AutoCloner

Multiple sequence alignment - TraesCS2A01G260800

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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	TraesCS2A01G260800	chr2A	100.000	3156	0	0	1	3156	410875058	410871903	0.000000e+00	5829
1	TraesCS2A01G260800	chr2A	95.714	140	5	1	2763	2902	20458440	20458578	1.140000e-54	224
2	TraesCS2A01G260800	chr2A	90.625	96	6	2	373	467	657809248	657809341	1.190000e-24	124
3	TraesCS2A01G260800	chr3B	97.722	2458	48	4	458	2908	2178648	2176192	0.000000e+00	4222
4	TraesCS2A01G260800	chr3B	89.706	204	20	1	2921	3123	20999708	20999505	3.120000e-65	259
5	TraesCS2A01G260800	chr4A	98.184	2092	35	3	458	2546	606645743	606643652	0.000000e+00	3650
6	TraesCS2A01G260800	chr4A	97.099	1482	32	5	1651	3125	21071916	21073393	0.000000e+00	2488
7	TraesCS2A01G260800	chr4A	98.432	1212	15	3	458	1667	21070119	21071328	0.000000e+00	2130
8	TraesCS2A01G260800	chr4A	90.749	227	17	4	2900	3123	596138876	596138651	1.840000e-77	300
9	TraesCS2A01G260800	chr2B	95.795	1189	43	5	1707	2893	702732912	702731729	0.000000e+00	1912
10	TraesCS2A01G260800	chr2B	96.692	665	21	1	563	1226	568465744	568465080	0.000000e+00	1105
11	TraesCS2A01G260800	chr2B	99.588	243	0	1	216	458	25668342	25668101	2.890000e-120	442
12	TraesCS2A01G260800	chr2B	97.391	230	3	2	1	228	25668900	25668672	3.820000e-104	388
13	TraesCS2A01G260800	chr2B	91.593	226	16	3	2900	3123	438612920	438613144	3.060000e-80	309
14	TraesCS2A01G260800	chr2B	88.496	226	24	2	2900	3123	787091726	787091951	4.010000e-69	272
15	TraesCS2A01G260800	chr4B	94.930	1144	45	9	1760	2900	110242885	110244018	0.000000e+00	1779
16	TraesCS2A01G260800	chr1D	92.366	1179	71	7	1239	2415	335349438	335348277	0.000000e+00	1661
17	TraesCS2A01G260800	chr1D	88.146	329	30	7	2578	2899	335289807	335289481	1.780000e-102	383
18	TraesCS2A01G260800	chr2D	87.067	1415	138	20	1241	2651	508251808	508253181	0.000000e+00	1557
19	TraesCS2A01G260800	chr2D	86.437	435	51	7	792	1223	508249726	508250155	1.330000e-128	470
20	TraesCS2A01G260800	chr7D	95.026	945	44	1	1369	2313	546774675	546773734	0.000000e+00	1482
21	TraesCS2A01G260800	chr7D	98.085	470	9	0	1239	1708	614645433	614645902	0.000000e+00	819
22	TraesCS2A01G260800	chr7D	95.739	399	16	1	2270	2668	614645901	614646298	2.650000e-180	641
23	TraesCS2A01G260800	chr7D	92.179	358	15	4	2309	2664	546770531	546770185	7.860000e-136	494
24	TraesCS2A01G260800	chr7D	88.382	241	15	3	2661	2900	614648231	614648459	8.620000e-71	278
25	TraesCS2A01G260800	chr7D	93.293	164	10	1	2737	2900	546769792	546769630	1.130000e-59	241
26	TraesCS2A01G260800	chrUn	87.584	1184	106	19	1471	2651	10110205	10111350	0.000000e+00	1334
27	TraesCS2A01G260800	chrUn	82.341	487	68	10	560	1033	10107602	10108083	1.050000e-109	407
28	TraesCS2A01G260800	chrUn	86.364	198	23	3	1239	1433	10110014	10110210	2.470000e-51	213
29	TraesCS2A01G260800	chrUn	93.023	86	4	1	373	458	300483082	300483165	1.190000e-24	124
30	TraesCS2A01G260800	chrUn	90.526	95	7	1	373	467	303730466	303730374	1.190000e-24	124
31	TraesCS2A01G260800	chrUn	93.023	86	4	1	373	458	312609477	312609560	1.190000e-24	124
32	TraesCS2A01G260800	chr1A	88.142	506	46	11	2405	2902	432856115	432855616	9.750000e-165	590
33	TraesCS2A01G260800	chr1A	89.565	230	19	4	2900	3126	554543565	554543338	1.430000e-73	287
34	TraesCS2A01G260800	chr1A	87.719	228	27	1	2900	3126	586114991	586114764	6.710000e-67	265
35	TraesCS2A01G260800	chr1A	93.939	165	9	1	1060	1223	432932453	432932289	6.760000e-62	248
36	TraesCS2A01G260800	chr6A	100.000	243	0	0	216	458	600012036	600012278	1.730000e-122	449
37	TraesCS2A01G260800	chr6A	99.074	216	1	1	1	215	600011051	600011266	1.370000e-103	387
38	TraesCS2A01G260800	chr6A	100.000	76	0	0	216	291	600011608	600011683	1.180000e-29	141
39	TraesCS2A01G260800	chr7A	89.199	287	20	3	2343	2627	630249164	630248887	6.480000e-92	348
40	TraesCS2A01G260800	chr7A	95.305	213	9	1	1369	1580	629817557	629817769	1.400000e-88	337
41	TraesCS2A01G260800	chr7A	93.023	86	4	1	373	458	667401679	667401762	1.190000e-24	124
42	TraesCS2A01G260800	chr5A	88.938	226	23	2	2900	3123	644862958	644863183	8.620000e-71	278
43	TraesCS2A01G260800	chr1B	88.938	226	23	2	2900	3123	83628643	83628868	8.620000e-71	278
44	TraesCS2A01G260800	chr6B	93.258	89	4	1	373	461	250789164	250789078	2.550000e-26	130
45	TraesCS2A01G260800	chr7B	90.722	97	6	2	373	469	122843915	122844008	3.300000e-25	126

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	TraesCS2A01G260800	chr2A	410871903	410875058	3155	True	5829.000000	5829	100.000000	1	3156	1	chr2A.!!$R1	3155
1	TraesCS2A01G260800	chr3B	2176192	2178648	2456	True	4222.000000	4222	97.722000	458	2908	1	chr3B.!!$R1	2450
2	TraesCS2A01G260800	chr4A	606643652	606645743	2091	True	3650.000000	3650	98.184000	458	2546	1	chr4A.!!$R2	2088
3	TraesCS2A01G260800	chr4A	21070119	21073393	3274	False	2309.000000	2488	97.765500	458	3125	2	chr4A.!!$F1	2667
4	TraesCS2A01G260800	chr2B	702731729	702732912	1183	True	1912.000000	1912	95.795000	1707	2893	1	chr2B.!!$R2	1186
5	TraesCS2A01G260800	chr2B	568465080	568465744	664	True	1105.000000	1105	96.692000	563	1226	1	chr2B.!!$R1	663
6	TraesCS2A01G260800	chr2B	25668101	25668900	799	True	415.000000	442	98.489500	1	458	2	chr2B.!!$R3	457
7	TraesCS2A01G260800	chr4B	110242885	110244018	1133	False	1779.000000	1779	94.930000	1760	2900	1	chr4B.!!$F1	1140
8	TraesCS2A01G260800	chr1D	335348277	335349438	1161	True	1661.000000	1661	92.366000	1239	2415	1	chr1D.!!$R2	1176
9	TraesCS2A01G260800	chr2D	508249726	508253181	3455	False	1013.500000	1557	86.752000	792	2651	2	chr2D.!!$F1	1859
10	TraesCS2A01G260800	chr7D	546769630	546774675	5045	True	739.000000	1482	93.499333	1369	2900	3	chr7D.!!$R1	1531
11	TraesCS2A01G260800	chr7D	614645433	614648459	3026	False	579.333333	819	94.068667	1239	2900	3	chr7D.!!$F1	1661
12	TraesCS2A01G260800	chrUn	10107602	10111350	3748	False	651.333333	1334	85.429667	560	2651	3	chrUn.!!$F3	2091
13	TraesCS2A01G260800	chr6A	600011051	600012278	1227	False	325.666667	449	99.691333	1	458	3	chr6A.!!$F1	457

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
505	1277	1.969923	CAAAGCATTTTCCCCTCCACA	59.030	47.619	0.0	0.00	35.03	4.17	F
1106	1986	3.736213	GTCGTCGACGTAGACATTACAA	58.264	45.455	34.4	10.55	40.98	2.41	F
1558	4075	1.909700	TGTCCACCTTTGATGAAGCC	58.090	50.000	0.0	0.00	33.84	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1558	4075	1.073763	TCATGACCTGTTGGACCCTTG	59.926	52.381	37.04	3.61	R
1960	5084	2.086869	CGATGGACTGCAAATTCTGGT	58.913	47.619	0.00	4.00	R
3128	11422	1.900016	GGTGGGGTGGACGGTTTTC	60.900	63.158	0.00	2.29	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
505	1277	1.969923	CAAAGCATTTTCCCCTCCACA	59.030	47.619	0.00	0.00	35.03	4.17
1106	1986	3.736213	GTCGTCGACGTAGACATTACAA	58.264	45.455	34.40	10.55	40.98	2.41
1558	4075	1.909700	TGTCCACCTTTGATGAAGCC	58.090	50.000	0.00	0.00	33.84	4.35
1840	4964	5.978814	ACTTTGATAGGCATACGAGAAACT	58.021	37.500	0.00	0.00	0.00	2.66
2019	5143	1.559682	GGGTCAAGAATACCTGGAGCA	59.440	52.381	0.00	0.00	43.52	4.26
2272	5401	7.041721	CACAACTGATGTCTAAGTAATGGCTA	58.958	38.462	0.00	0.00	41.46	3.93
2500	8845	5.523552	TGTGCTGGACAATGAGTATTAATCG	59.476	40.000	0.00	0.00	0.00	3.34
2959	11252	0.106521	GGCAGTGGGTTTTGTGCAAT	59.893	50.000	0.00	0.00	37.68	3.56
2963	11256	3.641648	CAGTGGGTTTTGTGCAATACTG	58.358	45.455	0.00	0.00	0.00	2.74
2964	11257	3.068024	CAGTGGGTTTTGTGCAATACTGT	59.932	43.478	0.00	0.00	32.02	3.55
2965	11258	3.068024	AGTGGGTTTTGTGCAATACTGTG	59.932	43.478	0.00	0.00	0.00	3.66
3047	11340	1.678101	GGATGCAAGTTGAGGTATGGC	59.322	52.381	7.16	0.00	0.00	4.40
3061	11354	5.486063	TGAGGTATGGCTTGGTCTAGTTTTA	59.514	40.000	0.00	0.00	0.00	1.52
3069	11362	6.183360	TGGCTTGGTCTAGTTTTACAAGTTTG	60.183	38.462	0.00	0.00	40.35	2.93
3088	11381	7.437713	AGTTTGGGACTAGATCATCACATTA	57.562	36.000	0.00	0.00	36.65	1.90
3089	11382	7.861629	AGTTTGGGACTAGATCATCACATTAA	58.138	34.615	0.00	0.00	36.65	1.40
3125	11419	2.916934	ACCTGGTTGCTATTACCTCCAA	59.083	45.455	0.00	0.00	36.60	3.53
3126	11420	3.279434	CCTGGTTGCTATTACCTCCAAC	58.721	50.000	0.00	0.00	36.60	3.77
3128	11422	2.285977	GGTTGCTATTACCTCCAACCG	58.714	52.381	5.74	0.00	45.17	4.44
3129	11423	2.093341	GGTTGCTATTACCTCCAACCGA	60.093	50.000	5.74	0.00	45.17	4.69
3130	11424	3.602483	GTTGCTATTACCTCCAACCGAA	58.398	45.455	0.00	0.00	33.33	4.30
3131	11425	3.985019	TGCTATTACCTCCAACCGAAA	57.015	42.857	0.00	0.00	0.00	3.46
3132	11426	4.289238	TGCTATTACCTCCAACCGAAAA	57.711	40.909	0.00	0.00	0.00	2.29
3133	11427	4.004982	TGCTATTACCTCCAACCGAAAAC	58.995	43.478	0.00	0.00	0.00	2.43
3134	11428	3.376234	GCTATTACCTCCAACCGAAAACC	59.624	47.826	0.00	0.00	0.00	3.27
3135	11429	1.881591	TTACCTCCAACCGAAAACCG	58.118	50.000	0.00	0.00	38.18	4.44
3136	11430	0.758123	TACCTCCAACCGAAAACCGT	59.242	50.000	0.00	0.00	36.31	4.83
3137	11431	0.533531	ACCTCCAACCGAAAACCGTC	60.534	55.000	0.00	0.00	36.31	4.79
3138	11432	1.232621	CCTCCAACCGAAAACCGTCC	61.233	60.000	0.00	0.00	36.31	4.79
3139	11433	0.533308	CTCCAACCGAAAACCGTCCA	60.533	55.000	0.00	0.00	36.31	4.02
3140	11434	0.814812	TCCAACCGAAAACCGTCCAC	60.815	55.000	0.00	0.00	36.31	4.02
3141	11435	1.650363	CAACCGAAAACCGTCCACC	59.350	57.895	0.00	0.00	36.31	4.61
3142	11436	1.526686	AACCGAAAACCGTCCACCC	60.527	57.895	0.00	0.00	36.31	4.61
3143	11437	2.670592	CCGAAAACCGTCCACCCC	60.671	66.667	0.00	0.00	36.31	4.95
3144	11438	2.111460	CGAAAACCGTCCACCCCA	59.889	61.111	0.00	0.00	0.00	4.96
3145	11439	2.255881	CGAAAACCGTCCACCCCAC	61.256	63.158	0.00	0.00	0.00	4.61
3146	11440	1.900016	GAAAACCGTCCACCCCACC	60.900	63.158	0.00	0.00	0.00	4.61
3147	11441	3.440162	AAAACCGTCCACCCCACCC	62.440	63.158	0.00	0.00	0.00	4.61
3149	11443	4.995058	ACCGTCCACCCCACCCAT	62.995	66.667	0.00	0.00	0.00	4.00
3150	11444	4.109675	CCGTCCACCCCACCCATC	62.110	72.222	0.00	0.00	0.00	3.51
3151	11445	4.467084	CGTCCACCCCACCCATCG	62.467	72.222	0.00	0.00	0.00	3.84
3152	11446	3.006728	GTCCACCCCACCCATCGA	61.007	66.667	0.00	0.00	0.00	3.59
3153	11447	3.006728	TCCACCCCACCCATCGAC	61.007	66.667	0.00	0.00	0.00	4.20
3154	11448	4.467084	CCACCCCACCCATCGACG	62.467	72.222	0.00	0.00	0.00	5.12
3155	11449	3.702048	CACCCCACCCATCGACGT	61.702	66.667	0.00	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
492	1264	1.354368	GAGTGGATGTGGAGGGGAAAA	59.646	52.381	0.00	0.00	0.00	2.29
996	1787	4.810790	GGACAGATTCCGTATACATCTGG	58.189	47.826	24.55	10.94	45.64	3.86
1106	1986	9.743057	CATACTTTCTTCGAGACATTCTAAGAT	57.257	33.333	0.00	0.00	37.43	2.40
1269	3785	5.710646	TCTAGAGTAGATTGGGAGAGCATT	58.289	41.667	0.00	0.00	0.00	3.56
1558	4075	1.073763	TCATGACCTGTTGGACCCTTG	59.926	52.381	0.00	0.00	37.04	3.61
1840	4964	2.965831	AGTCTGTACTGGACTTGCAAGA	59.034	45.455	32.50	9.84	40.65	3.02
1960	5084	2.086869	CGATGGACTGCAAATTCTGGT	58.913	47.619	0.00	0.00	0.00	4.00
2019	5143	9.154632	TGTCAGATAAGTATGTATACACCCAAT	57.845	33.333	7.96	0.00	35.74	3.16
2272	5401	6.183360	GGCTGTAGCAAAATAATACCACCATT	60.183	38.462	6.18	0.00	44.36	3.16
2500	8845	6.851609	TGAATAACCACAGTGCATTACATTC	58.148	36.000	0.00	0.82	0.00	2.67
2785	11077	2.418197	GCACGACCATGTTTCTAGGCTA	60.418	50.000	0.00	0.00	0.00	3.93
2945	11238	2.223923	GCACAGTATTGCACAAAACCCA	60.224	45.455	0.00	0.00	42.49	4.51
2999	11292	4.017958	TGATGTTTTAGTCCCAGGCCAATA	60.018	41.667	5.01	0.00	0.00	1.90
3047	11340	6.544564	TCCCAAACTTGTAAAACTAGACCAAG	59.455	38.462	0.00	3.72	38.71	3.61
3061	11354	5.013079	TGTGATGATCTAGTCCCAAACTTGT	59.987	40.000	0.00	0.00	39.55	3.16
3069	11362	6.712095	TGCATTTAATGTGATGATCTAGTCCC	59.288	38.462	6.81	0.00	0.00	4.46
3088	11381	3.075432	ACCAGGTACCCTAACTTGCATTT	59.925	43.478	8.74	0.00	29.64	2.32
3089	11382	2.647802	ACCAGGTACCCTAACTTGCATT	59.352	45.455	8.74	0.00	29.64	3.56
3110	11403	3.985019	TTCGGTTGGAGGTAATAGCAA	57.015	42.857	0.00	0.00	0.00	3.91
3125	11419	2.111669	GGGTGGACGGTTTTCGGT	59.888	61.111	0.00	0.00	44.45	4.69
3126	11420	2.670592	GGGGTGGACGGTTTTCGG	60.671	66.667	0.00	0.00	44.45	4.30
3127	11421	2.111460	TGGGGTGGACGGTTTTCG	59.889	61.111	0.00	0.00	45.88	3.46
3128	11422	1.900016	GGTGGGGTGGACGGTTTTC	60.900	63.158	0.00	0.00	0.00	2.29
3129	11423	2.196502	GGTGGGGTGGACGGTTTT	59.803	61.111	0.00	0.00	0.00	2.43
3130	11424	3.893399	GGGTGGGGTGGACGGTTT	61.893	66.667	0.00	0.00	0.00	3.27
3132	11426	4.995058	ATGGGTGGGGTGGACGGT	62.995	66.667	0.00	0.00	0.00	4.83
3133	11427	4.109675	GATGGGTGGGGTGGACGG	62.110	72.222	0.00	0.00	0.00	4.79
3134	11428	4.467084	CGATGGGTGGGGTGGACG	62.467	72.222	0.00	0.00	0.00	4.79
3135	11429	3.006728	TCGATGGGTGGGGTGGAC	61.007	66.667	0.00	0.00	0.00	4.02
3136	11430	3.006728	GTCGATGGGTGGGGTGGA	61.007	66.667	0.00	0.00	0.00	4.02
3137	11431	4.467084	CGTCGATGGGTGGGGTGG	62.467	72.222	0.00	0.00	0.00	4.61
3138	11432	3.702048	ACGTCGATGGGTGGGGTG	61.702	66.667	9.90	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.