AutoCloner

Multiple sequence alignment - TraesCS1D01G015000

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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	TraesCS1D01G015000	chr1D	100.000	2929	0	0	1	2929	7130945	7128017	0.000000e+00	5409.0
1	TraesCS1D01G015000	chr1D	92.232	1223	62	15	1	1204	7652161	7653369	0.000000e+00	1701.0
2	TraesCS1D01G015000	chr1D	88.793	928	65	20	1234	2141	7653370	7654278	0.000000e+00	1101.0
3	TraesCS1D01G015000	chr1D	84.848	297	45	0	2508	2804	347409381	347409677	1.710000e-77	300.0
4	TraesCS1D01G015000	chr1D	73.768	568	119	24	1316	1865	492500901	492500346	2.300000e-46	196.0
5	TraesCS1D01G015000	chr1B	92.877	2485	128	11	1	2477	9416473	9414030	0.000000e+00	3563.0
6	TraesCS1D01G015000	chr1B	94.714	454	24	0	2476	2929	9413987	9413534	0.000000e+00	706.0
7	TraesCS1D01G015000	chr1B	83.838	297	48	0	2508	2804	468510558	468510854	1.720000e-72	283.0
8	TraesCS1D01G015000	chr1B	79.710	207	40	2	2598	2803	637594625	637594420	6.540000e-32	148.0
9	TraesCS1D01G015000	chr1A	90.625	992	61	15	696	1685	8677822	8676861	0.000000e+00	1288.0
10	TraesCS1D01G015000	chr1A	89.263	801	59	9	1679	2455	8675624	8674827	0.000000e+00	977.0
11	TraesCS1D01G015000	chr1A	96.198	263	8	2	1	263	8678286	8678026	2.090000e-116	429.0
12	TraesCS1D01G015000	chr1A	83.838	297	48	0	2508	2804	448034393	448034689	1.720000e-72	283.0
13	TraesCS1D01G015000	chr1A	87.952	166	17	2	2476	2638	8674744	8674579	2.980000e-45	193.0
14	TraesCS1D01G015000	chr1A	73.250	557	124	21	1316	1865	590832633	590832095	2.320000e-41	180.0
15	TraesCS1D01G015000	chr1A	86.792	106	12	1	2703	2808	8674576	8674473	1.840000e-22	117.0
16	TraesCS1D01G015000	chr5A	75.748	635	120	25	1299	1923	691531564	691530954	3.690000e-74	289.0
17	TraesCS1D01G015000	chrUn	75.902	610	117	24	1317	1920	126691396	126691981	4.780000e-73	285.0
18	TraesCS1D01G015000	chr2B	73.980	588	126	24	1320	1896	761707163	761707734	2.290000e-51	213.0
19	TraesCS1D01G015000	chr2D	72.945	584	140	18	1320	1896	620812257	620812829	1.390000e-43	187.0
20	TraesCS1D01G015000	chr4D	97.561	41	1	0	1177	1217	36590472	36590432	1.460000e-08	71.3
21	TraesCS1D01G015000	chr4D	92.857	42	3	0	1176	1217	36590475	36590516	8.760000e-06	62.1
22	TraesCS1D01G015000	chr7D	90.566	53	4	1	1166	1218	177996720	177996771	5.240000e-08	69.4
23	TraesCS1D01G015000	chr3D	90.385	52	4	1	1167	1217	606883425	606883476	1.880000e-07	67.6
24	TraesCS1D01G015000	chr4A	92.857	42	3	0	1176	1217	565723510	565723469	8.760000e-06	62.1
25	TraesCS1D01G015000	chr5D	92.683	41	3	0	1177	1217	29135288	29135248	3.150000e-05	60.2
26	TraesCS1D01G015000	chr6A	90.909	44	2	1	1182	1225	13808184	13808225	1.130000e-04	58.4

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	TraesCS1D01G015000	chr1D	7128017	7130945	2928	True	5409.0	5409	100.0000	1	2929	1	chr1D.!!$R1	2928
1	TraesCS1D01G015000	chr1D	7652161	7654278	2117	False	1401.0	1701	90.5125	1	2141	2	chr1D.!!$F2	2140
2	TraesCS1D01G015000	chr1B	9413534	9416473	2939	True	2134.5	3563	93.7955	1	2929	2	chr1B.!!$R2	2928
3	TraesCS1D01G015000	chr1A	8674473	8678286	3813	True	600.8	1288	90.1660	1	2808	5	chr1A.!!$R2	2807
4	TraesCS1D01G015000	chr5A	691530954	691531564	610	True	289.0	289	75.7480	1299	1923	1	chr5A.!!$R1	624
5	TraesCS1D01G015000	chrUn	126691396	126691981	585	False	285.0	285	75.9020	1317	1920	1	chrUn.!!$F1	603
6	TraesCS1D01G015000	chr2B	761707163	761707734	571	False	213.0	213	73.9800	1320	1896	1	chr2B.!!$F1	576

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
324	327	0.31904	CCGGTCCATACATGAGCTCG	60.319	60.0	9.64	0.0	0.0	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2176	3471	1.064825	ATCACCGTCAAGGAAGGGTT	58.935	50.0	3.37	0.0	45.0	4.11	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
23	24	0.934496	TCCAAACGTGCGTGAAAGAG	59.066	50.000	0.00	0.00	0.00	2.85
185	187	9.743057	TGAGGTATGTTAACATTTGTTTTTCAG	57.257	29.630	25.31	0.00	39.31	3.02
324	327	0.319040	CCGGTCCATACATGAGCTCG	60.319	60.000	9.64	0.00	0.00	5.03
328	331	2.544694	GGTCCATACATGAGCTCGTGAG	60.545	54.545	36.58	24.95	36.72	3.51
446	456	3.361786	TCCGCTATATTCATCGGATCCA	58.638	45.455	13.41	0.00	44.99	3.41
459	469	1.595382	GATCCATTGTCGAGCGGGG	60.595	63.158	0.00	0.00	0.00	5.73
460	470	2.996168	GATCCATTGTCGAGCGGGGG	62.996	65.000	0.00	0.00	0.00	5.40
501	513	2.480555	GCTGGCATGTTTCGTCCG	59.519	61.111	0.00	0.00	0.00	4.79
722	742	3.545124	ATCTGTCAAACCCGCGGCA	62.545	57.895	22.85	10.46	0.00	5.69
846	866	7.395206	TCATGGCCCTCTATTAATCAAATCATG	59.605	37.037	0.00	0.00	0.00	3.07
850	870	7.665559	GGCCCTCTATTAATCAAATCATGTACA	59.334	37.037	0.00	0.00	0.00	2.90
861	881	2.394930	TCATGTACATGACGGGGTTG	57.605	50.000	30.29	7.65	42.42	3.77
864	884	2.747396	TGTACATGACGGGGTTGTAC	57.253	50.000	0.00	11.11	43.74	2.90
1021	1044	3.777106	TGAACAAGACTGGAGAGCATT	57.223	42.857	0.00	0.00	0.00	3.56
1060	1083	1.339610	CATCAGAGATCGACTGGGTCC	59.660	57.143	17.98	0.00	36.22	4.46
1119	1142	2.224450	CGGTTGTGGTAAGGGTCTTCTT	60.224	50.000	0.00	0.00	0.00	2.52
1152	1175	2.292845	TGCATGTGTTTGAATTCGCTCA	59.707	40.909	0.04	1.94	0.00	4.26
1171	1194	6.999272	TCGCTCAATTAGTAGATCTTACTCCT	59.001	38.462	0.00	0.00	0.00	3.69
1174	1197	8.085909	GCTCAATTAGTAGATCTTACTCCTTCC	58.914	40.741	0.00	0.00	0.00	3.46
1179	1202	6.251255	AGTAGATCTTACTCCTTCCGTAGT	57.749	41.667	0.00	0.00	0.00	2.73
1227	1250	7.907841	TTACAGATGTAGTAGGCTATTTCCA	57.092	36.000	0.00	0.00	0.00	3.53
1232	1255	5.786264	TGTAGTAGGCTATTTCCAGCTAC	57.214	43.478	0.00	3.57	41.50	3.58
1369	1396	0.390866	ACAGCATCAGTCGAAGCAGG	60.391	55.000	0.00	0.00	38.33	4.85
1470	1497	1.623811	ACGGTGGCTACTCTCAACATT	59.376	47.619	0.00	0.00	0.00	2.71
1682	2958	1.609555	CTACAGGGTACGCCTGATCTC	59.390	57.143	27.37	0.00	38.52	2.75
1832	3108	1.858739	CGTGGGGAAAGGATTGGGGA	61.859	60.000	0.00	0.00	0.00	4.81
1896	3172	1.818674	GAGGTGCCTTGGGTATGTTTG	59.181	52.381	0.00	0.00	0.00	2.93
1938	3214	4.025396	CAGTGATTGACTAACATCGGATGC	60.025	45.833	17.61	2.02	31.73	3.91
2021	3305	0.530744	CACTAGCTACTTGACCGCCA	59.469	55.000	0.00	0.00	0.00	5.69
2031	3315	2.301870	ACTTGACCGCCAGTGATCTTTA	59.698	45.455	0.00	0.00	0.00	1.85
2042	3326	6.907212	CGCCAGTGATCTTTATTGTGTTATTC	59.093	38.462	0.00	0.00	0.00	1.75
2098	3391	3.195610	TGAACTTCGTGCTAGGATGACAT	59.804	43.478	5.54	0.00	0.00	3.06
2150	3445	5.045869	TGGTTTGTATTAAGAGGGACTGAGG	60.046	44.000	0.00	0.00	41.55	3.86
2158	3453	2.048127	GGGACTGAGGCACGTGAC	60.048	66.667	22.23	18.98	0.00	3.67
2219	3514	0.250166	ACCTTGTGGTACTTGGCGAC	60.250	55.000	0.00	0.00	46.43	5.19
2329	3642	2.793946	CTAACACCGCCATGCAGC	59.206	61.111	0.00	0.00	0.00	5.25
2412	3725	1.699730	TGCCGATCTAAATCCTCCGA	58.300	50.000	0.00	0.00	0.00	4.55
2538	3913	1.476488	AGTGCCTTTGTTCTTTTGCGT	59.524	42.857	0.00	0.00	0.00	5.24
2557	3935	4.108299	AATGGGACGCCGATGCCA	62.108	61.111	0.00	0.00	45.13	4.92
2573	3951	0.321122	GCCATTGCCTCTCGGATAGG	60.321	60.000	5.11	5.11	37.17	2.57
2641	4019	1.300620	CAACAACTCGGCCTCGTCA	60.301	57.895	0.00	0.00	37.69	4.35
2689	4067	0.961019	GGCAAGCCATGAAAGTCACA	59.039	50.000	6.14	0.00	35.81	3.58
2698	4076	3.348309	CATGAAAGTCACATCGAATGCG	58.652	45.455	0.00	0.00	39.35	4.73
2701	4079	1.695893	AAGTCACATCGAATGCGCCG	61.696	55.000	4.18	0.37	37.46	6.46
2731	4109	2.761195	CCCATCAGCGTCGACGAGA	61.761	63.158	39.74	32.80	43.02	4.04
2759	4137	0.895530	GTCCTCACCGAATCTCACCA	59.104	55.000	0.00	0.00	0.00	4.17
2808	4186	0.824759	ACCTGATCGTAGCCTTCCAC	59.175	55.000	0.00	0.00	0.00	4.02
2874	4252	7.764695	TGATATACCGGCGATTTTACATATG	57.235	36.000	9.30	0.00	0.00	1.78
2893	4271	2.580962	TGCCTTTGTGCACAGTTGATA	58.419	42.857	20.59	0.24	36.04	2.15
2905	4283	1.835531	CAGTTGATACCCGGGTTACCT	59.164	52.381	35.42	17.63	33.28	3.08
2906	4284	2.113807	AGTTGATACCCGGGTTACCTC	58.886	52.381	35.42	22.60	33.28	3.85
2907	4285	1.139654	GTTGATACCCGGGTTACCTCC	59.860	57.143	35.42	14.81	33.28	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	5.965922	ACAAATCATAGGCTTAAACAAGGC	58.034	37.500	0.00	2.95	44.73	4.35
273	276	3.089284	CGACCCATTAGCCCTTTCTTTT	58.911	45.455	0.00	0.00	0.00	2.27
324	327	3.365265	CCAGCCAAACCGCCTCAC	61.365	66.667	0.00	0.00	0.00	3.51
328	331	2.142357	GAAAGACCAGCCAAACCGCC	62.142	60.000	0.00	0.00	0.00	6.13
377	380	6.803807	GCAAGAAAACGAGATTTATGAGCTTT	59.196	34.615	0.00	0.00	0.00	3.51
446	456	2.505982	CATCCCCCGCTCGACAAT	59.494	61.111	0.00	0.00	0.00	2.71
459	469	0.246086	CCAGCTCGCTATCTCCATCC	59.754	60.000	0.00	0.00	0.00	3.51
460	470	0.965439	ACCAGCTCGCTATCTCCATC	59.035	55.000	0.00	0.00	0.00	3.51
804	824	3.559655	GCCATGATGCACGTTTACATAGA	59.440	43.478	0.00	0.00	0.00	1.98
806	826	2.616376	GGCCATGATGCACGTTTACATA	59.384	45.455	0.00	0.00	0.00	2.29
846	866	2.231964	TGAGTACAACCCCGTCATGTAC	59.768	50.000	7.10	7.10	46.11	2.90
850	870	1.933021	TCTGAGTACAACCCCGTCAT	58.067	50.000	0.00	0.00	0.00	3.06
855	875	2.027192	TGAGCAATCTGAGTACAACCCC	60.027	50.000	0.00	0.00	0.00	4.95
1021	1044	0.683504	GGGCGGGTAGACTTCTCAGA	60.684	60.000	0.00	0.00	0.00	3.27
1060	1083	4.749310	AGAGACGGCGCCAGCTTG	62.749	66.667	28.98	12.44	44.37	4.01
1080	1103	1.308998	CGCCTTGTTTCCTCACAACT	58.691	50.000	0.00	0.00	33.04	3.16
1119	1142	0.518195	CACATGCATGTCAACAGCGA	59.482	50.000	29.23	0.00	39.39	4.93
1152	1175	9.287373	CTACGGAAGGAGTAAGATCTACTAATT	57.713	37.037	0.00	0.00	37.25	1.40
1171	1194	6.600882	AAGACCTTTTAGATCACTACGGAA	57.399	37.500	0.00	0.00	0.00	4.30
1210	1233	4.277672	CGTAGCTGGAAATAGCCTACTACA	59.722	45.833	0.00	0.00	44.76	2.74
1269	1292	5.244755	TGCTAGCTATGTCAACAATTGTGA	58.755	37.500	17.23	9.07	0.00	3.58
1274	1297	5.760253	GGTGTATGCTAGCTATGTCAACAAT	59.240	40.000	17.23	0.00	0.00	2.71
1470	1497	6.239487	CCATTATCCCGTATGTACTTGAAGGA	60.239	42.308	0.00	0.00	0.00	3.36
1682	2958	6.183360	CCATGATGCCTCCTTTGTAGTTTAAG	60.183	42.308	0.00	0.00	0.00	1.85
2098	3391	5.698089	CAGACAAGCTCAAGATGTGTAGAAA	59.302	40.000	0.00	0.00	0.00	2.52
2150	3445	3.712881	GGTTCGGCTGTCACGTGC	61.713	66.667	11.67	6.86	0.00	5.34
2176	3471	1.064825	ATCACCGTCAAGGAAGGGTT	58.935	50.000	3.37	0.00	45.00	4.11
2209	3504	1.320344	ATCAGGAGCGTCGCCAAGTA	61.320	55.000	14.86	0.00	0.00	2.24
2270	3583	4.083862	GCCTCAGGGTCACCGTCC	62.084	72.222	0.00	0.00	43.47	4.79
2289	3602	3.138798	GTGGAGCAGCATGGCCAG	61.139	66.667	13.05	4.54	35.86	4.85
2329	3642	2.178876	TATGGGTCCACGGTGCAGTG	62.179	60.000	1.68	0.00	41.53	3.66
2339	3652	1.570857	CCTGCTGGGTTATGGGTCCA	61.571	60.000	0.71	0.00	0.00	4.02
2364	3677	3.482436	GACTATGATCGAGGGTGAGAGT	58.518	50.000	0.00	0.00	0.00	3.24
2412	3725	4.654091	AGCTGCGCCAATTAATTTGTAT	57.346	36.364	4.18	0.00	33.15	2.29
2426	3739	0.788391	AACGTACACTAAAGCTGCGC	59.212	50.000	0.00	0.00	0.00	6.09
2538	3913	2.513666	GCATCGGCGTCCCATTGA	60.514	61.111	6.85	0.00	0.00	2.57
2573	3951	1.034292	GGTTGCCCCTCATGCTTCTC	61.034	60.000	0.00	0.00	0.00	2.87
2641	4019	1.221840	GGTCGTCATGGCCACATCT	59.778	57.895	8.16	0.00	34.35	2.90
2689	4067	1.591594	CCACTACGGCGCATTCGAT	60.592	57.895	10.83	0.00	38.10	3.59
2731	4109	1.990060	CGGTGAGGACAGGGTGGAT	60.990	63.158	0.00	0.00	0.00	3.41
2759	4137	1.471540	TGGACCTCCAGAAGCTCCT	59.528	57.895	0.00	0.00	42.01	3.69
2808	4186	6.101650	TGTAGTCATGGCAGGTATATGAAG	57.898	41.667	0.00	0.00	33.10	3.02
2874	4252	2.351738	GGTATCAACTGTGCACAAAGGC	60.352	50.000	21.98	7.33	0.00	4.35
2905	4283	5.192927	ACTCTTATCAAAATTCCATGCGGA	58.807	37.500	0.00	0.00	40.60	5.54
2906	4284	5.505173	ACTCTTATCAAAATTCCATGCGG	57.495	39.130	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.