AutoCloner

Multiple sequence alignment - TraesCS1A01G221400

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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	TraesCS1A01G221400	chr1A	100.000	3329	0	0	1	3329	390637795	390641123	0.000000e+00	6148
1	TraesCS1A01G221400	chr1D	95.053	2365	91	13	865	3220	310773798	310776145	0.000000e+00	3696
2	TraesCS1A01G221400	chr1D	86.176	774	85	19	12	770	202476085	202475319	0.000000e+00	817
3	TraesCS1A01G221400	chr1D	93.750	112	7	0	3218	3329	310776268	310776379	5.710000e-38	169
4	TraesCS1A01G221400	chr1D	93.182	88	6	0	770	857	310773419	310773506	2.700000e-26	130
5	TraesCS1A01G221400	chr1B	93.096	2419	103	18	856	3258	420415192	420417562	0.000000e+00	3483
6	TraesCS1A01G221400	chr1B	86.229	777	91	13	1	769	162354845	162354077	0.000000e+00	828
7	TraesCS1A01G221400	chr6D	88.571	770	79	7	9	771	162111306	162110539	0.000000e+00	926
8	TraesCS1A01G221400	chr6D	87.611	791	82	13	1	780	6001530	6002315	0.000000e+00	904
9	TraesCS1A01G221400	chr6D	89.451	692	61	10	2	686	254819008	254818322	0.000000e+00	863
10	TraesCS1A01G221400	chr3D	88.046	778	79	10	5	774	496182336	496181565	0.000000e+00	909
11	TraesCS1A01G221400	chr3D	76.754	456	81	18	1790	2242	108288190	108287757	7.180000e-57	231
12	TraesCS1A01G221400	chr6A	86.632	778	90	11	1	772	597326953	597327722	0.000000e+00	848
13	TraesCS1A01G221400	chr3A	86.118	778	97	9	1	772	693980563	693979791	0.000000e+00	828
14	TraesCS1A01G221400	chr3B	85.974	770	91	13	12	774	602244246	602245005	0.000000e+00	808
15	TraesCS1A01G221400	chr2D	77.426	474	91	13	1777	2242	618302366	618301901	5.470000e-68	268
16	TraesCS1A01G221400	chr2B	77.704	453	90	8	1777	2222	754977651	754977203	1.970000e-67	267
17	TraesCS1A01G221400	chr5A	77.124	459	87	16	1790	2242	697052507	697052061	1.980000e-62	250
18	TraesCS1A01G221400	chr4D	76.344	465	89	17	1790	2242	509096156	509095701	2.580000e-56	230
19	TraesCS1A01G221400	chr4B	76.923	364	50	19	1894	2253	658179800	658180133	3.410000e-40	176

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	TraesCS1A01G221400	chr1A	390637795	390641123	3328	False	6148.000000	6148	100.000	1	3329	1	chr1A.!!$F1	3328
1	TraesCS1A01G221400	chr1D	310773419	310776379	2960	False	1331.666667	3696	93.995	770	3329	3	chr1D.!!$F1	2559
2	TraesCS1A01G221400	chr1D	202475319	202476085	766	True	817.000000	817	86.176	12	770	1	chr1D.!!$R1	758
3	TraesCS1A01G221400	chr1B	420415192	420417562	2370	False	3483.000000	3483	93.096	856	3258	1	chr1B.!!$F1	2402
4	TraesCS1A01G221400	chr1B	162354077	162354845	768	True	828.000000	828	86.229	1	769	1	chr1B.!!$R1	768
5	TraesCS1A01G221400	chr6D	162110539	162111306	767	True	926.000000	926	88.571	9	771	1	chr6D.!!$R1	762
6	TraesCS1A01G221400	chr6D	6001530	6002315	785	False	904.000000	904	87.611	1	780	1	chr6D.!!$F1	779
7	TraesCS1A01G221400	chr6D	254818322	254819008	686	True	863.000000	863	89.451	2	686	1	chr6D.!!$R2	684
8	TraesCS1A01G221400	chr3D	496181565	496182336	771	True	909.000000	909	88.046	5	774	1	chr3D.!!$R2	769
9	TraesCS1A01G221400	chr6A	597326953	597327722	769	False	848.000000	848	86.632	1	772	1	chr6A.!!$F1	771
10	TraesCS1A01G221400	chr3A	693979791	693980563	772	True	828.000000	828	86.118	1	772	1	chr3A.!!$R1	771
11	TraesCS1A01G221400	chr3B	602244246	602245005	759	False	808.000000	808	85.974	12	774	1	chr3B.!!$F1	762

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
637	662	0.103937	CAAAAGCGGCCCAAACTTGA	59.896	50.000	0.00	0.00	3.02	F
787	814	0.179119	GCCTAATACGTGTGCCGAGT	60.179	55.000	0.00	40.70	4.18	F
2022	2333	1.008538	CGCTGGCGAAACAAAAGCT	60.009	52.632	9.51	42.83	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2007	2318	0.030101	CGGAAGCTTTTGTTTCGCCA	59.970	50.000	40.01	5.69	R
2284	2595	1.798813	CAGGACCGCACAAAGAACTAC	59.201	52.381	0.00	2.73	R
2842	3171	1.566298	ATCTGAAGTCCCCCAGCCAC	61.566	60.000	0.00	5.01	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
32	35	6.817184	AGTAGCACATACTCCATCGTTTAAT	58.183	36.000	0.00	0.00	40.99	1.40
46	49	7.336679	TCCATCGTTTAATCACTTGATGAACAT	59.663	33.333	14.32	0.00	41.93	2.71
118	121	1.724623	GCAGTCGTCGCACTTAATGAA	59.275	47.619	0.00	0.00	0.00	2.57
225	228	0.685660	TAGATCCGAGCGGCTAGAGA	59.314	55.000	11.90	7.59	34.68	3.10
244	250	2.125147	GCCACTACCTGCATGCGA	60.125	61.111	14.09	1.21	0.00	5.10
329	335	2.435938	CAGCCGGGCGAGCTTAAA	60.436	61.111	14.39	0.00	38.95	1.52
481	498	4.947147	AACGGCAGCGAGGGCAAA	62.947	61.111	0.00	0.00	43.41	3.68
539	562	1.064240	GGGGGCGAATAGAAAAAGGGA	60.064	52.381	0.00	0.00	0.00	4.20
582	607	1.446792	CAAGAGAGGACACGCGCAT	60.447	57.895	5.73	0.00	0.00	4.73
637	662	0.103937	CAAAAGCGGCCCAAACTTGA	59.896	50.000	0.00	0.00	0.00	3.02
644	669	2.434331	CCCAAACTTGAGCCGGGA	59.566	61.111	2.18	0.00	39.44	5.14
645	670	1.000896	CCCAAACTTGAGCCGGGAT	60.001	57.895	2.18	0.00	39.44	3.85
646	671	1.315257	CCCAAACTTGAGCCGGGATG	61.315	60.000	2.18	0.00	39.44	3.51
708	733	2.752075	TCATGCATTGGGCCATCTAA	57.248	45.000	7.26	0.00	43.89	2.10
750	776	1.359848	GACGCATCCAAACGAGATGT	58.640	50.000	0.00	0.00	42.58	3.06
787	814	0.179119	GCCTAATACGTGTGCCGAGT	60.179	55.000	0.00	0.00	40.70	4.18
801	828	2.561956	CGAGTCCGGGTGTGACACT	61.562	63.158	16.07	0.00	35.15	3.55
866	1177	7.708051	TCTGACAACAGCACTTAGAGATATAC	58.292	38.462	0.00	0.00	43.17	1.47
893	1204	8.095452	AGGTAGAAGATGGAGTACAAATCATT	57.905	34.615	0.00	0.00	0.00	2.57
904	1215	9.137459	TGGAGTACAAATCATTTTCTACCAAAA	57.863	29.630	0.00	0.00	0.00	2.44
975	1286	4.214980	TCAGCTCGCAGAAAAGAAAAAG	57.785	40.909	0.00	0.00	34.09	2.27
976	1287	3.003689	TCAGCTCGCAGAAAAGAAAAAGG	59.996	43.478	0.00	0.00	34.09	3.11
977	1288	2.294512	AGCTCGCAGAAAAGAAAAAGGG	59.705	45.455	0.00	0.00	34.09	3.95
996	1307	2.698274	GGGAAAAAGCCTTTGGTCTTCA	59.302	45.455	0.00	0.00	0.00	3.02
1059	1370	4.157958	CGGGGAGACGACGACGAC	62.158	72.222	15.32	8.08	42.66	4.34
1060	1371	4.157958	GGGGAGACGACGACGACG	62.158	72.222	17.60	17.60	42.66	5.12
1108	1419	2.835431	CGAGGACCCATCGGCTCT	60.835	66.667	0.00	0.00	36.54	4.09
1137	1448	4.282873	CGAACCTTTTTGTTCTCTTCTGC	58.717	43.478	0.00	0.00	41.95	4.26
1147	1458	4.051922	TGTTCTCTTCTGCTTCGTTTCTC	58.948	43.478	0.00	0.00	0.00	2.87
1148	1459	4.202161	TGTTCTCTTCTGCTTCGTTTCTCT	60.202	41.667	0.00	0.00	0.00	3.10
1433	1744	2.436115	GAAGCGGTACCTGGCCAC	60.436	66.667	10.90	0.00	0.00	5.01
1765	2076	4.143333	CCACCGTCGGCTACCTGG	62.143	72.222	12.28	7.37	0.00	4.45
2022	2333	1.008538	CGCTGGCGAAACAAAAGCT	60.009	52.632	9.51	0.00	42.83	3.74
2025	2336	1.770957	CTGGCGAAACAAAAGCTTCC	58.229	50.000	0.00	0.00	0.00	3.46
2127	2438	2.627945	GTCATGTACCCGAGCATCAAA	58.372	47.619	0.00	0.00	33.17	2.69
2284	2595	4.479993	CTGCTTCCTCGGCTGGGG	62.480	72.222	4.49	4.49	0.00	4.96
2366	2677	7.915293	TCGTTTTTATAGGCAAAAGATCAGA	57.085	32.000	0.00	0.00	0.00	3.27
2454	2768	6.705302	TCTCTTCTTGCATAGACAGTCAAAT	58.295	36.000	2.66	0.00	30.90	2.32
2469	2783	4.346734	GTCAAATGACGACAGCATGATT	57.653	40.909	0.00	0.00	35.71	2.57
2470	2784	4.093514	GTCAAATGACGACAGCATGATTG	58.906	43.478	0.00	0.00	35.71	2.67
2471	2785	5.478976	GTCAAATGACGACAGCATGATTGC	61.479	45.833	0.00	0.00	41.18	3.56
2472	2786	7.816941	GTCAAATGACGACAGCATGATTGCA	62.817	44.000	0.00	0.00	42.32	4.08
2528	2844	9.788960	AAAATTTGAAACTCTACTGTTTGACTC	57.211	29.630	0.00	0.00	39.86	3.36
2542	2858	4.631377	TGTTTGACTCGAGGATTATGCTTG	59.369	41.667	18.41	0.00	0.00	4.01
2557	2873	0.380378	GCTTGGTGACAGCGACAAAA	59.620	50.000	0.00	0.00	44.54	2.44
2568	2884	4.844267	ACAGCGACAAAATTTCACTACAC	58.156	39.130	0.00	0.00	0.00	2.90
2673	2996	2.888863	CAGTCCCCTCTGCGACTC	59.111	66.667	0.00	0.00	37.23	3.36
2828	3154	1.966451	CGAAGTTGAGGCGGGCTTT	60.966	57.895	5.24	0.00	0.00	3.51
2833	3159	0.321298	GTTGAGGCGGGCTTTACAGA	60.321	55.000	5.24	0.00	0.00	3.41
2842	3171	2.939103	CGGGCTTTACAGAAGATGAAGG	59.061	50.000	0.00	0.00	0.00	3.46
2957	3286	6.322712	TCTGCAATTCAATCCATCATGATGAA	59.677	34.615	32.71	21.25	41.20	2.57
2958	3287	7.015195	TCTGCAATTCAATCCATCATGATGAAT	59.985	33.333	32.71	22.38	41.20	2.57
2961	3290	7.544566	GCAATTCAATCCATCATGATGAATACC	59.455	37.037	32.71	16.20	41.20	2.73
2964	3293	8.715190	TTCAATCCATCATGATGAATACCAAT	57.285	30.769	32.71	13.32	41.20	3.16
2965	3294	8.117813	TCAATCCATCATGATGAATACCAATG	57.882	34.615	32.71	15.57	41.20	2.82
2966	3295	7.945664	TCAATCCATCATGATGAATACCAATGA	59.054	33.333	32.71	17.46	41.20	2.57
2971	3300	9.772973	CCATCATGATGAATACCAATGAAAAAT	57.227	29.630	32.71	0.00	41.20	1.82
2974	3303	9.970395	TCATGATGAATACCAATGAAAAATAGC	57.030	29.630	0.00	0.00	0.00	2.97
2975	3304	9.752961	CATGATGAATACCAATGAAAAATAGCA	57.247	29.630	0.00	0.00	0.00	3.49
2976	3305	9.976511	ATGATGAATACCAATGAAAAATAGCAG	57.023	29.630	0.00	0.00	0.00	4.24
2977	3306	8.970020	TGATGAATACCAATGAAAAATAGCAGT	58.030	29.630	0.00	0.00	0.00	4.40
3241	3704	2.092429	TGAAGGGACAGGCACCAATATC	60.092	50.000	0.00	0.00	0.00	1.63
3266	3729	7.660208	TCGTAGTCTATAGAGCAACATGTGATA	59.340	37.037	1.64	0.00	0.00	2.15
3271	3734	8.310382	GTCTATAGAGCAACATGTGATATCCTT	58.690	37.037	1.64	0.00	0.00	3.36
3304	3767	5.626543	GTGTGTGTGTATGCTTCAAAAGATG	59.373	40.000	0.00	0.00	0.00	2.90
3317	3780	2.559668	CAAAAGATGAGCCACCATGTGT	59.440	45.455	0.00	0.00	0.00	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	23	6.652900	TGTTCATCAAGTGATTAAACGATGGA	59.347	34.615	0.00	0.00	36.54	3.41
32	35	3.534554	CGGATGGATGTTCATCAAGTGA	58.465	45.455	13.64	0.00	43.82	3.41
163	166	2.693591	AGATACACGAATGATGGTCGGT	59.306	45.455	0.00	0.00	42.82	4.69
171	174	1.533129	CGCCGACAGATACACGAATGA	60.533	52.381	0.00	0.00	0.00	2.57
225	228	1.746615	CGCATGCAGGTAGTGGCTT	60.747	57.895	19.57	0.00	0.00	4.35
326	332	1.153588	GCGGATCCGGTCGGTTTTA	60.154	57.895	33.98	0.00	40.19	1.52
362	368	1.745115	GCCACCTGATTAGCGCACA	60.745	57.895	11.47	3.15	0.00	4.57
430	436	4.299547	TTGTGCAGCTCGGACGCT	62.300	61.111	0.00	0.00	39.19	5.07
464	470	4.947147	TTTGCCCTCGCTGCCGTT	62.947	61.111	0.00	0.00	35.36	4.44
465	471	4.947147	TTTTGCCCTCGCTGCCGT	62.947	61.111	0.00	0.00	35.36	5.68
481	498	1.650528	CCCTCCACTCTTCTCCACTT	58.349	55.000	0.00	0.00	0.00	3.16
522	545	2.885266	GGGATCCCTTTTTCTATTCGCC	59.115	50.000	24.69	0.00	0.00	5.54
539	562	2.507854	CCGTCGGTGGCATAGGGAT	61.508	63.158	2.08	0.00	0.00	3.85
566	589	1.433879	GTATGCGCGTGTCCTCTCT	59.566	57.895	13.61	0.00	0.00	3.10
568	591	2.102357	CGTATGCGCGTGTCCTCT	59.898	61.111	13.61	0.00	0.00	3.69
602	627	2.765689	TTTGGGGTGAAATGGACAGT	57.234	45.000	0.00	0.00	0.00	3.55
644	669	0.393077	CTATCCGCTTTCGACCCCAT	59.607	55.000	0.00	0.00	38.10	4.00
645	670	0.685131	TCTATCCGCTTTCGACCCCA	60.685	55.000	0.00	0.00	38.10	4.96
646	671	0.462789	TTCTATCCGCTTTCGACCCC	59.537	55.000	0.00	0.00	38.10	4.95
686	711	3.247948	AGATGGCCCAATGCATGAATA	57.752	42.857	0.00	0.00	43.89	1.75
687	712	2.097110	AGATGGCCCAATGCATGAAT	57.903	45.000	0.00	0.00	43.89	2.57
695	720	4.998051	ACGGATAAATTAGATGGCCCAAT	58.002	39.130	0.00	0.00	0.00	3.16
787	814	2.842462	AGCAGTGTCACACCCGGA	60.842	61.111	0.73	0.00	34.49	5.14
796	823	1.537135	GGAGCTAATCCGAGCAGTGTC	60.537	57.143	0.00	0.00	45.43	3.67
834	861	8.621532	TCTAAGTGCTGTTGTCAGATTTTTAT	57.378	30.769	0.00	0.00	43.76	1.40
838	865	5.858381	TCTCTAAGTGCTGTTGTCAGATTT	58.142	37.500	0.00	0.00	43.76	2.17
848	875	7.999545	TCTACCTTGTATATCTCTAAGTGCTGT	59.000	37.037	0.00	0.00	0.00	4.40
866	1177	7.331026	TGATTTGTACTCCATCTTCTACCTTG	58.669	38.462	0.00	0.00	0.00	3.61
945	1256	0.792640	CTGCGAGCTGATTCAAACGT	59.207	50.000	0.00	0.00	0.00	3.99
956	1267	2.294512	CCCTTTTTCTTTTCTGCGAGCT	59.705	45.455	0.00	0.00	0.00	4.09
975	1286	2.698274	TGAAGACCAAAGGCTTTTTCCC	59.302	45.455	10.36	5.76	0.00	3.97
976	1287	3.717707	GTGAAGACCAAAGGCTTTTTCC	58.282	45.455	10.36	2.08	0.00	3.13
977	1288	3.181490	ACGTGAAGACCAAAGGCTTTTTC	60.181	43.478	10.36	11.93	0.00	2.29
996	1307	1.062685	CGAGCTCTGCGTCATACGT	59.937	57.895	12.85	0.00	44.73	3.57
1137	1448	7.902403	GCAAAGAATCTTATGAGAGAAACGAAG	59.098	37.037	0.00	0.00	34.85	3.79
1147	1458	2.600792	GCGCGGCAAAGAATCTTATGAG	60.601	50.000	8.83	0.00	0.00	2.90
1148	1459	1.330521	GCGCGGCAAAGAATCTTATGA	59.669	47.619	8.83	0.00	0.00	2.15
1264	1575	2.170187	AGAGGAGGCAAAGTATCAGCAG	59.830	50.000	0.00	0.00	0.00	4.24
1568	1879	3.052620	ATCTGGTCGAGCGTCACGG	62.053	63.158	10.46	0.00	0.00	4.94
1668	1979	1.878775	CGGCTTGCCCTTGAAGAAG	59.121	57.895	6.02	0.00	0.00	2.85
1771	2082	4.657824	CACGGCCCTCACGTCGTT	62.658	66.667	0.00	0.00	43.58	3.85
2007	2318	0.030101	CGGAAGCTTTTGTTTCGCCA	59.970	50.000	0.00	0.00	40.01	5.69
2127	2438	2.665603	GCCTTCTTCTCCAGCGGT	59.334	61.111	0.00	0.00	0.00	5.68
2284	2595	1.798813	CAGGACCGCACAAAGAACTAC	59.201	52.381	0.00	0.00	0.00	2.73
2425	2739	6.471146	ACTGTCTATGCAAGAAGAGAAACAT	58.529	36.000	0.00	0.00	35.47	2.71
2528	2844	2.868583	CTGTCACCAAGCATAATCCTCG	59.131	50.000	0.00	0.00	0.00	4.63
2542	2858	3.042887	GTGAAATTTTGTCGCTGTCACC	58.957	45.455	0.00	0.00	0.00	4.02
2557	2873	6.293626	GCAATGTCAGTTCTGTGTAGTGAAAT	60.294	38.462	0.00	0.00	0.00	2.17
2568	2884	6.373186	ACATATGATGCAATGTCAGTTCTG	57.627	37.500	10.38	0.00	30.54	3.02
2672	2995	1.974265	TGTTTGCGATGTCAAAGGGA	58.026	45.000	0.00	0.00	36.71	4.20
2673	2996	2.791383	TTGTTTGCGATGTCAAAGGG	57.209	45.000	0.00	0.00	36.71	3.95
2828	3154	2.237143	CCAGCCACCTTCATCTTCTGTA	59.763	50.000	0.00	0.00	0.00	2.74
2833	3159	1.693640	CCCCAGCCACCTTCATCTT	59.306	57.895	0.00	0.00	0.00	2.40
2842	3171	1.566298	ATCTGAAGTCCCCCAGCCAC	61.566	60.000	0.00	0.00	0.00	5.01
2957	3286	5.598417	GGGGACTGCTATTTTTCATTGGTAT	59.402	40.000	0.00	0.00	0.00	2.73
2958	3287	4.953579	GGGGACTGCTATTTTTCATTGGTA	59.046	41.667	0.00	0.00	0.00	3.25
2961	3290	4.026052	AGGGGGACTGCTATTTTTCATTG	58.974	43.478	0.00	0.00	0.00	2.82
2964	3293	3.825908	AAGGGGGACTGCTATTTTTCA	57.174	42.857	0.00	0.00	0.00	2.69
2965	3294	6.599356	TTTTAAGGGGGACTGCTATTTTTC	57.401	37.500	0.00	0.00	0.00	2.29
3118	3453	9.425248	TTCTAATGCTTAGGATTTGGATTCATT	57.575	29.630	3.97	0.00	34.00	2.57
3188	3526	2.892852	ACTGGAATCATGTGGTGTTTGG	59.107	45.455	0.00	0.00	0.00	3.28
3241	3704	6.061231	TCACATGTTGCTCTATAGACTACG	57.939	41.667	0.00	0.00	0.00	3.51
3266	3729	5.376625	ACACACACACAATTAGTCAAGGAT	58.623	37.500	0.00	0.00	0.00	3.24
3271	3734	5.304778	AGCATACACACACACAATTAGTCA	58.695	37.500	0.00	0.00	0.00	3.41
3304	3767	1.755179	ATGCTAACACATGGTGGCTC	58.245	50.000	6.82	0.00	37.94	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.