AutoCloner

Multiple sequence alignment - TraesCS5D01G147500

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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	TraesCS5D01G147500	chr5D	100.000	3298	0	0	1	3298	233749997	233746700	0.000000e+00	6091
1	TraesCS5D01G147500	chr5D	88.304	684	60	9	3	679	439014871	439015541	0.000000e+00	802
2	TraesCS5D01G147500	chr5D	86.758	219	24	5	1057	1272	233742501	233742285	4.250000e-59	239
3	TraesCS5D01G147500	chr5A	92.131	2656	102	33	679	3296	321001039	321003625	0.000000e+00	3648
4	TraesCS5D01G147500	chr5A	86.207	232	26	6	1045	1272	321019884	321020113	2.540000e-61	246
5	TraesCS5D01G147500	chr5B	93.414	1488	64	20	1656	3116	271110767	271112247	0.000000e+00	2174
6	TraesCS5D01G147500	chr5B	94.484	979	39	8	679	1655	271109772	271110737	0.000000e+00	1495
7	TraesCS5D01G147500	chr5B	87.215	219	23	5	1057	1272	271140958	271141174	9.140000e-61	244
8	TraesCS5D01G147500	chr5B	93.043	115	8	0	3116	3230	271112408	271112522	5.660000e-38	169
9	TraesCS5D01G147500	chr4A	88.429	700	63	8	1	683	636393307	636394005	0.000000e+00	828
10	TraesCS5D01G147500	chr3D	87.391	690	53	16	1	679	472200969	472201635	0.000000e+00	761
11	TraesCS5D01G147500	chr3D	85.651	676	69	17	18	679	144255712	144256373	0.000000e+00	686
12	TraesCS5D01G147500	chr3D	83.531	674	73	18	20	679	43540525	43539876	2.190000e-166	595
13	TraesCS5D01G147500	chr2D	87.278	676	68	12	8	679	643845388	643846049	0.000000e+00	756
14	TraesCS5D01G147500	chr1D	87.332	671	65	11	23	683	22505870	22505210	0.000000e+00	750
15	TraesCS5D01G147500	chr1D	85.857	700	55	17	1	679	483837922	483838598	0.000000e+00	704
16	TraesCS5D01G147500	chr7B	85.714	665	69	17	22	677	626060716	626061363	0.000000e+00	678
17	TraesCS5D01G147500	chr7B	89.136	405	20	5	1543	1947	116071210	116071590	1.780000e-132	483
18	TraesCS5D01G147500	chr3A	84.911	676	77	15	16	677	717822630	717821966	0.000000e+00	660
19	TraesCS5D01G147500	chr3A	84.339	613	78	14	20	622	42452501	42451897	4.740000e-163	584
20	TraesCS5D01G147500	chr4D	90.196	408	16	5	1543	1950	361163692	361164075	8.160000e-141	510
21	TraesCS5D01G147500	chr4D	88.971	408	21	5	1543	1950	361190121	361190504	1.780000e-132	483
22	TraesCS5D01G147500	chr6A	89.877	405	17	5	1543	1947	29402735	29403115	1.770000e-137	499
23	TraesCS5D01G147500	chr6A	88.753	409	22	5	1539	1947	612718212	612718596	2.300000e-131	479
24	TraesCS5D01G147500	chr6B	88.642	405	22	5	1543	1947	49502424	49502804	3.850000e-129	472
25	TraesCS5D01G147500	chr7D	88.642	405	21	6	1546	1950	592270025	592269646	1.390000e-128	470
26	TraesCS5D01G147500	chr3B	87.901	405	25	6	1546	1950	711740033	711739653	3.880000e-124	455

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	TraesCS5D01G147500	chr5D	233746700	233749997	3297	True	6091.000000	6091	100.000	1	3298	1	chr5D.!!$R2	3297
1	TraesCS5D01G147500	chr5D	439014871	439015541	670	False	802.000000	802	88.304	3	679	1	chr5D.!!$F1	676
2	TraesCS5D01G147500	chr5A	321001039	321003625	2586	False	3648.000000	3648	92.131	679	3296	1	chr5A.!!$F1	2617
3	TraesCS5D01G147500	chr5B	271109772	271112522	2750	False	1279.333333	2174	93.647	679	3230	3	chr5B.!!$F2	2551
4	TraesCS5D01G147500	chr4A	636393307	636394005	698	False	828.000000	828	88.429	1	683	1	chr4A.!!$F1	682
5	TraesCS5D01G147500	chr3D	472200969	472201635	666	False	761.000000	761	87.391	1	679	1	chr3D.!!$F2	678
6	TraesCS5D01G147500	chr3D	144255712	144256373	661	False	686.000000	686	85.651	18	679	1	chr3D.!!$F1	661
7	TraesCS5D01G147500	chr3D	43539876	43540525	649	True	595.000000	595	83.531	20	679	1	chr3D.!!$R1	659
8	TraesCS5D01G147500	chr2D	643845388	643846049	661	False	756.000000	756	87.278	8	679	1	chr2D.!!$F1	671
9	TraesCS5D01G147500	chr1D	22505210	22505870	660	True	750.000000	750	87.332	23	683	1	chr1D.!!$R1	660
10	TraesCS5D01G147500	chr1D	483837922	483838598	676	False	704.000000	704	85.857	1	679	1	chr1D.!!$F1	678
11	TraesCS5D01G147500	chr7B	626060716	626061363	647	False	678.000000	678	85.714	22	677	1	chr7B.!!$F2	655
12	TraesCS5D01G147500	chr3A	717821966	717822630	664	True	660.000000	660	84.911	16	677	1	chr3A.!!$R2	661
13	TraesCS5D01G147500	chr3A	42451897	42452501	604	True	584.000000	584	84.339	20	622	1	chr3A.!!$R1	602

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
356	357	0.247537	CGATGACGACGACGATGACA	60.248	55.000	15.32	8.67	42.66	3.58	F
386	408	1.093159	CGACTACACCCGCTTCTACT	58.907	55.000	0.00	0.00	0.00	2.57	F
932	1016	1.677518	CGTTCCATTCCGTTCCATCCA	60.678	52.381	0.00	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1635	1720	0.678048	AGAAAATGACAGCGGCTCCC	60.678	55.000	0.00	0.00	4.30	R
2093	2220	1.300620	CACCTCTTTGCCGTCGTGA	60.301	57.895	0.00	0.00	4.35	R
2814	2947	0.909610	TTCCCAGCACGGAATCTCCT	60.910	55.000	0.57	36.98	3.69	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
114	115	4.180946	CGACGAGTCCGCCCTCAG	62.181	72.222	0.00	0.00	39.95	3.35
356	357	0.247537	CGATGACGACGACGATGACA	60.248	55.000	15.32	8.67	42.66	3.58
362	363	1.154282	GACGACGATGACAGCGACA	60.154	57.895	21.46	0.00	0.00	4.35
386	408	1.093159	CGACTACACCCGCTTCTACT	58.907	55.000	0.00	0.00	0.00	2.57
441	495	4.581868	AGGCGTAGTTTGGCATAGTTTAA	58.418	39.130	0.00	0.00	0.00	1.52
471	525	3.249799	TCAGTCGTAGTTTGCATGGTTTG	59.750	43.478	0.00	0.00	0.00	2.93
511	576	6.497785	TTTAACAAAGTTTCACCGAGTTCA	57.502	33.333	0.00	0.00	0.00	3.18
542	609	5.378292	TTGCCGAGTTTGCACATATTTTA	57.622	34.783	0.00	0.00	38.72	1.52
554	621	4.085466	GCACATATTTTATACGCGACGTCA	60.085	41.667	15.93	0.00	41.54	4.35
555	622	5.388061	GCACATATTTTATACGCGACGTCAT	60.388	40.000	15.93	3.76	41.54	3.06
594	662	3.032339	CCGGCGACTAGGAGCTAC	58.968	66.667	9.30	0.00	0.00	3.58
756	838	4.846168	ACATTCTTAGAAGGTTCCCTCC	57.154	45.455	6.44	0.00	30.89	4.30
792	874	2.388661	CCCTATCCTGCCCTAGGGTTG	61.389	61.905	28.96	20.23	46.28	3.77
834	916	2.513753	CCCAACACACTCATAAAGGCA	58.486	47.619	0.00	0.00	0.00	4.75
836	918	3.411446	CCAACACACTCATAAAGGCAGA	58.589	45.455	0.00	0.00	0.00	4.26
837	919	3.189287	CCAACACACTCATAAAGGCAGAC	59.811	47.826	0.00	0.00	0.00	3.51
932	1016	1.677518	CGTTCCATTCCGTTCCATCCA	60.678	52.381	0.00	0.00	0.00	3.41
934	1018	3.023832	GTTCCATTCCGTTCCATCCAAT	58.976	45.455	0.00	0.00	0.00	3.16
1297	1381	3.485877	GCTCTTCCCATTCGACGAATTTG	60.486	47.826	20.12	13.78	28.87	2.32
1635	1720	5.580691	TGAAACTTTGTATCCTATCTGCACG	59.419	40.000	0.00	0.00	0.00	5.34
1713	1832	8.880878	AATAAAACAAGAATGTGGGTTTGTAC	57.119	30.769	0.00	0.00	40.46	2.90
1964	2091	3.077359	AGTTTACATGTCTTCAGCCTGC	58.923	45.455	0.00	0.00	0.00	4.85
1965	2092	2.813754	GTTTACATGTCTTCAGCCTGCA	59.186	45.455	0.00	0.00	0.00	4.41
1966	2093	2.099141	TACATGTCTTCAGCCTGCAC	57.901	50.000	0.00	0.00	0.00	4.57
2142	2269	0.108567	GAGGAAGAAGGCGAGGACAC	60.109	60.000	0.00	0.00	0.00	3.67
2171	2298	4.357947	GACACGGCGCCTCTGACA	62.358	66.667	26.68	0.00	0.00	3.58
2206	2333	3.716006	CAGCCTCGTGGTGCAACG	61.716	66.667	4.54	4.54	44.92	4.10
2273	2400	1.476007	GGATCTGCTGGAGGCCGTAT	61.476	60.000	0.00	0.00	40.92	3.06
2343	2470	5.473796	GAACCTCTGTTCGTTTTACACAA	57.526	39.130	0.00	0.00	41.35	3.33
2399	2530	1.905922	GACTGTCGCCTGAAGCAAGC	61.906	60.000	0.00	0.00	44.04	4.01
2439	2570	3.278574	AGTGCTGTTCAGTTAGTTGCAA	58.721	40.909	0.00	0.00	0.00	4.08
2511	2642	0.169451	TTCTGACATGCAGCAATGCG	59.831	50.000	0.00	0.00	44.52	4.73
2562	2693	2.044123	ATCTCGGACTTGAAATGCCC	57.956	50.000	0.00	0.00	0.00	5.36
2577	2708	3.857157	ATGCCCGTACCATTAATCTGT	57.143	42.857	0.00	0.00	0.00	3.41
2607	2738	1.783071	TCCTACATGACGGTGCCATA	58.217	50.000	0.00	0.00	0.00	2.74
2650	2781	0.464036	TGCACCGTCAGAGAAAGTGT	59.536	50.000	0.00	0.00	0.00	3.55
2658	2789	3.490933	CGTCAGAGAAAGTGTCAAGGACA	60.491	47.826	0.00	0.00	40.50	4.02
2822	2955	9.113838	TGAAATATACTGCAGAAAAGGAGATTC	57.886	33.333	23.35	12.25	0.00	2.52
2823	2956	8.457238	AAATATACTGCAGAAAAGGAGATTCC	57.543	34.615	23.35	0.00	36.58	3.01
2825	2958	2.039084	ACTGCAGAAAAGGAGATTCCGT	59.961	45.455	23.35	0.00	42.75	4.69
2827	2960	1.131315	GCAGAAAAGGAGATTCCGTGC	59.869	52.381	0.00	0.00	42.75	5.34
2842	2986	4.448537	TCCGTGCTGGGAATTTTATTTG	57.551	40.909	0.00	0.00	38.76	2.32
2851	2995	9.249053	TGCTGGGAATTTTATTTGTACAGAATA	57.751	29.630	0.00	1.50	0.00	1.75
2878	3022	4.448537	AGAGTCAAGAAGATGGACGAAG	57.551	45.455	0.00	0.00	36.68	3.79
2902	3046	6.615726	AGTTGAGGGAATATAGCTGTAAAGGA	59.384	38.462	0.00	0.00	0.00	3.36
3068	3219	5.163591	TGCATCTCATTCTGCTAATGTTTGG	60.164	40.000	10.77	3.80	39.16	3.28
3075	3226	5.627499	TTCTGCTAATGTTTGGATGTGTC	57.373	39.130	0.00	0.00	0.00	3.67
3089	3240	5.541845	TGGATGTGTCTGTAAGTTCAGAAG	58.458	41.667	6.60	0.00	44.48	2.85
3160	3471	6.974932	ATATTGCTCAGGCTAATACAATCG	57.025	37.500	7.29	0.00	39.59	3.34
3164	3475	4.751600	TGCTCAGGCTAATACAATCGATTG	59.248	41.667	31.51	31.51	40.29	2.67
3292	3603	8.012957	ACCTCCTAATTACAATACTCACTCTG	57.987	38.462	0.00	0.00	0.00	3.35
3293	3604	7.839705	ACCTCCTAATTACAATACTCACTCTGA	59.160	37.037	0.00	0.00	0.00	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	3.710722	CTTCACCGGGAGCAGCCT	61.711	66.667	6.32	0.00	36.66	4.58
114	115	1.615424	TAGTCCTCCTTGGCCCACC	60.615	63.158	0.00	0.00	35.26	4.61
356	357	2.265904	TGTAGTCGCCACTGTCGCT	61.266	57.895	0.00	0.00	33.62	4.93
362	363	4.065281	GCGGGTGTAGTCGCCACT	62.065	66.667	0.00	0.00	45.42	4.00
386	408	1.522092	CCTACATGCCGAGAAGCCA	59.478	57.895	0.00	0.00	0.00	4.75
411	454	3.711541	AAACTACGCCTAGCCGCCG	62.712	63.158	0.00	0.00	0.00	6.46
441	495	3.367025	GCAAACTACGACTGAATTACGCT	59.633	43.478	0.00	0.00	0.00	5.07
554	621	2.754658	AGGTCGCCCGAGTTCGAT	60.755	61.111	2.59	0.00	43.02	3.59
555	622	3.744719	CAGGTCGCCCGAGTTCGA	61.745	66.667	2.59	0.00	43.02	3.71
756	838	0.919710	AGGGTAGGCTTTAGCTTGGG	59.080	55.000	0.00	0.00	41.70	4.12
792	874	1.796617	GCATGCGTTGGAAGATTCTGC	60.797	52.381	0.00	0.00	0.00	4.26
834	916	4.039357	CGAGTGACGTGGCGGTCT	62.039	66.667	0.00	0.00	37.81	3.85
854	936	2.283604	GGGTTTTCGGTGGGGCAT	60.284	61.111	0.00	0.00	0.00	4.40
914	998	2.889170	TTGGATGGAACGGAATGGAA	57.111	45.000	0.00	0.00	0.00	3.53
932	1016	4.202212	GGTTTTATATTTCGGCAGGCCATT	60.202	41.667	5.01	0.00	35.37	3.16
934	1018	2.691011	GGTTTTATATTTCGGCAGGCCA	59.309	45.455	5.01	0.00	35.37	5.36
1276	1360	3.932710	TCAAATTCGTCGAATGGGAAGAG	59.067	43.478	20.62	6.69	32.14	2.85
1297	1381	3.498397	TGAAGCCAACAATCGTCTCTTTC	59.502	43.478	0.00	0.00	0.00	2.62
1540	1625	2.425312	ACAGTGCAGATAGGAGACGAAG	59.575	50.000	0.00	0.00	0.00	3.79
1635	1720	0.678048	AGAAAATGACAGCGGCTCCC	60.678	55.000	0.00	0.00	0.00	4.30
1964	2091	2.518349	GTGGTGGTGGTGGTGGTG	60.518	66.667	0.00	0.00	0.00	4.17
1965	2092	3.816090	GGTGGTGGTGGTGGTGGT	61.816	66.667	0.00	0.00	0.00	4.16
1966	2093	3.814906	TGGTGGTGGTGGTGGTGG	61.815	66.667	0.00	0.00	0.00	4.61
2093	2220	1.300620	CACCTCTTTGCCGTCGTGA	60.301	57.895	0.00	0.00	0.00	4.35
2171	2298	2.672307	AAGACGTCCTCGCCGAGT	60.672	61.111	13.83	0.00	41.18	4.18
2273	2400	3.110358	CGAAGAACATATCAACGGCGTA	58.890	45.455	15.20	0.00	0.00	4.42
2309	2436	1.872679	GAGGTTCGTCGATCACCGC	60.873	63.158	9.84	7.18	38.37	5.68
2366	2494	2.797156	CGACAGTCACTTGAAGAACTGG	59.203	50.000	24.80	12.35	0.00	4.00
2399	2530	2.027377	ACTTCATCTCCACTGGCTCTTG	60.027	50.000	0.00	0.00	0.00	3.02
2439	2570	1.109323	GCTTTCAGCCAACCCACAGT	61.109	55.000	0.00	0.00	34.48	3.55
2511	2642	4.577875	TGGGATTTCATTTTTGATGCACC	58.422	39.130	0.00	0.00	0.00	5.01
2577	2708	7.207383	CACCGTCATGTAGGAACAATAATCTA	58.793	38.462	14.41	0.00	39.58	1.98
2607	2738	4.477213	ACTAACACTAGGTGGCCCATTAAT	59.523	41.667	0.00	0.00	37.94	1.40
2650	2781	5.607939	TTTGTCTTCTGTACTGTCCTTGA	57.392	39.130	0.00	0.00	0.00	3.02
2658	2789	7.865706	AACTTGTCATTTTGTCTTCTGTACT	57.134	32.000	0.00	0.00	0.00	2.73
2690	2823	2.271497	CAGGCTTCTCTGCTGGGG	59.729	66.667	0.00	0.00	0.00	4.96
2796	2929	9.113838	GAATCTCCTTTTCTGCAGTATATTTCA	57.886	33.333	14.67	0.00	0.00	2.69
2814	2947	0.909610	TTCCCAGCACGGAATCTCCT	60.910	55.000	0.57	0.00	36.98	3.69
2822	2955	4.186856	ACAAATAAAATTCCCAGCACGG	57.813	40.909	0.00	0.00	0.00	4.94
2823	2956	5.704888	TGTACAAATAAAATTCCCAGCACG	58.295	37.500	0.00	0.00	0.00	5.34
2825	2958	7.531857	TTCTGTACAAATAAAATTCCCAGCA	57.468	32.000	0.00	0.00	0.00	4.41
2842	2986	9.515020	CTTCTTGACTCTTCTGATATTCTGTAC	57.485	37.037	0.00	0.00	0.00	2.90
2851	2995	5.394005	CGTCCATCTTCTTGACTCTTCTGAT	60.394	44.000	0.00	0.00	0.00	2.90
2860	3004	4.307432	TCAACTTCGTCCATCTTCTTGAC	58.693	43.478	0.00	0.00	0.00	3.18
2863	3007	3.307059	CCCTCAACTTCGTCCATCTTCTT	60.307	47.826	0.00	0.00	0.00	2.52
2878	3022	6.827727	TCCTTTACAGCTATATTCCCTCAAC	58.172	40.000	0.00	0.00	0.00	3.18
2894	3038	6.404844	CGAAGACAAGAGAGCTATCCTTTACA	60.405	42.308	4.34	0.00	0.00	2.41
2902	3046	2.757868	ACTGCGAAGACAAGAGAGCTAT	59.242	45.455	0.00	0.00	0.00	2.97
2908	3052	2.447244	AAGGACTGCGAAGACAAGAG	57.553	50.000	0.00	0.00	0.00	2.85
3068	3219	8.764524	ATAACTTCTGAACTTACAGACACATC	57.235	34.615	0.00	0.00	44.94	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.