AutoCloner

Multiple sequence alignment - TraesCS5D01G070600

Loading Multiple Alignment...

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	TraesCS5D01G070600	chr5D	100.000	2774	0	0	1	2774	68237329	68240102	0.000000e+00	5123.0
1	TraesCS5D01G070600	chr5D	95.217	230	10	1	2360	2589	486284817	486285045	2.030000e-96	363.0
2	TraesCS5D01G070600	chr5B	92.365	2829	113	58	2	2774	74306590	74309371	0.000000e+00	3932.0
3	TraesCS5D01G070600	chr5A	91.619	2112	79	43	2	2035	59140157	59138066	0.000000e+00	2830.0
4	TraesCS5D01G070600	chr5A	85.797	345	33	7	2030	2364	59041233	59040895	4.400000e-93	351.0
5	TraesCS5D01G070600	chr5A	87.978	183	15	7	2595	2774	59040898	59040720	2.800000e-50	209.0
6	TraesCS5D01G070600	chr7A	96.035	227	8	1	2363	2589	424976365	424976590	4.360000e-98	368.0
7	TraesCS5D01G070600	chr6B	95.652	230	9	1	2360	2589	347227148	347227376	4.360000e-98	368.0
8	TraesCS5D01G070600	chr3D	94.239	243	11	3	2355	2595	590076779	590077020	4.360000e-98	368.0
9	TraesCS5D01G070600	chr3D	95.217	230	10	1	2360	2589	269465502	269465730	2.030000e-96	363.0
10	TraesCS5D01G070600	chr2D	95.652	230	9	1	2360	2589	541547536	541547308	4.360000e-98	368.0
11	TraesCS5D01G070600	chr1B	95.259	232	10	1	2358	2589	453879441	453879211	1.570000e-97	366.0
12	TraesCS5D01G070600	chr1D	96.000	225	8	1	2365	2589	448103379	448103156	5.650000e-97	364.0
13	TraesCS5D01G070600	chr1D	97.561	41	1	0	2109	2149	16506343	16506383	1.380000e-08	71.3
14	TraesCS5D01G070600	chr1D	86.441	59	6	2	2107	2165	414138608	414138552	2.310000e-06	63.9
15	TraesCS5D01G070600	chr2A	81.553	103	12	5	2100	2197	635522347	635522447	8.240000e-11	78.7
16	TraesCS5D01G070600	chr4A	93.878	49	2	1	2102	2149	606786795	606786747	3.830000e-09	73.1
17	TraesCS5D01G070600	chr4A	87.500	64	5	3	2099	2161	474121256	474121317	1.380000e-08	71.3
18	TraesCS5D01G070600	chr1A	92.308	52	2	2	2099	2149	428997337	428997287	3.830000e-09	73.1
19	TraesCS5D01G070600	chr1A	89.474	57	6	0	2086	2142	575401451	575401507	3.830000e-09	73.1
20	TraesCS5D01G070600	chr3B	93.478	46	3	0	2195	2240	580887990	580887945	4.960000e-08	69.4

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	TraesCS5D01G070600	chr5D	68237329	68240102	2773	False	5123	5123	100.0000	1	2774	1	chr5D.!!$F1	2773
1	TraesCS5D01G070600	chr5B	74306590	74309371	2781	False	3932	3932	92.3650	2	2774	1	chr5B.!!$F1	2772
2	TraesCS5D01G070600	chr5A	59138066	59140157	2091	True	2830	2830	91.6190	2	2035	1	chr5A.!!$R1	2033
3	TraesCS5D01G070600	chr5A	59040720	59041233	513	True	280	351	86.8875	2030	2774	2	chr5A.!!$R2	744

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
620	621	2.105821	CTCTGTATCGTCTCTCCCCTCT	59.894	54.545	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2448	2571	1.346538	GAGCGCTCGACATTGAAGC	59.653	57.895	23.61	0.0	0.0	3.86	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
62	63	2.825836	CCATGGAGCTGAACCGGC	60.826	66.667	5.56	0.00	35.73	6.13
620	621	2.105821	CTCTGTATCGTCTCTCCCCTCT	59.894	54.545	0.00	0.00	0.00	3.69
621	622	2.510382	TCTGTATCGTCTCTCCCCTCTT	59.490	50.000	0.00	0.00	0.00	2.85
640	647	5.326200	TCTTCTCGGTCCTCTTAAATGAC	57.674	43.478	0.00	0.00	0.00	3.06
775	786	3.360867	AGTTGAGACGAGATGATCTGGT	58.639	45.455	9.94	9.94	38.17	4.00
776	787	4.527944	AGTTGAGACGAGATGATCTGGTA	58.472	43.478	10.13	0.00	35.54	3.25
824	864	3.464907	ACATGCACTGCTGATCATCTAC	58.535	45.455	1.98	0.00	0.00	2.59
826	866	3.900966	TGCACTGCTGATCATCTACTT	57.099	42.857	1.98	0.00	0.00	2.24
827	867	3.528532	TGCACTGCTGATCATCTACTTG	58.471	45.455	1.98	0.00	0.00	3.16
828	868	3.055602	TGCACTGCTGATCATCTACTTGT	60.056	43.478	1.98	0.00	0.00	3.16
829	869	4.160252	TGCACTGCTGATCATCTACTTGTA	59.840	41.667	1.98	0.00	0.00	2.41
830	870	4.505922	GCACTGCTGATCATCTACTTGTAC	59.494	45.833	0.00	0.00	0.00	2.90
831	871	5.680922	GCACTGCTGATCATCTACTTGTACT	60.681	44.000	0.00	0.00	0.00	2.73
832	872	6.460261	GCACTGCTGATCATCTACTTGTACTA	60.460	42.308	0.00	0.00	0.00	1.82
833	873	7.656412	CACTGCTGATCATCTACTTGTACTAT	58.344	38.462	0.00	0.00	0.00	2.12
834	874	7.807433	CACTGCTGATCATCTACTTGTACTATC	59.193	40.741	0.00	0.00	0.00	2.08
835	875	7.040062	ACTGCTGATCATCTACTTGTACTATCC	60.040	40.741	0.00	0.00	0.00	2.59
836	876	6.777580	TGCTGATCATCTACTTGTACTATCCA	59.222	38.462	0.00	0.00	0.00	3.41
837	877	7.452813	TGCTGATCATCTACTTGTACTATCCAT	59.547	37.037	0.00	0.00	0.00	3.41
838	878	7.973388	GCTGATCATCTACTTGTACTATCCATC	59.027	40.741	0.00	0.00	0.00	3.51
839	879	8.045176	TGATCATCTACTTGTACTATCCATCG	57.955	38.462	0.00	0.00	0.00	3.84
1073	1121	3.584406	TGGGACAAACACAAACACAAG	57.416	42.857	0.00	0.00	31.92	3.16
1074	1122	2.267426	GGGACAAACACAAACACAAGC	58.733	47.619	0.00	0.00	0.00	4.01
1075	1123	2.267426	GGACAAACACAAACACAAGCC	58.733	47.619	0.00	0.00	0.00	4.35
1076	1124	2.094234	GGACAAACACAAACACAAGCCT	60.094	45.455	0.00	0.00	0.00	4.58
1077	1125	3.179048	GACAAACACAAACACAAGCCTC	58.821	45.455	0.00	0.00	0.00	4.70
1146	1205	2.161609	CACCAGGAAACAAATACGAGCC	59.838	50.000	0.00	0.00	0.00	4.70
1177	1241	0.965866	TCGATCCCACTTCACGAGCT	60.966	55.000	0.00	0.00	0.00	4.09
1203	1267	3.050275	GTCAGCGTCAGGCCAACC	61.050	66.667	5.01	0.00	45.17	3.77
1238	1313	1.739338	ATGACGACCCGGAGCTCATC	61.739	60.000	17.19	6.27	0.00	2.92
1728	1809	1.581954	CGAGTTCGACCAGCTCACT	59.418	57.895	0.00	0.00	43.02	3.41
2054	2169	9.972106	AAAGGATCAGATGATAAAAGAAGAAGT	57.028	29.630	0.00	0.00	34.37	3.01
2135	2250	3.005554	CTCAAATGAGCTCGGTGAACAT	58.994	45.455	9.64	0.00	35.13	2.71
2216	2331	9.934190	AAAAGTTTCACATGTATGCAAATTTTC	57.066	25.926	0.00	0.00	30.03	2.29
2251	2366	4.766891	ACATTCGTGGAGATGTGGAAAAAT	59.233	37.500	0.00	0.00	0.00	1.82
2276	2393	2.029649	AGCGATGCTCTGCAAAAATTGT	60.030	40.909	0.00	0.00	43.62	2.71
2361	2484	6.528014	TCATCACAAAATTTTGCACACATC	57.472	33.333	26.94	0.00	41.79	3.06
2364	2487	8.089597	TCATCACAAAATTTTGCACACATCTAT	58.910	29.630	26.94	4.44	41.79	1.98
2365	2488	9.356433	CATCACAAAATTTTGCACACATCTATA	57.644	29.630	26.94	1.89	41.79	1.31
2395	2518	7.718334	ACCAATATAAAAAGACCCAAAGGAG	57.282	36.000	0.00	0.00	36.73	3.69
2420	2543	3.855255	TCCAATTAATCTCGGCCATCA	57.145	42.857	2.24	0.00	0.00	3.07
2425	2548	5.149273	CAATTAATCTCGGCCATCAAATCG	58.851	41.667	2.24	0.00	0.00	3.34
2477	2600	0.091344	CGAGCGCTCAACACGTTTAG	59.909	55.000	34.69	12.34	0.00	1.85
2479	2602	0.878523	AGCGCTCAACACGTTTAGCA	60.879	50.000	2.64	0.00	39.16	3.49
2508	2631	8.971321	CAGTTAATTTCATGCCAAATATAGTGC	58.029	33.333	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.994247	ATCCATGTCTGCCACCTGAA	59.006	50.000	0.00	0.00	0.00	3.02
62	63	2.747855	GCTGCCCAAGGAGAACGG	60.748	66.667	0.00	0.00	0.00	4.44
433	434	4.111016	TACGTCACGCCGGAGCTG	62.111	66.667	5.05	3.22	36.60	4.24
620	621	5.235516	GTTGTCATTTAAGAGGACCGAGAA	58.764	41.667	0.00	0.00	0.00	2.87
621	622	4.617530	CGTTGTCATTTAAGAGGACCGAGA	60.618	45.833	0.00	0.00	0.00	4.04
775	786	6.589907	CAGCAGTAATTAGTGTGTGACATGTA	59.410	38.462	19.15	0.00	0.00	2.29
776	787	5.409520	CAGCAGTAATTAGTGTGTGACATGT	59.590	40.000	19.15	0.00	0.00	3.21
839	879	6.441274	TCAATGGGACTTTATACGTATCGAC	58.559	40.000	12.24	2.78	0.00	4.20
983	1024	0.450583	CATGAGTGATTGCGCTTGCT	59.549	50.000	9.73	0.00	40.12	3.91
1067	1115	1.676635	ATGCATGCGAGGCTTGTGT	60.677	52.632	14.09	0.00	36.33	3.72
1069	1117	3.060020	GCATGCATGCGAGGCTTGT	62.060	57.895	33.99	0.00	44.67	3.16
1101	1153	2.500098	GTTGTGGGTAGGTGAGCTGATA	59.500	50.000	0.00	0.00	0.00	2.15
1164	1223	1.143305	CACTGAAGCTCGTGAAGTGG	58.857	55.000	5.15	0.00	35.66	4.00
1177	1241	0.317854	CTGACGCTGACGACACTGAA	60.318	55.000	0.00	0.00	43.93	3.02
1203	1267	0.690192	TCATGGTACTGGTGGTGGTG	59.310	55.000	0.00	0.00	0.00	4.17
1238	1313	4.168291	GCGCAAGGAGGAGGAGGG	62.168	72.222	0.30	0.00	38.28	4.30
1519	1600	4.241555	GATCCCGCACGCCTCCAT	62.242	66.667	0.00	0.00	0.00	3.41
1839	1947	7.009357	CGCTTACTAGTTTGATCAAGGAACTAC	59.991	40.741	12.45	6.10	38.49	2.73
2251	2366	3.913548	TTTTGCAGAGCATCGCTTTTA	57.086	38.095	0.00	0.00	39.88	1.52
2394	2517	3.406764	GCCGAGATTAATTGGATCTGCT	58.593	45.455	9.96	0.00	34.13	4.24
2395	2518	2.485814	GGCCGAGATTAATTGGATCTGC	59.514	50.000	9.96	8.37	34.13	4.26
2420	2543	4.335416	AGGTCATTGGATTGACACGATTT	58.665	39.130	6.88	0.00	46.32	2.17
2425	2548	4.872691	CAGTCTAGGTCATTGGATTGACAC	59.127	45.833	6.88	0.00	46.32	3.67
2441	2564	2.857152	GCTCGACATTGAAGCAGTCTAG	59.143	50.000	0.00	0.00	0.00	2.43
2448	2571	1.346538	GAGCGCTCGACATTGAAGC	59.653	57.895	23.61	0.00	0.00	3.86
2479	2602	9.701098	CTATATTTGGCATGAAATTAACTGCAT	57.299	29.630	0.00	0.00	36.34	3.96
2530	2653	8.893727	GCATGCGGATATTAAGTAGGATTTTAT	58.106	33.333	0.00	0.00	0.00	1.40
2531	2654	7.880713	TGCATGCGGATATTAAGTAGGATTTTA	59.119	33.333	14.09	0.00	0.00	1.52
2532	2655	6.714810	TGCATGCGGATATTAAGTAGGATTTT	59.285	34.615	14.09	0.00	0.00	1.82
2533	2656	6.149474	GTGCATGCGGATATTAAGTAGGATTT	59.851	38.462	14.09	0.00	0.00	2.17
2534	2657	5.643777	GTGCATGCGGATATTAAGTAGGATT	59.356	40.000	14.09	0.00	0.00	3.01
2605	2740	3.931468	TGTTTTTGCAACACACATTGAGG	59.069	39.130	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.