AutoCloner

Multiple sequence alignment - TraesCS1A01G067800

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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	TraesCS1A01G067800	chr1A	100.000	3125	0	0	1	3125	49355130	49358254	0.000000e+00	5771
1	TraesCS1A01G067800	chr1A	87.270	2388	284	12	2	2380	49347103	49349479	0.000000e+00	2708
2	TraesCS1A01G067800	chr1A	84.975	2376	316	20	2	2355	49293731	49296087	0.000000e+00	2372
3	TraesCS1A01G067800	chr1D	95.900	3049	85	7	2	3048	50108941	50111951	0.000000e+00	4902
4	TraesCS1A01G067800	chr1D	86.516	2388	298	17	2	2380	49973574	49975946	0.000000e+00	2604
5	TraesCS1A01G067800	chr1D	85.152	2364	324	12	2	2355	49956610	49958956	0.000000e+00	2396
6	TraesCS1A01G067800	chr1D	86.990	2106	255	15	10	2110	50022942	50025033	0.000000e+00	2353
7	TraesCS1A01G067800	chr1D	89.509	1773	181	3	339	2110	50008020	50009788	0.000000e+00	2239
8	TraesCS1A01G067800	chr1D	88.766	1086	87	17	1537	2612	80651710	80652770	0.000000e+00	1297
9	TraesCS1A01G067800	chr1D	89.974	379	33	5	2644	3020	80652770	80653145	4.690000e-133	484
10	TraesCS1A01G067800	chr1B	96.699	2696	69	8	434	3125	70694934	70697613	0.000000e+00	4468
11	TraesCS1A01G067800	chr1B	84.645	2377	319	24	2	2355	70334129	70336482	0.000000e+00	2326
12	TraesCS1A01G067800	chr1B	85.224	1252	153	15	1140	2375	70497481	70498716	0.000000e+00	1258
13	TraesCS1A01G067800	chr1B	94.855	447	23	0	2	448	70690257	70690703	0.000000e+00	699

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	TraesCS1A01G067800	chr1A	49355130	49358254	3124	False	5771.0	5771	100.000	1	3125	1	chr1A.!!$F3	3124
1	TraesCS1A01G067800	chr1A	49347103	49349479	2376	False	2708.0	2708	87.270	2	2380	1	chr1A.!!$F2	2378
2	TraesCS1A01G067800	chr1A	49293731	49296087	2356	False	2372.0	2372	84.975	2	2355	1	chr1A.!!$F1	2353
3	TraesCS1A01G067800	chr1D	50108941	50111951	3010	False	4902.0	4902	95.900	2	3048	1	chr1D.!!$F5	3046
4	TraesCS1A01G067800	chr1D	49973574	49975946	2372	False	2604.0	2604	86.516	2	2380	1	chr1D.!!$F2	2378
5	TraesCS1A01G067800	chr1D	49956610	49958956	2346	False	2396.0	2396	85.152	2	2355	1	chr1D.!!$F1	2353
6	TraesCS1A01G067800	chr1D	50022942	50025033	2091	False	2353.0	2353	86.990	10	2110	1	chr1D.!!$F4	2100
7	TraesCS1A01G067800	chr1D	50008020	50009788	1768	False	2239.0	2239	89.509	339	2110	1	chr1D.!!$F3	1771
8	TraesCS1A01G067800	chr1D	80651710	80653145	1435	False	890.5	1297	89.370	1537	3020	2	chr1D.!!$F6	1483
9	TraesCS1A01G067800	chr1B	70694934	70697613	2679	False	4468.0	4468	96.699	434	3125	1	chr1B.!!$F4	2691
10	TraesCS1A01G067800	chr1B	70334129	70336482	2353	False	2326.0	2326	84.645	2	2355	1	chr1B.!!$F1	2353
11	TraesCS1A01G067800	chr1B	70497481	70498716	1235	False	1258.0	1258	85.224	1140	2375	1	chr1B.!!$F2	1235

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
302	303	0.249238	CTACTGCTCCAGATGGCGTC	60.249	60.0	0.0	0.0	35.18	5.19	F
1020	1024	0.253044	TGGGTAAGCTGACTGATGCC	59.747	55.0	0.0	0.0	0.00	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1787	1795	1.847798	ATTAGGCACCAACCCGCTGA	61.848	55.0	0.0	0.0	0.0	4.26	R
2812	2855	2.708216	TGTACGTGATGGCATTGGAT	57.292	45.0	0.0	0.0	0.0	3.41	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
42	43	2.033141	ATGAACTGCTGCTGCCGT	59.967	55.556	13.47	10.06	38.26	5.68
46	47	1.709147	GAACTGCTGCTGCCGTATGG	61.709	60.000	12.73	0.00	35.61	2.74
159	160	0.521291	TCTGCTGCGCAAAACATACC	59.479	50.000	13.05	0.00	38.41	2.73
293	294	2.407428	CGCTCGACCTACTGCTCCA	61.407	63.158	0.00	0.00	0.00	3.86
301	302	1.680522	CCTACTGCTCCAGATGGCGT	61.681	60.000	0.00	0.00	35.18	5.68
302	303	0.249238	CTACTGCTCCAGATGGCGTC	60.249	60.000	0.00	0.00	35.18	5.19
303	304	2.004808	TACTGCTCCAGATGGCGTCG	62.005	60.000	0.13	0.00	35.18	5.12
304	305	3.068064	TGCTCCAGATGGCGTCGA	61.068	61.111	0.00	0.00	34.44	4.20
305	306	2.184322	GCTCCAGATGGCGTCGAA	59.816	61.111	0.00	0.00	34.44	3.71
306	307	1.880340	GCTCCAGATGGCGTCGAAG	60.880	63.158	0.00	0.00	34.44	3.79
307	308	1.227089	CTCCAGATGGCGTCGAAGG	60.227	63.158	0.00	5.40	34.44	3.46
317	318	1.446272	CGTCGAAGGAAGGAGGTGC	60.446	63.158	0.00	0.00	0.00	5.01
366	370	1.361668	CGGTCATCCACGGCTTCTTG	61.362	60.000	0.00	0.00	0.00	3.02
403	407	3.562973	AGACAAGGCATGCAATCTATTCG	59.437	43.478	21.36	0.00	0.00	3.34
487	491	0.316204	GTGCAAAGCTGGAGCAATGT	59.684	50.000	9.25	0.00	45.16	2.71
523	527	1.019673	CCTTCGGCAGATGGTTGATG	58.980	55.000	10.15	0.00	37.04	3.07
525	529	2.569059	CTTCGGCAGATGGTTGATGAT	58.431	47.619	0.00	0.00	0.00	2.45
595	599	1.830847	ACTTTGGGCCGGTGGAAAC	60.831	57.895	1.90	0.00	0.00	2.78
678	682	1.187087	ACTCGTTCATGGACTCCCTC	58.813	55.000	1.86	0.00	0.00	4.30
740	744	2.056223	CCATGGCTGGAAAGGGCAG	61.056	63.158	0.00	0.00	46.37	4.85
996	1000	8.969260	ATTCAACTCTAATATCTGCACATTGA	57.031	30.769	0.00	0.00	0.00	2.57
1020	1024	0.253044	TGGGTAAGCTGACTGATGCC	59.747	55.000	0.00	0.00	0.00	4.40
1188	1192	1.670811	CGTCCAAACACTGCACTCTTT	59.329	47.619	0.00	0.00	0.00	2.52
1511	1518	7.389607	ACCTACAACTGTTACATATGAAACCAC	59.610	37.037	10.38	0.00	0.00	4.16
1592	1599	5.471456	AGATGATCGAAAGTGGAATAATGGC	59.529	40.000	0.00	0.00	0.00	4.40
1787	1795	4.039004	TGATTTGTTTGCTGCATTACCAGT	59.961	37.500	1.84	0.00	35.28	4.00
2162	2178	4.095483	CAGATAAGCCTTGTCATGGTTCAC	59.905	45.833	3.95	0.00	0.00	3.18
2413	2454	7.164803	GGATTTCATCCCTGAGTTAATAGAGG	58.835	42.308	0.00	0.00	43.88	3.69
2483	2526	5.411053	GCTCAATGCTGTCTCTTTCTAAACT	59.589	40.000	0.00	0.00	38.95	2.66
2484	2527	6.591834	GCTCAATGCTGTCTCTTTCTAAACTA	59.408	38.462	0.00	0.00	38.95	2.24
2485	2528	7.412455	GCTCAATGCTGTCTCTTTCTAAACTAC	60.412	40.741	0.00	0.00	38.95	2.73
2486	2529	7.441836	TCAATGCTGTCTCTTTCTAAACTACA	58.558	34.615	0.00	0.00	0.00	2.74
2487	2530	7.600375	TCAATGCTGTCTCTTTCTAAACTACAG	59.400	37.037	0.00	0.00	36.74	2.74
2488	2531	6.406692	TGCTGTCTCTTTCTAAACTACAGT	57.593	37.500	0.00	0.00	36.20	3.55
2489	2532	6.448006	TGCTGTCTCTTTCTAAACTACAGTC	58.552	40.000	0.00	0.00	36.20	3.51
2507	2550	9.086758	ACTACAGTCTACAGTAACAAATTACCT	57.913	33.333	0.00	0.00	41.54	3.08
2609	2652	4.688879	GTGTGTGACTTATTCGAACATGGA	59.311	41.667	0.00	0.00	0.00	3.41
2640	2683	4.944317	CCTAATCTTGGGTTCAGTTCCTTC	59.056	45.833	0.00	0.00	0.00	3.46
2754	2797	7.414436	TGTTTGTAAGTGCTTCATGTTACTTC	58.586	34.615	8.92	4.59	35.26	3.01
2812	2855	4.597507	AGGGTCAGTACCTGATTTTCTGAA	59.402	41.667	0.00	0.00	45.95	3.02
2927	2975	6.808008	TTCTTCATCTGTCAAGTTGATTCC	57.192	37.500	9.18	0.00	33.24	3.01
2969	3017	0.323178	ATCAGGGCTGGTTGCTGAAG	60.323	55.000	0.00	0.00	42.39	3.02
3066	3115	2.607631	GGGGGAATTTGTCGTATCGA	57.392	50.000	0.00	0.00	0.00	3.59
3087	3136	2.953821	GGTGTGCCAACCGACATG	59.046	61.111	0.00	0.00	34.09	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
159	160	0.855349	GCATATTGACAGCCTCGTCG	59.145	55.000	0.00	0.00	38.84	5.12
210	211	3.264193	TGTTGTATGAGAAGGCATCAGGT	59.736	43.478	0.00	0.00	0.00	4.00
293	294	0.970937	TCCTTCCTTCGACGCCATCT	60.971	55.000	0.00	0.00	0.00	2.90
301	302	1.229209	AGGCACCTCCTTCCTTCGA	60.229	57.895	0.00	0.00	44.75	3.71
302	303	1.078848	CAGGCACCTCCTTCCTTCG	60.079	63.158	0.00	0.00	44.75	3.79
303	304	1.377856	GCAGGCACCTCCTTCCTTC	60.378	63.158	0.00	0.00	44.75	3.46
304	305	1.846712	GAGCAGGCACCTCCTTCCTT	61.847	60.000	0.00	0.00	44.75	3.36
305	306	2.204059	AGCAGGCACCTCCTTCCT	60.204	61.111	0.00	0.00	44.75	3.36
306	307	2.270527	GAGCAGGCACCTCCTTCC	59.729	66.667	0.00	0.00	44.75	3.46
307	308	2.270527	GGAGCAGGCACCTCCTTC	59.729	66.667	14.13	0.00	44.75	3.46
317	318	4.181010	CCATGTCGGGGGAGCAGG	62.181	72.222	0.00	0.00	0.00	4.85
331	335	0.764890	ACCGTGCTATATGCCACCAT	59.235	50.000	3.03	0.00	42.00	3.55
366	370	3.753797	CCTTGTCTACTTTGCCTTCCTTC	59.246	47.826	0.00	0.00	0.00	3.46
403	407	1.269413	CCCTTGCCGCATCATTTCATC	60.269	52.381	0.00	0.00	0.00	2.92
487	491	3.740115	GAAGGAACAACTCTGCCTTGTA	58.260	45.455	0.00	0.00	40.64	2.41
595	599	3.745975	TCTCTGAACATTTTACGCACCTG	59.254	43.478	0.00	0.00	0.00	4.00
647	651	2.821546	TGAACGAGTTCCAAGTGACAG	58.178	47.619	12.76	0.00	38.77	3.51
678	682	1.250328	TGGTTCTTCCATGCTTGCAG	58.750	50.000	0.87	0.00	41.93	4.41
740	744	5.467063	GTGTAGGAGACAATATTAGGCTTGC	59.533	44.000	0.00	0.00	40.66	4.01
996	1000	4.521146	CATCAGTCAGCTTACCCATTCTT	58.479	43.478	0.00	0.00	0.00	2.52
1020	1024	5.678583	ACCATCTGACTGAACTTATCCATG	58.321	41.667	0.00	0.00	0.00	3.66
1159	1163	3.067106	CAGTGTTTGGACGAGCAATACT	58.933	45.455	0.00	0.00	0.00	2.12
1188	1192	7.791029	TGCATAGACTGTCCATTATTGAACTA	58.209	34.615	3.76	0.00	0.00	2.24
1511	1518	5.268544	CAGCACGAAATAATCCATTCAGTG	58.731	41.667	0.00	0.00	35.34	3.66
1657	1665	5.231568	CACGTAATTTCTGGAATAGGACGAC	59.768	44.000	14.14	0.00	34.82	4.34
1787	1795	1.847798	ATTAGGCACCAACCCGCTGA	61.848	55.000	0.00	0.00	0.00	4.26
2162	2178	3.885901	TCTACATCGTTGAGAGGGAGATG	59.114	47.826	0.00	2.63	44.89	2.90
2409	2450	4.887071	TGCAAACACTGTTAATTCACCTCT	59.113	37.500	0.00	0.00	0.00	3.69
2413	2454	7.639461	CCAAAAATGCAAACACTGTTAATTCAC	59.361	33.333	0.00	0.00	0.00	3.18
2483	2526	9.081204	TGAGGTAATTTGTTACTGTAGACTGTA	57.919	33.333	0.00	0.00	0.00	2.74
2484	2527	7.959175	TGAGGTAATTTGTTACTGTAGACTGT	58.041	34.615	0.00	0.00	0.00	3.55
2485	2528	7.545965	CCTGAGGTAATTTGTTACTGTAGACTG	59.454	40.741	0.00	0.00	0.00	3.51
2486	2529	7.453752	TCCTGAGGTAATTTGTTACTGTAGACT	59.546	37.037	0.00	0.00	0.00	3.24
2487	2530	7.544915	GTCCTGAGGTAATTTGTTACTGTAGAC	59.455	40.741	0.00	0.00	0.00	2.59
2488	2531	7.310237	GGTCCTGAGGTAATTTGTTACTGTAGA	60.310	40.741	0.00	0.00	0.00	2.59
2489	2532	6.817140	GGTCCTGAGGTAATTTGTTACTGTAG	59.183	42.308	0.00	0.00	0.00	2.74
2507	2550	7.914427	TTATAAGATAGCTTTGAGGTCCTGA	57.086	36.000	0.00	0.00	35.56	3.86
2609	2652	5.271598	TGAACCCAAGATTAGGCATTCATT	58.728	37.500	0.00	0.00	29.82	2.57
2754	2797	3.070018	GAGATACATCCCTGGAAATGCG	58.930	50.000	0.00	0.00	0.00	4.73
2812	2855	2.708216	TGTACGTGATGGCATTGGAT	57.292	45.000	0.00	0.00	0.00	3.41
3064	3113	2.449525	CGGTTGGCACACCGTATCG	61.450	63.158	23.89	3.39	43.96	2.92
3065	3114	3.481661	CGGTTGGCACACCGTATC	58.518	61.111	23.89	0.00	43.96	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.