AutoCloner

Multiple sequence alignment - TraesCS5D01G070500

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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	TraesCS5D01G070500	chr5D	100.000	3403	0	0	1	3403	68238966	68235564	0.000000e+00	6285.0
1	TraesCS5D01G070500	chr5D	97.879	330	7	0	3064	3393	485707963	485707634	3.810000e-159	571.0
2	TraesCS5D01G070500	chr5D	96.226	318	11	1	2697	3014	354807151	354806835	1.400000e-143	520.0
3	TraesCS5D01G070500	chr5A	91.436	2172	85	40	1	2116	59138488	59140614	0.000000e+00	2887.0
4	TraesCS5D01G070500	chr5B	90.039	2309	116	54	1	2262	74308235	74305994	0.000000e+00	2885.0
5	TraesCS5D01G070500	chr5B	95.912	318	12	1	2696	3013	387152414	387152098	6.510000e-142	514.0
6	TraesCS5D01G070500	chr5B	95.094	265	13	0	2423	2687	405238928	405239192	5.250000e-113	418.0
7	TraesCS5D01G070500	chr5B	93.478	276	17	1	2419	2693	310319901	310319626	3.160000e-110	409.0
8	TraesCS5D01G070500	chr5B	90.099	101	9	1	2202	2302	74305996	74305897	2.760000e-26	130.0
9	TraesCS5D01G070500	chr3D	97.866	328	7	0	3066	3393	7429106	7428779	4.930000e-158	568.0
10	TraesCS5D01G070500	chr3D	97.590	332	7	1	3067	3398	507868666	507868336	4.930000e-158	568.0
11	TraesCS5D01G070500	chr3D	97.561	328	8	0	3067	3394	273267474	273267147	2.290000e-156	562.0
12	TraesCS5D01G070500	chr3D	95.652	345	13	2	3049	3393	248906771	248907113	1.380000e-153	553.0
13	TraesCS5D01G070500	chr3D	94.074	270	14	2	2419	2687	7428776	7429044	3.160000e-110	409.0
14	TraesCS5D01G070500	chr6A	97.859	327	7	0	3067	3393	470260645	470260319	1.770000e-157	566.0
15	TraesCS5D01G070500	chr6A	94.118	272	15	1	2420	2690	110490854	110491125	2.440000e-111	412.0
16	TraesCS5D01G070500	chr6A	85.938	64	9	0	2121	2184	184388303	184388240	6.090000e-08	69.4
17	TraesCS5D01G070500	chr6A	96.970	33	1	0	2150	2182	73562858	73562826	4.740000e-04	56.5
18	TraesCS5D01G070500	chr6A	100.000	28	0	0	2399	2426	212809095	212809122	6.000000e-03	52.8
19	TraesCS5D01G070500	chr6D	97.561	328	8	0	3067	3394	153351765	153352092	2.290000e-156	562.0
20	TraesCS5D01G070500	chr6D	96.894	322	10	0	2693	3014	199149487	199149808	1.070000e-149	540.0
21	TraesCS5D01G070500	chr6D	93.796	274	16	1	2415	2687	304697898	304698171	8.790000e-111	411.0
22	TraesCS5D01G070500	chr6D	94.737	38	1	1	2146	2183	463669241	463669205	1.320000e-04	58.4
23	TraesCS5D01G070500	chr1D	97.561	328	8	0	3067	3394	267864408	267864081	2.290000e-156	562.0
24	TraesCS5D01G070500	chr6B	96.429	336	11	1	3058	3393	544762255	544762589	1.380000e-153	553.0
25	TraesCS5D01G070500	chr6B	95.899	317	12	1	2697	3013	500564432	500564117	2.340000e-141	512.0
26	TraesCS5D01G070500	chr6B	93.455	275	18	0	2423	2697	130722675	130722401	3.160000e-110	409.0
27	TraesCS5D01G070500	chr7D	96.855	318	10	0	2697	3014	386079356	386079039	1.800000e-147	532.0
28	TraesCS5D01G070500	chr3B	95.356	323	14	1	2691	3013	19658404	19658725	2.340000e-141	512.0
29	TraesCS5D01G070500	chr3B	95.899	317	12	1	2697	3013	713579590	713579275	2.340000e-141	512.0
30	TraesCS5D01G070500	chr1B	95.584	317	13	1	2697	3013	373130345	373130030	1.090000e-139	507.0
31	TraesCS5D01G070500	chr1B	94.529	329	16	2	2687	3014	475477191	475476864	1.090000e-139	507.0
32	TraesCS5D01G070500	chr1A	93.750	272	16	1	2420	2690	305208538	305208809	1.140000e-109	407.0
33	TraesCS5D01G070500	chr1A	93.750	272	15	2	2420	2690	351081384	351081654	1.140000e-109	407.0
34	TraesCS5D01G070500	chr1A	93.750	272	16	1	2420	2690	473462821	473463092	1.140000e-109	407.0
35	TraesCS5D01G070500	chr4D	82.812	64	9	2	2121	2183	481346356	481346294	4.740000e-04	56.5

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	TraesCS5D01G070500	chr5D	68235564	68238966	3402	True	6285.0	6285	100.000	1	3403	1	chr5D.!!$R1	3402
1	TraesCS5D01G070500	chr5A	59138488	59140614	2126	False	2887.0	2887	91.436	1	2116	1	chr5A.!!$F1	2115
2	TraesCS5D01G070500	chr5B	74305897	74308235	2338	True	1507.5	2885	90.069	1	2302	2	chr5B.!!$R3	2301

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
654	693	0.450583	CATGAGTGATTGCGCTTGCT	59.549	50.0	9.73	0.0	40.12	3.91	F
1673	1752	0.179111	CGCCGAACTCATTAGCCTGA	60.179	55.0	0.00	0.0	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1869	1952	0.670162	GATCATCAATGGCAACCGGG	59.330	55.0	6.32	0.0	0.0	5.73	R
3065	3212	0.531200	AACCGGAAAGGAGCGAGTAG	59.469	55.0	9.46	0.0	45.0	2.57	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
118	119	4.241555	GATCCCGCACGCCTCCAT	62.242	66.667	0.00	0.00	0.00	3.41
399	406	4.168291	GCGCAAGGAGGAGGAGGG	62.168	72.222	0.30	0.00	38.28	4.30
434	452	0.690192	TCATGGTACTGGTGGTGGTG	59.310	55.000	0.00	0.00	0.00	4.17
473	496	1.143305	CACTGAAGCTCGTGAAGTGG	58.857	55.000	5.15	0.00	35.66	4.00
536	562	2.500098	GTTGTGGGTAGGTGAGCTGATA	59.500	50.000	0.00	0.00	0.00	2.15
567	597	2.278596	GCATGCATGCGAGGCTTG	60.279	61.111	33.99	4.73	44.67	4.01
568	598	3.060020	GCATGCATGCGAGGCTTGT	62.060	57.895	33.99	0.00	44.67	3.16
570	600	1.676635	ATGCATGCGAGGCTTGTGT	60.677	52.632	14.09	0.00	36.33	3.72
654	693	0.450583	CATGAGTGATTGCGCTTGCT	59.549	50.000	9.73	0.00	40.12	3.91
798	838	6.441274	TCAATGGGACTTTATACGTATCGAC	58.559	40.000	12.24	2.78	0.00	4.20
860	909	5.163824	CCAGCAGTAATTAGTGTGTGACATG	60.164	44.000	19.15	0.00	0.00	3.21
862	911	6.589907	CAGCAGTAATTAGTGTGTGACATGTA	59.410	38.462	19.15	0.00	0.00	2.29
1016	1095	4.617530	CGTTGTCATTTAAGAGGACCGAGA	60.618	45.833	0.00	0.00	0.00	4.04
1017	1096	5.235516	GTTGTCATTTAAGAGGACCGAGAA	58.764	41.667	0.00	0.00	0.00	2.87
1204	1283	4.111016	TACGTCACGCCGGAGCTG	62.111	66.667	5.05	3.22	36.60	4.24
1575	1654	2.747855	GCTGCCCAAGGAGAACGG	60.748	66.667	0.00	0.00	0.00	4.44
1637	1716	0.994247	ATCCATGTCTGCCACCTGAA	59.006	50.000	0.00	0.00	0.00	3.02
1647	1726	1.078759	GCCACCTGAACACTCGATCG	61.079	60.000	9.36	9.36	0.00	3.69
1653	1732	1.872679	GAACACTCGATCGACCGGC	60.873	63.158	15.15	0.00	0.00	6.13
1655	1734	4.907034	CACTCGATCGACCGGCCG	62.907	72.222	21.04	21.04	0.00	6.13
1673	1752	0.179111	CGCCGAACTCATTAGCCTGA	60.179	55.000	0.00	0.00	0.00	3.86
1735	1818	3.335579	GGTAACAATGGGTCAGTGAGAC	58.664	50.000	0.00	0.00	46.83	3.36
1750	1833	8.641499	GTCAGTGAGACGTAATTTAAACAATG	57.359	34.615	0.00	0.00	37.53	2.82
1751	1834	8.492748	GTCAGTGAGACGTAATTTAAACAATGA	58.507	33.333	0.00	0.00	37.53	2.57
1785	1868	5.297547	TCTCGTGCTGTTTATTCAACTCTT	58.702	37.500	0.00	0.00	36.21	2.85

Showing 1 to 25 of 653 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
399	406	1.739338	ATGACGACCCGGAGCTCATC	61.739	60.000	17.19	6.27	0.00	2.92
434	452	3.050275	GTCAGCGTCAGGCCAACC	61.050	66.667	5.01	0.00	45.17	3.77
491	514	2.161609	CACCAGGAAACAAATACGAGCC	59.838	50.000	0.00	0.00	0.00	4.70
560	590	3.179048	GACAAACACAAACACAAGCCTC	58.821	45.455	0.00	0.00	0.00	4.70
561	591	2.094234	GGACAAACACAAACACAAGCCT	60.094	45.455	0.00	0.00	0.00	4.58
563	593	2.267426	GGGACAAACACAAACACAAGC	58.733	47.619	0.00	0.00	0.00	4.01
564	594	3.584406	TGGGACAAACACAAACACAAG	57.416	42.857	0.00	0.00	31.92	3.16
798	838	8.045176	TGATCATCTACTTGTACTATCCATCG	57.955	38.462	0.00	0.00	0.00	3.84
801	841	6.777580	TGCTGATCATCTACTTGTACTATCCA	59.222	38.462	0.00	0.00	0.00	3.41
802	842	7.040062	ACTGCTGATCATCTACTTGTACTATCC	60.040	40.741	0.00	0.00	0.00	2.59
803	843	7.807433	CACTGCTGATCATCTACTTGTACTATC	59.193	40.741	0.00	0.00	0.00	2.08
804	844	7.656412	CACTGCTGATCATCTACTTGTACTAT	58.344	38.462	0.00	0.00	0.00	2.12
805	845	6.460261	GCACTGCTGATCATCTACTTGTACTA	60.460	42.308	0.00	0.00	0.00	1.82
806	846	5.680922	GCACTGCTGATCATCTACTTGTACT	60.681	44.000	0.00	0.00	0.00	2.73
807	847	4.505922	GCACTGCTGATCATCTACTTGTAC	59.494	45.833	0.00	0.00	0.00	2.90
808	848	4.160252	TGCACTGCTGATCATCTACTTGTA	59.840	41.667	1.98	0.00	0.00	2.41
809	849	3.055602	TGCACTGCTGATCATCTACTTGT	60.056	43.478	1.98	0.00	0.00	3.16
810	850	3.528532	TGCACTGCTGATCATCTACTTG	58.471	45.455	1.98	0.00	0.00	3.16
811	851	3.900966	TGCACTGCTGATCATCTACTT	57.099	42.857	1.98	0.00	0.00	2.24
812	852	3.134262	ACATGCACTGCTGATCATCTACT	59.866	43.478	1.98	0.00	0.00	2.57
813	853	3.464907	ACATGCACTGCTGATCATCTAC	58.535	45.455	1.98	0.00	0.00	2.59
860	909	4.336993	AGTTGAGACGAGATGATCTGGTAC	59.663	45.833	10.13	5.27	35.54	3.34
862	911	3.360867	AGTTGAGACGAGATGATCTGGT	58.639	45.455	9.94	9.94	38.17	4.00
997	1070	5.326200	TCTTCTCGGTCCTCTTAAATGAC	57.674	43.478	0.00	0.00	0.00	3.06
1016	1095	2.510382	TCTGTATCGTCTCTCCCCTCTT	59.490	50.000	0.00	0.00	0.00	2.85

Showing 1 to 25 of 633 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.