GGTCACGCGAATGAAAATGAAAA	59.022	39.130	15.93	0.00	0.00	2.29
269	271	5.049612	ACATCATTCATTTGCATAGAGCTCG	60.050	40.000	8.37	0.00	45.94	5.03
270	272	3.811497	TCATTCATTTGCATAGAGCTCGG	59.189	43.478	8.37	3.31	45.94	4.63
286	288	1.746220	CTCGGTCTCTCGGAAGTGAAT	59.254	52.381	0.00	0.00	32.67	2.57
344	346	1.569479	GCGAGCACCAGGACTTGAAC	61.569	60.000	0.00	0.00	0.00	3.18
345	347	0.951040	CGAGCACCAGGACTTGAACC	60.951	60.000	0.00	0.00	0.00	3.62
368	370	3.124856	AGTGGGCTGGGTATAACACTA	57.875	47.619	0.00	0.00	37.41	2.74
381	383	6.015688	GGGTATAACACTATTCTCGACCATCA	60.016	42.308	0.00	0.00	0.00	3.07
439	442	8.466617	ACTTGTCTCCGATAGAAGTACATAAT	57.533	34.615	0.00	0.00	35.47	1.28
440	443	8.353684	ACTTGTCTCCGATAGAAGTACATAATG	58.646	37.037	0.00	0.00	35.47	1.90
442	445	6.264518	TGTCTCCGATAGAAGTACATAATGCA	59.735	38.462	0.00	0.00	35.47	3.96
519	522	5.239306	TCAGTTTCAAGCAACACCTTATCAG	59.761	40.000	0.00	0.00	0.00	2.90
533	536	3.255149	CCTTATCAGGCTGCAAATCCATC	59.745	47.826	10.34	0.00	31.53	3.51
951	971	3.632333	TCACACTCCATAGATCGACCTT	58.368	45.455	0.00	0.00	0.00	3.50
955	975	1.967066	CTCCATAGATCGACCTTGGCT	59.033	52.381	3.77	0.00	0.00	4.75
1446	1471	1.141019	CACCGTTCCCGTCGATGAT	59.859	57.895	6.11	0.00	0.00	2.45
1494	1519	1.562008	TCCATGGAAAATACCGGCTCA	59.438	47.619	13.46	0.00	0.00	4.26
1802	1836	8.863049	GTCAGCATAATAAAATTGTGGAACTTG	58.137	33.333	0.00	0.00	38.04	3.16
1823	1883	2.113860	ACCCATCAAATCCTGTGACG	57.886	50.000	0.00	0.00	0.00	4.35
1930	1996	7.487822	AAATTCACAGAAGATCCTAGACTGA	57.512	36.000	0.00	0.00	33.53	3.41
1946	2012	4.111577	AGACTGATGGGAAAAGGATACCA	58.888	43.478	0.00	0.00	37.41	3.25
2051	2127	0.250793	TGGTCCATGTACGCCGATTT	59.749	50.000	0.00	0.00	0.00	2.17
2287	2385	5.350504	AGATCTAGTGTGATTGTGGAAGG	57.649	43.478	0.00	0.00	0.00	3.46
2355	2453	3.333029	ACAGTGCAAGGCTTTGTTTTT	57.667	38.095	10.54	0.00	36.65	1.94
2434	2532	7.276218	CACATATTCATGGGTTGATGTCAAAAC	59.724	37.037	0.00	0.00	35.58	2.43
2555	2663	2.109128	TGTGTGGATATTGGTGGTGGTT	59.891	45.455	0.00	0.00	0.00	3.67
2596	2704	9.543231	TCTCTCCTATCCATATTAATTACCGTT	57.457	33.333	0.00	0.00	0.00	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.521947	AGTATTAGTGACACGGGCTTC	57.478	47.619	0.00	0.00	0.00	3.86
6	7	5.330571	CGTTATGCGAAGTATTAGTGACACG	60.331	44.000	0.00	0.00	44.77	4.49
7	8	5.948348	CGTTATGCGAAGTATTAGTGACAC	58.052	41.667	0.00	0.00	44.77	3.67
27	28	2.060050	TTCCCACAACCACAATCGTT	57.940	45.000	0.00	0.00	0.00	3.85
29	30	1.334599	CGTTTCCCACAACCACAATCG	60.335	52.381	0.00	0.00	0.00	3.34
31	32	0.387565	GCGTTTCCCACAACCACAAT	59.612	50.000	0.00	0.00	0.00	2.71
34	35	1.792118	GAGGCGTTTCCCACAACCAC	61.792	60.000	0.00	0.00	34.51	4.16
35	36	1.527380	GAGGCGTTTCCCACAACCA	60.527	57.895	0.00	0.00	34.51	3.67
46	47	0.916086	TCCATGGTATTGGAGGCGTT	59.084	50.000	12.58	0.00	40.90	4.84
69	70	8.658609	CGTTTAATTTATTCGGAAACTCCTACA	58.341	33.333	0.00	0.00	33.30	2.74
76	77	5.740569	GGAGGCGTTTAATTTATTCGGAAAC	59.259	40.000	0.00	0.00	0.00	2.78
85	86	8.524487	ACATACAAAATGGAGGCGTTTAATTTA	58.476	29.630	0.00	0.00	0.00	1.40
86	87	7.382898	ACATACAAAATGGAGGCGTTTAATTT	58.617	30.769	0.00	0.00	0.00	1.82
87	88	6.930731	ACATACAAAATGGAGGCGTTTAATT	58.069	32.000	0.00	0.00	0.00	1.40
88	89	6.151985	TGACATACAAAATGGAGGCGTTTAAT	59.848	34.615	0.00	0.00	0.00	1.40
89	90	5.473846	TGACATACAAAATGGAGGCGTTTAA	59.526	36.000	0.00	0.00	0.00	1.52
193	194	1.144969	TTTCATTCGCGTGACCAGTC	58.855	50.000	5.77	0.00	0.00	3.51
269	271	1.066858	TGCATTCACTTCCGAGAGACC	60.067	52.381	0.00	0.00	0.00	3.85
270	272	1.996191	GTGCATTCACTTCCGAGAGAC	59.004	52.381	0.00	0.00	40.03	3.36
286	288	2.028203	TCAGGATTTCTGACGATGTGCA	60.028	45.455	0.00	0.00	46.71	4.57
344	346	2.775384	TGTTATACCCAGCCCACTAAGG	59.225	50.000	0.00	0.00	37.03	2.69
345	347	3.454812	AGTGTTATACCCAGCCCACTAAG	59.545	47.826	0.00	0.00	31.80	2.18
368	370	2.289444	ACAACCGTTGATGGTCGAGAAT	60.289	45.455	18.19	0.00	42.89	2.40
381	383	3.389925	TCCGAGAACATTACAACCGTT	57.610	42.857	0.00	0.00	0.00	4.44
422	424	6.455647	TCCTTGCATTATGTACTTCTATCGG	58.544	40.000	0.00	0.00	0.00	4.18
439	442	1.317613	AGTGACGCATTTTCCTTGCA	58.682	45.000	0.00	0.00	40.14	4.08
440	443	2.053627	CAAGTGACGCATTTTCCTTGC	58.946	47.619	0.00	0.00	36.74	4.01
442	445	2.293399	GGACAAGTGACGCATTTTCCTT	59.707	45.455	0.00	0.00	0.00	3.36
519	522	1.226773	GCGTGATGGATTTGCAGCC	60.227	57.895	0.00	0.00	0.00	4.85
533	536	3.041940	GGGGACAAGTGACGCGTG	61.042	66.667	20.70	3.72	0.00	5.34
584	587	1.101331	GAAGGCATCTTCTTGCTGGG	58.899	55.000	0.00	0.00	44.43	4.45
828	847	2.811101	CTCCAGACTAGCGGCAGG	59.189	66.667	1.45	0.00	0.00	4.85
955	975	0.723414	CTCGAGCTTACGTACGGTGA	59.277	55.000	21.06	1.01	34.70	4.02
1237	1262	4.865761	GAGCATGGCGGCGTCGTA	62.866	66.667	12.58	0.04	39.27	3.43
1277	1302	0.318784	GTCGGCGAAGTTGAGACACT	60.319	55.000	12.92	0.00	32.57	3.55
1330	1355	2.027625	GGACGTCTGCAAAGTCGGG	61.028	63.158	16.46	0.00	37.26	5.14
1446	1471	0.251916	CGGATTGGCTACAGGTTCCA	59.748	55.000	0.00	0.00	0.00	3.53
1802	1836	2.420022	CGTCACAGGATTTGATGGGTTC	59.580	50.000	0.00	0.00	0.00	3.62
1823	1883	1.944709	ACTCCGTTTGTTTGCAGGTAC	59.055	47.619	0.00	0.00	0.00	3.34
2051	2127	0.913934	TGCCTAGGCCACATCTTCCA	60.914	55.000	30.81	5.05	41.09	3.53
2087	2163	0.846693	AGGGATCCAGCGGCTTTAAT	59.153	50.000	15.23	0.00	0.00	1.40
2278	2376	1.071699	GCACACTAGTCCCTTCCACAA	59.928	52.381	0.00	0.00	0.00	3.33
2287	2385	4.396166	ACAATTATTGCAGCACACTAGTCC	59.604	41.667	4.68	0.00	0.00	3.85
2355	2453	2.241176	ACAACCAGTTCTCCACAAAGGA	59.759	45.455	0.00	0.00	46.75	3.36
2374	2472	6.489603	AGGAACATGATACAACCCATTTACA	58.510	36.000	0.00	0.00	0.00	2.41
2446	2544	4.081309	AGGCATCAGAAAACCCATGAAATG	60.081	41.667	0.00	0.00	46.21	2.32
2460	2564	1.973515	AGTCTTCACACAGGCATCAGA	59.026	47.619	0.00	0.00	0.00	3.27
2496	2604	0.807667	GCTCCGTCACTATGCACCAG	60.808	60.000	0.00	0.00	0.00	4.00
2636	2744	7.302524	TGTCGTTGATTTAGCATACTTTTTCC	58.697	34.615	0.00	0.00	0.00	3.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.