AutoCloner

Multiple sequence alignment - TraesCS3B01G192800

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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	TraesCS3B01G192800	chr3B	100.000	2720	0	0	535	3254	207243835	207241116	0.000000e+00	5024.0
1	TraesCS3B01G192800	chr3B	100.000	256	0	0	1	256	207244369	207244114	1.060000e-129	473.0
2	TraesCS3B01G192800	chr2D	95.486	1994	75	6	803	2796	70292074	70294052	0.000000e+00	3169.0
3	TraesCS3B01G192800	chr2D	84.298	484	31	14	2670	3129	70038814	70039276	6.450000e-117	431.0
4	TraesCS3B01G192800	chr2D	92.000	225	14	4	2806	3027	70307559	70307782	2.440000e-81	313.0
5	TraesCS3B01G192800	chr2D	90.840	131	11	1	2502	2632	70293884	70294013	1.200000e-39	174.0
6	TraesCS3B01G192800	chr2D	75.000	412	71	25	1700	2104	69919580	69919966	9.340000e-36	161.0
7	TraesCS3B01G192800	chr2D	78.970	233	39	9	1692	1919	70034865	70035092	2.020000e-32	150.0
8	TraesCS3B01G192800	chr2D	92.683	41	1	2	1336	1375	70034485	70034524	1.260000e-04	58.4
9	TraesCS3B01G192800	chr2B	91.040	2076	139	18	730	2798	106206326	106204291	0.000000e+00	2760.0
10	TraesCS3B01G192800	chr2B	91.509	318	26	1	2818	3134	106202235	106201918	1.390000e-118	436.0
11	TraesCS3B01G192800	chr2B	80.508	236	34	11	1700	1929	106377015	106376786	1.550000e-38	171.0
12	TraesCS3B01G192800	chr2B	94.231	104	6	0	535	638	106213777	106213674	3.360000e-35	159.0
13	TraesCS3B01G192800	chr2B	89.423	104	8	2	154	256	106213944	106213843	9.480000e-26	128.0
14	TraesCS3B01G192800	chr2B	82.418	91	12	4	556	645	106214483	106214396	3.480000e-10	76.8
15	TraesCS3B01G192800	chr2B	91.837	49	1	3	1331	1377	106377402	106377355	7.540000e-07	65.8
16	TraesCS3B01G192800	chr3D	94.903	1334	35	10	1932	3239	143640987	143639661	0.000000e+00	2056.0
17	TraesCS3B01G192800	chr3A	99.042	939	9	0	1360	2298	163694087	163693149	0.000000e+00	1685.0
18	TraesCS3B01G192800	chr3A	97.267	622	12	3	582	1203	163695021	163694405	0.000000e+00	1050.0
19	TraesCS3B01G192800	chr3A	93.260	727	22	7	2400	3101	163683784	163683060	0.000000e+00	1046.0
20	TraesCS3B01G192800	chr3A	94.553	257	11	2	1	256	163695398	163695144	8.460000e-106	394.0
21	TraesCS3B01G192800	chr3A	96.503	143	5	0	3097	3239	163659519	163659377	1.510000e-58	237.0
22	TraesCS3B01G192800	chr3A	92.453	53	3	1	753	804	163694925	163694873	1.250000e-09	75.0
23	TraesCS3B01G192800	chr5D	95.745	141	6	0	1	141	459967786	459967926	9.080000e-56	228.0
24	TraesCS3B01G192800	chr4A	92.500	40	3	0	3131	3170	709966048	709966009	1.260000e-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	TraesCS3B01G192800	chr3B	207241116	207244369	3253	True	2748.500000	5024	100.00000	1	3254	2	chr3B.!!$R1	3253
1	TraesCS3B01G192800	chr2D	70292074	70294052	1978	False	1671.500000	3169	93.16300	803	2796	2	chr2D.!!$F4	1993
2	TraesCS3B01G192800	chr2D	70034485	70039276	4791	False	213.133333	431	85.31700	1336	3129	3	chr2D.!!$F3	1793
3	TraesCS3B01G192800	chr2B	106201918	106206326	4408	True	1598.000000	2760	91.27450	730	3134	2	chr2B.!!$R1	2404
4	TraesCS3B01G192800	chr3D	143639661	143640987	1326	True	2056.000000	2056	94.90300	1932	3239	1	chr3D.!!$R1	1307
5	TraesCS3B01G192800	chr3A	163683060	163683784	724	True	1046.000000	1046	93.26000	2400	3101	1	chr3A.!!$R2	701
6	TraesCS3B01G192800	chr3A	163693149	163695398	2249	True	801.000000	1685	95.82875	1	2298	4	chr3A.!!$R3	2297

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	End Stability	Orientation
196	197	0.181114	CATGTGATCCGATGGTGGGT	59.819	55.0	4.51	F
201	202	0.318762	GATCCGATGGTGGGTAGAGC	59.681	60.0	4.09	F
1695	1919	2.171237	CCCTTCTGGCTGTGACATGATA	59.829	50.0	2.15	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1044	1053	0.615331	GCAGGTGGGTCAAGATCTCA	59.385	55.000	0.00	0.00	3.27	R
2136	2360	1.733041	GCGCTGCGTCAGTCTAACA	60.733	57.895	24.04	33.43	2.41	R
2968	8494	0.871722	TGCACTTGTATGTGAACGCC	59.128	50.000	0.00	40.12	5.68	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
40	41	3.306919	CCCCAAAATCACATGTGAAAGGG	60.307	47.826	31.35	31.35	43.58	3.95
104	105	5.011227	GGTAAATGGTAAAAGGCCAACAGAA	59.989	40.000	5.01	0.00	39.72	3.02
196	197	0.181114	CATGTGATCCGATGGTGGGT	59.819	55.000	0.00	0.00	0.00	4.51
201	202	0.318762	GATCCGATGGTGGGTAGAGC	59.681	60.000	0.00	0.00	0.00	4.09
246	248	4.635473	TCTAACCCCCTCTTGATTCATCT	58.365	43.478	0.00	0.00	0.00	2.90
248	250	2.850833	ACCCCCTCTTGATTCATCTCA	58.149	47.619	0.00	0.00	0.00	3.27
249	251	2.507471	ACCCCCTCTTGATTCATCTCAC	59.493	50.000	0.00	0.00	0.00	3.51
253	255	5.782331	CCCCCTCTTGATTCATCTCACTATA	59.218	44.000	0.00	0.00	0.00	1.31
254	256	6.443206	CCCCCTCTTGATTCATCTCACTATAT	59.557	42.308	0.00	0.00	0.00	0.86
255	257	7.364585	CCCCCTCTTGATTCATCTCACTATATC	60.365	44.444	0.00	0.00	0.00	1.63
556	558	5.852282	AAGGATTTTGCCGTGCTTTATAT	57.148	34.783	0.00	0.00	0.00	0.86
557	559	5.852282	AGGATTTTGCCGTGCTTTATATT	57.148	34.783	0.00	0.00	0.00	1.28
558	560	6.220726	AGGATTTTGCCGTGCTTTATATTT	57.779	33.333	0.00	0.00	0.00	1.40
559	561	6.639563	AGGATTTTGCCGTGCTTTATATTTT	58.360	32.000	0.00	0.00	0.00	1.82
560	562	6.756542	AGGATTTTGCCGTGCTTTATATTTTC	59.243	34.615	0.00	0.00	0.00	2.29
561	563	6.533367	GGATTTTGCCGTGCTTTATATTTTCA	59.467	34.615	0.00	0.00	0.00	2.69
562	564	7.224557	GGATTTTGCCGTGCTTTATATTTTCAT	59.775	33.333	0.00	0.00	0.00	2.57
563	565	7.897575	TTTTGCCGTGCTTTATATTTTCATT	57.102	28.000	0.00	0.00	0.00	2.57
564	566	7.897575	TTTGCCGTGCTTTATATTTTCATTT	57.102	28.000	0.00	0.00	0.00	2.32
565	567	7.897575	TTGCCGTGCTTTATATTTTCATTTT	57.102	28.000	0.00	0.00	0.00	1.82
566	568	7.288317	TGCCGTGCTTTATATTTTCATTTTG	57.712	32.000	0.00	0.00	0.00	2.44
567	569	7.093354	TGCCGTGCTTTATATTTTCATTTTGA	58.907	30.769	0.00	0.00	0.00	2.69
568	570	7.600375	TGCCGTGCTTTATATTTTCATTTTGAA	59.400	29.630	0.00	0.00	34.03	2.69
569	571	8.439286	GCCGTGCTTTATATTTTCATTTTGAAA	58.561	29.630	0.00	0.00	43.84	2.69
612	614	6.767456	AGGAAATTGCCATGACAAAACATAA	58.233	32.000	4.92	0.00	32.27	1.90
756	758	9.553064	TGCCATGTTACAAGTTCAAAATAAAAT	57.447	25.926	0.00	0.00	0.00	1.82
817	820	6.546403	TCGCTGGAACTTACTAGACATCTAAT	59.454	38.462	0.00	0.00	0.00	1.73
832	835	6.475727	AGACATCTAATGTTCGTCCAATAACG	59.524	38.462	0.00	0.00	45.03	3.18
1044	1053	4.386867	TCTTGGCGAAGATCTTATCGTT	57.613	40.909	16.10	0.00	41.01	3.85
1695	1919	2.171237	CCCTTCTGGCTGTGACATGATA	59.829	50.000	0.00	0.00	0.00	2.15
2136	2360	4.817909	CCCGGGGGCTCTAAGGGT	62.818	72.222	14.71	0.00	37.36	4.34
2496	5859	2.049888	AGCAAATAGAGCCTTGGCTC	57.950	50.000	28.67	28.67	37.11	4.70
2613	5976	1.005097	AGGACCAAGCTTGATGCATGA	59.995	47.619	28.05	0.00	42.37	3.07
2657	6020	1.091537	AATTATGCAACCGGACCACG	58.908	50.000	9.46	0.00	43.80	4.94
2679	6042	2.995258	CGGGTTCAATTTGCAGAATTGG	59.005	45.455	22.68	10.88	38.00	3.16
2680	6043	3.554752	CGGGTTCAATTTGCAGAATTGGT	60.555	43.478	22.68	0.00	38.00	3.67
2803	6317	5.619132	TGGTGCTTTATCTCTGATGATGA	57.381	39.130	0.00	0.00	0.00	2.92
2804	6318	5.993055	TGGTGCTTTATCTCTGATGATGAA	58.007	37.500	0.00	0.00	0.00	2.57
2968	8494	9.352163	GTTTTTGCGAAACACAATATAAACAAG	57.648	29.630	0.00	0.00	30.83	3.16
2991	8517	3.485216	GCGTTCACATACAAGTGCATACC	60.485	47.826	0.00	0.00	39.35	2.73
3003	8529	9.715119	ATACAAGTGCATACCCTCATATCTATA	57.285	33.333	0.00	0.00	0.00	1.31
3095	8621	4.356405	TCACATGTTGGTCTCACTCATT	57.644	40.909	0.00	0.00	0.00	2.57
3135	8661	5.141182	GTCATCCCCACTATCTCAACTAGA	58.859	45.833	0.00	0.00	39.02	2.43
3187	8713	2.677542	TGTATCTATCACGAGCCCCT	57.322	50.000	0.00	0.00	0.00	4.79
3196	8722	0.250295	CACGAGCCCCTCAACTTCAA	60.250	55.000	0.00	0.00	0.00	2.69
3241	8767	5.585500	TTATTTCGCTATATTGTCACGCC	57.415	39.130	0.00	0.00	0.00	5.68
3242	8768	1.483316	TTCGCTATATTGTCACGCCG	58.517	50.000	0.00	0.00	0.00	6.46
3243	8769	0.937699	TCGCTATATTGTCACGCCGC	60.938	55.000	0.00	0.00	0.00	6.53
3244	8770	1.860078	GCTATATTGTCACGCCGCC	59.140	57.895	0.00	0.00	0.00	6.13
3245	8771	0.878523	GCTATATTGTCACGCCGCCA	60.879	55.000	0.00	0.00	0.00	5.69
3246	8772	1.139989	CTATATTGTCACGCCGCCAG	58.860	55.000	0.00	0.00	0.00	4.85
3247	8773	0.878523	TATATTGTCACGCCGCCAGC	60.879	55.000	0.00	0.00	38.52	4.85
3248	8774	2.867793	ATATTGTCACGCCGCCAGCA	62.868	55.000	0.00	0.00	44.04	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	4.111255	TCACATGTGATTTTGGGGAAGA	57.889	40.909	24.56	0.00	34.14	2.87
104	105	7.186804	CGTGCCGACTTCATTTATAGATTTTT	58.813	34.615	0.00	0.00	0.00	1.94
140	141	3.914312	TGAAACTCACTAGAGGCGAAAG	58.086	45.455	0.00	0.00	46.44	2.62
141	142	4.330944	TTGAAACTCACTAGAGGCGAAA	57.669	40.909	0.00	0.00	46.44	3.46
142	143	4.330944	TTTGAAACTCACTAGAGGCGAA	57.669	40.909	0.00	0.00	46.44	4.70
196	197	0.963962	AAGTCCCAACGAACGCTCTA	59.036	50.000	0.00	0.00	0.00	2.43
201	202	1.068474	CTAGCAAGTCCCAACGAACG	58.932	55.000	0.00	0.00	0.00	3.95
534	536	5.852282	ATATAAAGCACGGCAAAATCCTT	57.148	34.783	0.00	0.00	0.00	3.36
535	537	5.852282	AATATAAAGCACGGCAAAATCCT	57.148	34.783	0.00	0.00	0.00	3.24
536	538	6.533367	TGAAAATATAAAGCACGGCAAAATCC	59.467	34.615	0.00	0.00	0.00	3.01
537	539	7.518731	TGAAAATATAAAGCACGGCAAAATC	57.481	32.000	0.00	0.00	0.00	2.17
538	540	8.491331	AATGAAAATATAAAGCACGGCAAAAT	57.509	26.923	0.00	0.00	0.00	1.82
539	541	7.897575	AATGAAAATATAAAGCACGGCAAAA	57.102	28.000	0.00	0.00	0.00	2.44
540	542	7.897575	AAATGAAAATATAAAGCACGGCAAA	57.102	28.000	0.00	0.00	0.00	3.68
541	543	7.600375	TCAAAATGAAAATATAAAGCACGGCAA	59.400	29.630	0.00	0.00	0.00	4.52
542	544	7.093354	TCAAAATGAAAATATAAAGCACGGCA	58.907	30.769	0.00	0.00	0.00	5.69
543	545	7.518731	TCAAAATGAAAATATAAAGCACGGC	57.481	32.000	0.00	0.00	0.00	5.68
564	566	8.783093	CCTACATGTGACTTCTATGTTTTTCAA	58.217	33.333	9.11	0.00	36.52	2.69
565	567	8.154203	TCCTACATGTGACTTCTATGTTTTTCA	58.846	33.333	9.11	0.00	36.52	2.69
566	568	8.547967	TCCTACATGTGACTTCTATGTTTTTC	57.452	34.615	9.11	0.00	36.52	2.29
567	569	8.918202	TTCCTACATGTGACTTCTATGTTTTT	57.082	30.769	9.11	0.00	36.52	1.94
568	570	8.918202	TTTCCTACATGTGACTTCTATGTTTT	57.082	30.769	9.11	0.00	36.52	2.43
569	571	9.520515	AATTTCCTACATGTGACTTCTATGTTT	57.479	29.630	9.11	0.00	36.52	2.83
570	572	8.950210	CAATTTCCTACATGTGACTTCTATGTT	58.050	33.333	9.11	0.00	36.52	2.71
571	573	7.066284	GCAATTTCCTACATGTGACTTCTATGT	59.934	37.037	9.11	0.00	38.48	2.29
572	574	7.412853	GCAATTTCCTACATGTGACTTCTATG	58.587	38.462	9.11	0.35	0.00	2.23
573	575	6.543831	GGCAATTTCCTACATGTGACTTCTAT	59.456	38.462	9.11	0.00	0.00	1.98
574	576	5.880332	GGCAATTTCCTACATGTGACTTCTA	59.120	40.000	9.11	0.00	0.00	2.10
575	577	4.702131	GGCAATTTCCTACATGTGACTTCT	59.298	41.667	9.11	0.00	0.00	2.85
576	578	4.458989	TGGCAATTTCCTACATGTGACTTC	59.541	41.667	9.11	0.00	0.00	3.01
577	579	4.406456	TGGCAATTTCCTACATGTGACTT	58.594	39.130	9.11	0.00	0.00	3.01
578	580	4.032960	TGGCAATTTCCTACATGTGACT	57.967	40.909	9.11	0.00	0.00	3.41
579	581	4.398988	TCATGGCAATTTCCTACATGTGAC	59.601	41.667	9.11	0.00	39.76	3.67
580	582	4.398988	GTCATGGCAATTTCCTACATGTGA	59.601	41.667	9.11	0.00	39.76	3.58
720	722	1.885887	GTAACATGGCAAGTTCCAGCA	59.114	47.619	11.83	0.00	39.89	4.41
817	820	4.269603	TCGAAAAACGTTATTGGACGAACA	59.730	37.500	0.00	0.00	45.47	3.18
832	835	5.566395	ACACGTCTTTTTGTCTTCGAAAAAC	59.434	36.000	0.00	1.17	36.75	2.43
916	925	4.568760	GGAATCTGTCTTGAATCGAACTCC	59.431	45.833	0.00	0.00	0.00	3.85
1044	1053	0.615331	GCAGGTGGGTCAAGATCTCA	59.385	55.000	0.00	0.00	0.00	3.27
2136	2360	1.733041	GCGCTGCGTCAGTCTAACA	60.733	57.895	24.04	0.00	33.43	2.41
2496	5859	3.001634	CACAATCGCATGCCTTACTACTG	59.998	47.826	13.15	1.19	0.00	2.74
2657	6020	2.368655	ATTCTGCAAATTGAACCCGC	57.631	45.000	0.00	0.00	0.00	6.13
2679	6042	2.128771	ACCCCATAAGCATCACACAC	57.871	50.000	0.00	0.00	0.00	3.82
2680	6043	2.897271	AACCCCATAAGCATCACACA	57.103	45.000	0.00	0.00	0.00	3.72
2803	6317	6.588719	TTACAGAACCAAATAGCAATGCTT	57.411	33.333	14.85	0.00	40.44	3.91
2804	6318	6.780457	ATTACAGAACCAAATAGCAATGCT	57.220	33.333	13.92	13.92	43.41	3.79
2968	8494	0.871722	TGCACTTGTATGTGAACGCC	59.128	50.000	0.00	0.00	40.12	5.68
3095	8621	7.128109	TGGGGATGACCTATTTAGTTGTATTGA	59.872	37.037	0.00	0.00	40.03	2.57
3187	8713	7.067372	ACACAATGATCAAAGAGTTGAAGTTGA	59.933	33.333	11.90	0.00	46.66	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.