AutoCloner

Multiple sequence alignment - TraesCS5B01G126200

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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	TraesCS5B01G126200	chr5B	100.000	3023	0	0	1	3023	230249524	230246502	0.000000e+00	5583.0
1	TraesCS5B01G126200	chr5B	94.118	85	5	0	584	668	36727196	36727280	2.450000e-26	130.0
2	TraesCS5B01G126200	chr5D	97.953	2638	36	6	1	2623	214920677	214918043	0.000000e+00	4556.0
3	TraesCS5B01G126200	chr5D	100.000	309	0	0	2715	3023	214918030	214917722	3.380000e-159	571.0
4	TraesCS5B01G126200	chr5D	96.552	58	2	0	2609	2666	214918088	214918031	2.480000e-16	97.1
5	TraesCS5B01G126200	chr5A	96.241	2687	56	14	1	2666	282588943	282586281	0.000000e+00	4361.0
6	TraesCS5B01G126200	chr5A	97.411	309	4	2	2715	3023	282586280	282585976	9.600000e-145	523.0
7	TraesCS5B01G126200	chr2D	89.094	2714	174	51	30	2642	567476248	567478940	0.000000e+00	3260.0
8	TraesCS5B01G126200	chr2D	91.584	202	17	0	2822	3023	567479085	567479286	2.290000e-71	279.0
9	TraesCS5B01G126200	chr2D	97.826	46	1	0	2609	2654	567478876	567478921	2.500000e-11	80.5
10	TraesCS5B01G126200	chr2B	88.775	2726	183	51	30	2654	680192918	680195621	0.000000e+00	3225.0
11	TraesCS5B01G126200	chr2B	90.777	206	15	3	2822	3023	680195788	680195993	3.840000e-69	272.0
12	TraesCS5B01G126200	chr2B	94.118	68	1	1	2578	2642	680195573	680195640	1.920000e-17	100.0
13	TraesCS5B01G126200	chr2A	89.241	1989	138	33	733	2665	706994904	706996872	0.000000e+00	2418.0
14	TraesCS5B01G126200	chr2A	89.720	428	21	11	330	735	706994352	706994778	2.670000e-145	525.0
15	TraesCS5B01G126200	chr2A	89.489	352	22	8	30	368	706994006	706994355	5.990000e-117	431.0
16	TraesCS5B01G126200	chr2A	91.584	202	17	0	2822	3023	706996986	706997187	2.290000e-71	279.0
17	TraesCS5B01G126200	chrUn	100.000	309	0	0	2715	3023	476965435	476965743	3.380000e-159	571.0
18	TraesCS5B01G126200	chrUn	100.000	49	0	0	2667	2715	354076946	354076898	1.150000e-14	91.6
19	TraesCS5B01G126200	chrUn	100.000	49	0	0	2667	2715	379970368	379970416	1.150000e-14	91.6
20	TraesCS5B01G126200	chrUn	100.000	49	0	0	2667	2715	452335546	452335594	1.150000e-14	91.6
21	TraesCS5B01G126200	chr4B	82.915	597	73	21	846	1431	135211254	135211832	7.480000e-141	510.0
22	TraesCS5B01G126200	chr4B	87.234	141	12	3	533	668	135210867	135211006	4.040000e-34	156.0
23	TraesCS5B01G126200	chr4D	82.333	600	78	21	846	1431	95780931	95781516	2.090000e-136	496.0
24	TraesCS5B01G126200	chr4D	87.234	141	12	3	533	668	95780563	95780702	4.040000e-34	156.0
25	TraesCS5B01G126200	chr4D	100.000	49	0	0	2667	2715	490365110	490365062	1.150000e-14	91.6
26	TraesCS5B01G126200	chr4A	87.558	434	45	4	1001	1431	483951403	483950976	7.530000e-136	494.0
27	TraesCS5B01G126200	chr4A	86.207	145	11	6	538	676	483951949	483951808	6.750000e-32	148.0
28	TraesCS5B01G126200	chr3D	81.181	271	44	5	1097	1362	362069952	362069684	8.490000e-51	211.0
29	TraesCS5B01G126200	chr6D	100.000	49	0	0	2667	2715	108492219	108492267	1.150000e-14	91.6
30	TraesCS5B01G126200	chr6D	100.000	49	0	0	2667	2715	135458433	135458481	1.150000e-14	91.6
31	TraesCS5B01G126200	chr6D	100.000	49	0	0	2667	2715	458921329	458921281	1.150000e-14	91.6
32	TraesCS5B01G126200	chr1D	100.000	49	0	0	2667	2715	254389071	254389119	1.150000e-14	91.6
33	TraesCS5B01G126200	chr1D	100.000	49	0	0	2667	2715	254390767	254390719	1.150000e-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	TraesCS5B01G126200	chr5B	230246502	230249524	3022	True	5583.000000	5583	100.000000	1	3023	1	chr5B.!!$R1	3022
1	TraesCS5B01G126200	chr5D	214917722	214920677	2955	True	1741.366667	4556	98.168333	1	3023	3	chr5D.!!$R1	3022
2	TraesCS5B01G126200	chr5A	282585976	282588943	2967	True	2442.000000	4361	96.826000	1	3023	2	chr5A.!!$R1	3022
3	TraesCS5B01G126200	chr2D	567476248	567479286	3038	False	1206.500000	3260	92.834667	30	3023	3	chr2D.!!$F1	2993
4	TraesCS5B01G126200	chr2B	680192918	680195993	3075	False	1199.000000	3225	91.223333	30	3023	3	chr2B.!!$F1	2993
5	TraesCS5B01G126200	chr2A	706994006	706997187	3181	False	913.250000	2418	90.008500	30	3023	4	chr2A.!!$F1	2993
6	TraesCS5B01G126200	chr4B	135210867	135211832	965	False	333.000000	510	85.074500	533	1431	2	chr4B.!!$F1	898
7	TraesCS5B01G126200	chr4D	95780563	95781516	953	False	326.000000	496	84.783500	533	1431	2	chr4D.!!$F1	898
8	TraesCS5B01G126200	chr4A	483950976	483951949	973	True	321.000000	494	86.882500	538	1431	2	chr4A.!!$R1	893

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
954	1301	0.967887	TCTCTTCTCTCCACTGCCCG	60.968	60.000	0.0	0.0	0.0	6.13	F
1248	1615	1.480137	CTGTCTTTCGAGGATGAGGCT	59.520	52.381	0.0	0.0	0.0	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1997	2390	0.188342	ACTGCCCCTGTTGTGGAATT	59.812	50.000	0.0	0.0	0.0	2.17	R
2713	3243	3.678072	GCGTACACTCACTCATTGCTTAA	59.322	43.478	0.0	0.0	0.0	1.85	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	Hairpin	End Stability
69	70	3.068024	CAGCTTGGTTACTTTGCTTGGAA	59.932	43.478	0.0	0.00	3.53
71	72	3.317993	GCTTGGTTACTTTGCTTGGAAGA	59.682	43.478	0.0	0.00	2.87
674	783	5.835280	TGATCATTCCTCATCAGCTACACTA	59.165	40.000	0.0	0.00	2.74
954	1301	0.967887	TCTCTTCTCTCCACTGCCCG	60.968	60.000	0.0	0.00	6.13
1248	1615	1.480137	CTGTCTTTCGAGGATGAGGCT	59.520	52.381	0.0	0.00	4.58
1465	1835	2.035469	TACGTGTACCTCCGCCCA	59.965	61.111	0.0	0.00	5.36
2136	2544	2.893489	ACAGGCTTGAATTGACCCTTTC	59.107	45.455	1.4	0.00	2.62
2216	2624	1.490910	CCATCCCCAGAGTACCCTTTC	59.509	57.143	0.0	0.00	2.62
2337	2755	1.831106	AGAGCGAGTGAGAGAGAGAGA	59.169	52.381	0.0	0.00	3.10
2338	2756	2.159043	AGAGCGAGTGAGAGAGAGAGAG	60.159	54.545	0.0	0.00	3.20
2558	3011	3.932710	TCTACACCTCACGCAATCAATTC	59.067	43.478	0.0	0.00	2.17
2666	3196	3.627395	ATGCATTCGTTCACCTAAGGA	57.373	42.857	0.0	0.00	3.36
2667	3197	3.410631	TGCATTCGTTCACCTAAGGAA	57.589	42.857	0.0	43.86	3.36
2668	3198	3.071479	TGCATTCGTTCACCTAAGGAAC	58.929	45.455	0.0	42.88	3.62
2680	3210	9.159364	GTTCACCTAAGGAACGATTTAATAACT	57.841	33.333	0.0	35.76	2.24
2700	3230	9.553064	AATAACTATCTTTGTAGCTCCAGAATG	57.447	33.333	0.0	0.00	2.67
2701	3231	6.552445	ACTATCTTTGTAGCTCCAGAATGT	57.448	37.500	0.0	0.00	2.71
2702	3232	6.951971	ACTATCTTTGTAGCTCCAGAATGTT	58.048	36.000	0.0	0.00	2.71
2703	3233	7.398024	ACTATCTTTGTAGCTCCAGAATGTTT	58.602	34.615	0.0	0.00	2.83
2704	3234	6.749923	ATCTTTGTAGCTCCAGAATGTTTC	57.250	37.500	0.0	0.00	2.78
2705	3235	5.620206	TCTTTGTAGCTCCAGAATGTTTCA	58.380	37.500	0.0	0.00	2.69
2706	3236	5.702670	TCTTTGTAGCTCCAGAATGTTTCAG	59.297	40.000	0.0	0.00	3.02
2707	3237	4.623932	TGTAGCTCCAGAATGTTTCAGT	57.376	40.909	0.0	0.00	3.41
2708	3238	4.973168	TGTAGCTCCAGAATGTTTCAGTT	58.027	39.130	0.0	0.00	3.16
2709	3239	5.376625	TGTAGCTCCAGAATGTTTCAGTTT	58.623	37.500	0.0	0.00	2.66
2710	3240	6.530120	TGTAGCTCCAGAATGTTTCAGTTTA	58.470	36.000	0.0	0.00	2.01
2711	3241	7.168219	TGTAGCTCCAGAATGTTTCAGTTTAT	58.832	34.615	0.0	0.00	1.40
2712	3242	6.506500	AGCTCCAGAATGTTTCAGTTTATG	57.493	37.500	0.0	0.00	1.90
2713	3243	6.006449	AGCTCCAGAATGTTTCAGTTTATGT	58.994	36.000	0.0	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	3.007398	CACCTGTTAAGAGGACAAGCTCT	59.993	47.826	24.66	0.0	36.51	4.09
71	72	2.039084	CCACCTGTTAAGAGGACAAGCT	59.961	50.000	24.66	0.0	36.51	3.74
201	206	0.324943	GAGGTGTATGGGCTGTGTGT	59.675	55.000	0.00	0.0	0.00	3.72
674	783	8.376270	GGTGCTAAGGTTGGAATATATAGTTCT	58.624	37.037	0.00	0.0	0.00	3.01
688	797	2.029918	GGCTTCAAAGGTGCTAAGGTTG	60.030	50.000	0.00	0.0	0.00	3.77
954	1301	3.944087	AGAGGTTCTTGTCTATGGCAAC	58.056	45.455	0.00	0.0	0.00	4.17
1440	1807	2.097825	GGAGGTACACGTACAGGTGAT	58.902	52.381	8.91	0.0	40.38	3.06
1441	1808	1.538047	GGAGGTACACGTACAGGTGA	58.462	55.000	8.91	0.0	40.38	4.02
1465	1835	3.382832	CTCCCCGGCGTTCAGAGT	61.383	66.667	6.01	0.0	0.00	3.24
1631	2009	7.337480	TGCATCTAAGATATGTTGCATGTTT	57.663	32.000	0.00	0.0	35.01	2.83
1994	2387	2.104622	CTGCCCCTGTTGTGGAATTTTT	59.895	45.455	0.00	0.0	0.00	1.94
1996	2389	1.341080	CTGCCCCTGTTGTGGAATTT	58.659	50.000	0.00	0.0	0.00	1.82
1997	2390	0.188342	ACTGCCCCTGTTGTGGAATT	59.812	50.000	0.00	0.0	0.00	2.17
1998	2391	0.188342	AACTGCCCCTGTTGTGGAAT	59.812	50.000	0.00	0.0	0.00	3.01
2136	2544	5.140454	TCCTCTTCCTTTTCCTTTTCCTTG	58.860	41.667	0.00	0.0	0.00	3.61
2611	3065	5.324409	AGAAGGTAAGGTGAATGCATTGAA	58.676	37.500	18.59	1.5	0.00	2.69
2674	3204	9.553064	CATTCTGGAGCTACAAAGATAGTTATT	57.447	33.333	0.00	0.0	0.00	1.40
2675	3205	8.709308	ACATTCTGGAGCTACAAAGATAGTTAT	58.291	33.333	0.00	0.0	0.00	1.89
2676	3206	8.079211	ACATTCTGGAGCTACAAAGATAGTTA	57.921	34.615	0.00	0.0	0.00	2.24
2677	3207	6.951971	ACATTCTGGAGCTACAAAGATAGTT	58.048	36.000	0.00	0.0	0.00	2.24
2678	3208	6.552445	ACATTCTGGAGCTACAAAGATAGT	57.448	37.500	0.00	0.0	0.00	2.12
2679	3209	7.550551	TGAAACATTCTGGAGCTACAAAGATAG	59.449	37.037	0.00	0.0	0.00	2.08
2680	3210	7.394016	TGAAACATTCTGGAGCTACAAAGATA	58.606	34.615	0.00	0.0	0.00	1.98
2681	3211	6.240894	TGAAACATTCTGGAGCTACAAAGAT	58.759	36.000	0.00	0.0	0.00	2.40
2682	3212	5.620206	TGAAACATTCTGGAGCTACAAAGA	58.380	37.500	0.00	0.0	0.00	2.52
2683	3213	5.471456	ACTGAAACATTCTGGAGCTACAAAG	59.529	40.000	0.00	0.0	33.45	2.77
2684	3214	5.376625	ACTGAAACATTCTGGAGCTACAAA	58.623	37.500	0.00	0.0	33.45	2.83
2685	3215	4.973168	ACTGAAACATTCTGGAGCTACAA	58.027	39.130	0.00	0.0	33.45	2.41
2686	3216	4.623932	ACTGAAACATTCTGGAGCTACA	57.376	40.909	0.00	0.0	33.45	2.74
2687	3217	5.948992	AAACTGAAACATTCTGGAGCTAC	57.051	39.130	0.00	0.0	33.45	3.58
2688	3218	7.168219	ACATAAACTGAAACATTCTGGAGCTA	58.832	34.615	0.00	0.0	33.45	3.32
2689	3219	6.006449	ACATAAACTGAAACATTCTGGAGCT	58.994	36.000	0.00	0.0	33.45	4.09
2690	3220	6.259550	ACATAAACTGAAACATTCTGGAGC	57.740	37.500	2.73	0.0	33.45	4.70
2691	3221	9.831737	CTTAACATAAACTGAAACATTCTGGAG	57.168	33.333	2.73	0.0	33.45	3.86
2692	3222	8.296713	GCTTAACATAAACTGAAACATTCTGGA	58.703	33.333	2.73	0.0	33.45	3.86
2693	3223	8.081633	TGCTTAACATAAACTGAAACATTCTGG	58.918	33.333	2.73	0.0	33.45	3.86
2694	3224	9.462174	TTGCTTAACATAAACTGAAACATTCTG	57.538	29.630	0.00	0.0	35.09	3.02
2697	3227	9.979578	TCATTGCTTAACATAAACTGAAACATT	57.020	25.926	0.00	0.0	0.00	2.71
2698	3228	9.630098	CTCATTGCTTAACATAAACTGAAACAT	57.370	29.630	0.00	0.0	0.00	2.71
2699	3229	8.629158	ACTCATTGCTTAACATAAACTGAAACA	58.371	29.630	0.00	0.0	0.00	2.83
2700	3230	8.905702	CACTCATTGCTTAACATAAACTGAAAC	58.094	33.333	0.00	0.0	0.00	2.78
2701	3231	8.845227	TCACTCATTGCTTAACATAAACTGAAA	58.155	29.630	0.00	0.0	0.00	2.69
2702	3232	8.389779	TCACTCATTGCTTAACATAAACTGAA	57.610	30.769	0.00	0.0	0.00	3.02
2703	3233	7.661437	ACTCACTCATTGCTTAACATAAACTGA	59.339	33.333	0.00	0.0	0.00	3.41
2704	3234	7.747799	CACTCACTCATTGCTTAACATAAACTG	59.252	37.037	0.00	0.0	0.00	3.16
2705	3235	7.445402	ACACTCACTCATTGCTTAACATAAACT	59.555	33.333	0.00	0.0	0.00	2.66
2706	3236	7.584987	ACACTCACTCATTGCTTAACATAAAC	58.415	34.615	0.00	0.0	0.00	2.01
2707	3237	7.744087	ACACTCACTCATTGCTTAACATAAA	57.256	32.000	0.00	0.0	0.00	1.40
2708	3238	7.062956	CGTACACTCACTCATTGCTTAACATAA	59.937	37.037	0.00	0.0	0.00	1.90
2709	3239	6.530181	CGTACACTCACTCATTGCTTAACATA	59.470	38.462	0.00	0.0	0.00	2.29
2710	3240	5.348724	CGTACACTCACTCATTGCTTAACAT	59.651	40.000	0.00	0.0	0.00	2.71
2711	3241	4.684242	CGTACACTCACTCATTGCTTAACA	59.316	41.667	0.00	0.0	0.00	2.41
2712	3242	4.434330	GCGTACACTCACTCATTGCTTAAC	60.434	45.833	0.00	0.0	0.00	2.01
2713	3243	3.678072	GCGTACACTCACTCATTGCTTAA	59.322	43.478	0.00	0.0	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.