AutoCloner

Multiple sequence alignment - TraesCS6D01G253500

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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	TraesCS6D01G253500	chr6D	100.000	3492	0	0	1	3492	357582026	357578535	0.000000e+00	6449.0
1	TraesCS6D01G253500	chr6B	90.500	1779	115	19	872	2641	539179664	539177931	0.000000e+00	2300.0
2	TraesCS6D01G253500	chr6B	92.723	481	26	9	2652	3131	48493691	48493219	0.000000e+00	686.0
3	TraesCS6D01G253500	chr6B	81.230	618	74	27	265	870	539180384	539179797	8.830000e-126	460.0
4	TraesCS6D01G253500	chr6B	93.902	164	9	1	2	165	394425674	394425836	2.690000e-61	246.0
5	TraesCS6D01G253500	chr6B	93.878	49	1	2	3444	3492	539177782	539177736	4.830000e-09	73.1
6	TraesCS6D01G253500	chr6A	93.558	652	31	4	1995	2643	499658741	499658098	0.000000e+00	961.0
7	TraesCS6D01G253500	chr6A	95.054	465	21	2	2672	3135	88810191	88809728	0.000000e+00	730.0
8	TraesCS6D01G253500	chr6A	98.745	239	3	0	3254	3492	499658107	499657869	3.220000e-115	425.0
9	TraesCS6D01G253500	chr6A	91.870	123	4	3	3134	3255	88809670	88809553	2.160000e-37	167.0
10	TraesCS6D01G253500	chr7B	92.797	472	27	6	2661	3131	125229322	125229787	0.000000e+00	676.0
11	TraesCS6D01G253500	chr7B	92.585	472	28	6	2661	3131	125265497	125265962	0.000000e+00	671.0
12	TraesCS6D01G253500	chr7B	92.585	472	28	6	2661	3131	125301563	125302028	0.000000e+00	671.0
13	TraesCS6D01G253500	chr7B	92.585	472	28	6	2661	3131	125335258	125335723	0.000000e+00	671.0
14	TraesCS6D01G253500	chr7B	93.496	123	5	3	3131	3252	125209308	125209428	2.770000e-41	180.0
15	TraesCS6D01G253500	chr5B	91.992	487	24	9	2652	3131	529047316	529046838	0.000000e+00	669.0
16	TraesCS6D01G253500	chr5B	94.309	123	6	1	3131	3252	529046775	529046653	1.650000e-43	187.0
17	TraesCS6D01G253500	chr2B	91.598	488	25	9	2652	3131	788538410	788537931	0.000000e+00	660.0
18	TraesCS6D01G253500	chr2B	93.413	167	10	1	2	168	385128225	385128060	2.690000e-61	246.0
19	TraesCS6D01G253500	chr2B	84.158	101	9	5	657	756	186941130	186941036	1.330000e-14	91.6
20	TraesCS6D01G253500	chr7A	91.758	364	20	5	2773	3135	719928208	719927854	6.730000e-137	497.0
21	TraesCS6D01G253500	chr7A	89.844	128	12	1	3129	3255	719927801	719927674	2.790000e-36	163.0
22	TraesCS6D01G253500	chr7A	79.710	207	25	10	2677	2879	696292371	696292178	2.190000e-27	134.0
23	TraesCS6D01G253500	chr7A	92.982	57	3	1	2652	2708	45698607	45698662	8.030000e-12	82.4
24	TraesCS6D01G253500	chr5A	77.804	838	135	24	1056	1878	504932838	504932037	1.470000e-128	470.0
25	TraesCS6D01G253500	chr5A	83.636	55	9	0	2031	2085	680859685	680859631	6.000000e-03	52.8
26	TraesCS6D01G253500	chrUn	93.413	167	10	1	2	168	446906825	446906660	2.690000e-61	246.0
27	TraesCS6D01G253500	chr7D	93.413	167	10	1	2	168	382001563	382001398	2.690000e-61	246.0
28	TraesCS6D01G253500	chr4D	93.902	164	9	1	2	165	123377578	123377740	2.690000e-61	246.0
29	TraesCS6D01G253500	chr4D	93.902	164	9	1	2	165	123588365	123588527	2.690000e-61	246.0
30	TraesCS6D01G253500	chr4D	92.683	123	7	2	3131	3252	464309086	464308965	3.580000e-40	176.0
31	TraesCS6D01G253500	chr2D	93.413	167	10	1	2	168	637325647	637325482	2.690000e-61	246.0
32	TraesCS6D01G253500	chr2D	92.982	57	3	1	2652	2708	45829629	45829684	8.030000e-12	82.4
33	TraesCS6D01G253500	chr1A	93.413	167	10	1	2	168	238146471	238146306	2.690000e-61	246.0
34	TraesCS6D01G253500	chr1A	93.413	167	10	1	2	168	334070751	334070586	2.690000e-61	246.0
35	TraesCS6D01G253500	chr1D	93.496	123	7	1	3131	3252	1815616	1815494	7.700000e-42	182.0
36	TraesCS6D01G253500	chr1D	89.474	133	10	4	3131	3261	445220934	445220804	7.750000e-37	165.0
37	TraesCS6D01G253500	chr1D	83.168	101	10	5	657	756	50887357	50887451	6.210000e-13	86.1
38	TraesCS6D01G253500	chr4B	94.017	117	7	0	3134	3250	621686739	621686855	9.960000e-41	178.0
39	TraesCS6D01G253500	chr5D	92.683	123	7	2	3131	3252	424652374	424652253	3.580000e-40	176.0
40	TraesCS6D01G253500	chr4A	84.158	101	9	5	657	756	127225164	127225070	1.330000e-14	91.6
41	TraesCS6D01G253500	chr3D	83.168	101	10	5	657	756	141668678	141668584	6.210000e-13	86.1
42	TraesCS6D01G253500	chr3D	82.178	101	11	5	657	756	53828525	53828431	2.890000e-11	80.5
43	TraesCS6D01G253500	chr2A	78.000	150	23	8	610	756	736539572	736539430	6.210000e-13	86.1

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	TraesCS6D01G253500	chr6D	357578535	357582026	3491	True	6449.000000	6449	100.0000	1	3492	1	chr6D.!!$R1	3491
1	TraesCS6D01G253500	chr6B	539177736	539180384	2648	True	944.366667	2300	88.5360	265	3492	3	chr6B.!!$R2	3227
2	TraesCS6D01G253500	chr6A	499657869	499658741	872	True	693.000000	961	96.1515	1995	3492	2	chr6A.!!$R2	1497
3	TraesCS6D01G253500	chr6A	88809553	88810191	638	True	448.500000	730	93.4620	2672	3255	2	chr6A.!!$R1	583
4	TraesCS6D01G253500	chr5B	529046653	529047316	663	True	428.000000	669	93.1505	2652	3252	2	chr5B.!!$R1	600
5	TraesCS6D01G253500	chr7A	719927674	719928208	534	True	330.000000	497	90.8010	2773	3255	2	chr7A.!!$R2	482
6	TraesCS6D01G253500	chr5A	504932037	504932838	801	True	470.000000	470	77.8040	1056	1878	1	chr5A.!!$R1	822

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
444	445	0.251341	GCCCCCAACTGATCTGTGTT	60.251	55.0	5.96	0.14	0.00	3.32	F
510	511	0.388649	ATATGACGATTCGAGCGGCC	60.389	55.0	13.95	0.00	35.47	6.13	F
736	747	0.537188	CATAGACACCGGTGCTCCTT	59.463	55.0	34.26	15.00	0.00	3.36	F
1130	1280	0.677731	ACGACATCCCAAGCACCATG	60.678	55.0	0.00	0.00	0.00	3.66	F
2170	2329	0.391130	ATAAGAAGCTGCGCACGGAA	60.391	50.0	5.66	0.00	0.00	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1477	1627	0.320247	GCTCAGTATGGCCATCTCCG	60.320	60.000	24.80	9.78	36.16	4.63	R
1946	2105	0.536687	CCTCGGGAGTGAGCGGTATA	60.537	60.000	0.00	0.00	34.56	1.47	R
1973	2132	1.354506	GCTCAGCCATTCGTGATGC	59.645	57.895	0.00	0.00	34.25	3.91	R
2203	2365	1.451387	GGTGGGGTAAGACATGCGG	60.451	63.158	0.00	0.00	0.00	5.69	R
3312	3552	0.031716	TAGAGTGCAGGCTCATCCCT	60.032	55.000	7.05	0.00	37.94	4.20	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.781681	AGGAGGTACATTTTGGACGG	57.218	50.000	0.00	0.00	29.95	4.79
20	21	2.262637	AGGAGGTACATTTTGGACGGA	58.737	47.619	0.00	0.00	29.95	4.69
21	22	2.844348	AGGAGGTACATTTTGGACGGAT	59.156	45.455	0.00	0.00	29.95	4.18
22	23	2.943033	GGAGGTACATTTTGGACGGATG	59.057	50.000	0.00	0.00	29.95	3.51
23	24	3.606687	GAGGTACATTTTGGACGGATGT	58.393	45.455	0.00	0.00	37.70	3.06
24	25	3.343617	AGGTACATTTTGGACGGATGTG	58.656	45.455	0.00	0.00	35.72	3.21
25	26	3.078837	GGTACATTTTGGACGGATGTGT	58.921	45.455	0.00	0.00	35.72	3.72
26	27	4.020039	AGGTACATTTTGGACGGATGTGTA	60.020	41.667	0.00	0.00	35.72	2.90
27	28	4.696402	GGTACATTTTGGACGGATGTGTAA	59.304	41.667	0.00	0.00	35.72	2.41
28	29	5.355910	GGTACATTTTGGACGGATGTGTAAT	59.644	40.000	0.00	0.00	35.72	1.89
29	30	5.975693	ACATTTTGGACGGATGTGTAATT	57.024	34.783	0.00	0.00	33.08	1.40
30	31	5.949735	ACATTTTGGACGGATGTGTAATTC	58.050	37.500	0.00	0.00	33.08	2.17
31	32	5.710099	ACATTTTGGACGGATGTGTAATTCT	59.290	36.000	0.00	0.00	33.08	2.40
32	33	6.208599	ACATTTTGGACGGATGTGTAATTCTT	59.791	34.615	0.00	0.00	33.08	2.52
33	34	5.873179	TTTGGACGGATGTGTAATTCTTC	57.127	39.130	0.00	0.00	0.00	2.87
34	35	4.545208	TGGACGGATGTGTAATTCTTCA	57.455	40.909	0.00	0.00	0.00	3.02
35	36	5.097742	TGGACGGATGTGTAATTCTTCAT	57.902	39.130	0.00	0.00	0.00	2.57
36	37	4.875536	TGGACGGATGTGTAATTCTTCATG	59.124	41.667	0.00	0.00	0.00	3.07
37	38	5.116180	GGACGGATGTGTAATTCTTCATGA	58.884	41.667	0.00	0.00	0.00	3.07
38	39	5.584649	GGACGGATGTGTAATTCTTCATGAA	59.415	40.000	8.12	8.12	39.24	2.57
39	40	6.238211	GGACGGATGTGTAATTCTTCATGAAG	60.238	42.308	26.56	26.56	38.18	3.02
40	41	6.173339	ACGGATGTGTAATTCTTCATGAAGT	58.827	36.000	29.80	16.71	38.18	3.01
41	42	6.655003	ACGGATGTGTAATTCTTCATGAAGTT	59.345	34.615	29.80	21.45	38.18	2.66
42	43	7.174946	ACGGATGTGTAATTCTTCATGAAGTTT	59.825	33.333	29.80	25.05	38.18	2.66
43	44	8.023128	CGGATGTGTAATTCTTCATGAAGTTTT	58.977	33.333	29.80	24.77	38.18	2.43

Showing 1 to 25 of 309 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.262637	TCCGTCCAAAATGTACCTCCT	58.737	47.619	0.00	0.00	0.00	3.69
2	3	3.374058	CACATCCGTCCAAAATGTACCTC	59.626	47.826	0.00	0.00	32.54	3.85
3	4	3.244770	ACACATCCGTCCAAAATGTACCT	60.245	43.478	0.00	0.00	32.54	3.08
4	5	3.078837	ACACATCCGTCCAAAATGTACC	58.921	45.455	0.00	0.00	32.54	3.34
6	7	6.882140	AGAATTACACATCCGTCCAAAATGTA	59.118	34.615	0.00	0.00	32.54	2.29
7	8	5.710099	AGAATTACACATCCGTCCAAAATGT	59.290	36.000	0.00	0.00	34.03	2.71
8	9	6.194796	AGAATTACACATCCGTCCAAAATG	57.805	37.500	0.00	0.00	0.00	2.32
10	11	5.765677	TGAAGAATTACACATCCGTCCAAAA	59.234	36.000	0.00	0.00	0.00	2.44
11	12	5.309638	TGAAGAATTACACATCCGTCCAAA	58.690	37.500	0.00	0.00	0.00	3.28
12	13	4.900684	TGAAGAATTACACATCCGTCCAA	58.099	39.130	0.00	0.00	0.00	3.53
13	14	4.545208	TGAAGAATTACACATCCGTCCA	57.455	40.909	0.00	0.00	0.00	4.02
14	15	5.116180	TCATGAAGAATTACACATCCGTCC	58.884	41.667	0.00	0.00	0.00	4.79
15	16	6.313905	ACTTCATGAAGAATTACACATCCGTC	59.686	38.462	36.15	0.00	40.79	4.79
16	17	6.173339	ACTTCATGAAGAATTACACATCCGT	58.827	36.000	36.15	11.28	40.79	4.69
17	18	6.668541	ACTTCATGAAGAATTACACATCCG	57.331	37.500	36.15	10.66	40.79	4.18
18	19	9.132521	CAAAACTTCATGAAGAATTACACATCC	57.867	33.333	36.15	0.00	40.79	3.51
19	20	8.642020	GCAAAACTTCATGAAGAATTACACATC	58.358	33.333	36.15	13.58	40.79	3.06
20	21	8.143193	TGCAAAACTTCATGAAGAATTACACAT	58.857	29.630	36.15	12.32	40.79	3.21
21	22	7.487484	TGCAAAACTTCATGAAGAATTACACA	58.513	30.769	36.15	23.42	40.79	3.72
22	23	7.928908	TGCAAAACTTCATGAAGAATTACAC	57.071	32.000	36.15	21.79	40.79	2.90
23	24	8.358895	TCATGCAAAACTTCATGAAGAATTACA	58.641	29.630	36.15	27.63	44.08	2.41
24	25	8.746922	TCATGCAAAACTTCATGAAGAATTAC	57.253	30.769	36.15	24.08	44.08	1.89
25	26	8.579006	ACTCATGCAAAACTTCATGAAGAATTA	58.421	29.630	36.15	19.09	45.64	1.40
26	27	7.439381	ACTCATGCAAAACTTCATGAAGAATT	58.561	30.769	36.15	26.55	45.64	2.17
27	28	6.989659	ACTCATGCAAAACTTCATGAAGAAT	58.010	32.000	36.15	23.06	45.64	2.40

Showing 1 to 25 of 336 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.