AutoCloner

Multiple sequence alignment - TraesCS2D01G191600

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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	TraesCS2D01G191600	chr2D	100.000	3028	0	0	1	3028	135600205	135603232	0.000000e+00	5592.0
1	TraesCS2D01G191600	chr2B	92.993	3097	110	41	1	3028	193389691	193392749	0.000000e+00	4418.0
2	TraesCS2D01G191600	chr2A	90.258	2556	108	48	1	2478	143722591	143725083	0.000000e+00	3210.0
3	TraesCS2D01G191600	chr2A	86.579	760	75	11	982	1731	143835490	143836232	0.000000e+00	813.0
4	TraesCS2D01G191600	chr2A	89.837	492	40	1	2544	3025	143725082	143725573	9.220000e-175	623.0
5	TraesCS2D01G191600	chr2A	96.552	58	2	0	2491	2548	161948620	161948677	2.480000e-16	97.1
6	TraesCS2D01G191600	chr2A	91.045	67	4	2	2491	2555	617636064	617636130	4.160000e-14	89.8
7	TraesCS2D01G191600	chr4A	96.552	58	2	0	2491	2548	548783071	548783014	2.480000e-16	97.1
8	TraesCS2D01G191600	chr6D	93.548	62	4	0	2494	2555	2956615	2956554	3.210000e-15	93.5
9	TraesCS2D01G191600	chr5A	94.915	59	3	0	2491	2549	382759465	382759523	3.210000e-15	93.5
10	TraesCS2D01G191600	chr5A	94.915	59	2	1	2491	2549	582386204	582386261	1.160000e-14	91.6
11	TraesCS2D01G191600	chr6B	92.188	64	5	0	2483	2546	543217446	543217509	1.160000e-14	91.6
12	TraesCS2D01G191600	chr4D	94.828	58	3	0	2491	2548	48595819	48595876	1.160000e-14	91.6

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	TraesCS2D01G191600	chr2D	135600205	135603232	3027	False	5592.0	5592	100.0000	1	3028	1	chr2D.!!$F1	3027
1	TraesCS2D01G191600	chr2B	193389691	193392749	3058	False	4418.0	4418	92.9930	1	3028	1	chr2B.!!$F1	3027
2	TraesCS2D01G191600	chr2A	143722591	143725573	2982	False	1916.5	3210	90.0475	1	3025	2	chr2A.!!$F4	3024
3	TraesCS2D01G191600	chr2A	143835490	143836232	742	False	813.0	813	86.5790	982	1731	1	chr2A.!!$F1	749

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	Hairpin	End Stability	Orientation
40	41	0.095935	CCAAGATTCTCTGCGTTGCG	59.904	55.0	0.0	4.85	F
639	667	0.386476	AACCGCTGACGTGACTACAA	59.614	50.0	37.7	2.41	F
963	1024	1.056660	CACTTGTCACCCTACCCTGT	58.943	55.0	0.0	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1713	1795	0.811281	GCCTGTAACAGTCCAATGCC	59.189	55.000	0.00	4.40	R
1950	2033	2.499693	ACAACCCCCAAAAAGACAGTTG	59.500	45.455	39.14	3.16	R
2851	2987	1.071605	GCTAGAAGACCGCAGTGTTG	58.928	55.000	27.73	3.33	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
37	38	1.537202	GTTGCCAAGATTCTCTGCGTT	59.463	47.619	3.75	0.00	0.00	4.84
38	39	1.159285	TGCCAAGATTCTCTGCGTTG	58.841	50.000	3.75	0.00	0.00	4.10
39	40	0.179179	GCCAAGATTCTCTGCGTTGC	60.179	55.000	0.00	0.00	0.00	4.17
40	41	0.095935	CCAAGATTCTCTGCGTTGCG	59.904	55.000	0.00	0.00	0.00	4.85
41	42	0.792640	CAAGATTCTCTGCGTTGCGT	59.207	50.000	0.00	0.00	0.00	5.24
82	83	4.212004	CCTTTCAGTCATGCGGTATACATG	59.788	45.833	5.01	0.44	45.08	3.21
107	109	2.604046	ATGATTGTGTCCTCGTAGCC	57.396	50.000	0.00	0.00	0.00	3.93
119	121	3.787001	GTAGCCCCTGCCTCGCTT	61.787	66.667	0.00	0.00	38.69	4.68
120	122	2.042333	TAGCCCCTGCCTCGCTTA	60.042	61.111	0.00	0.00	38.69	3.09
121	123	2.134287	TAGCCCCTGCCTCGCTTAG	61.134	63.158	0.00	0.00	38.69	2.18
124	126	4.554036	CCCTGCCTCGCTTAGGGC	62.554	72.222	0.00	0.00	46.65	5.19
184	186	2.754658	TCGCTCTTCTCCCCGTCC	60.755	66.667	0.00	0.00	0.00	4.79
185	187	4.194720	CGCTCTTCTCCCCGTCCG	62.195	72.222	0.00	0.00	0.00	4.79
186	188	3.069318	GCTCTTCTCCCCGTCCGT	61.069	66.667	0.00	0.00	0.00	4.69
187	189	3.066233	GCTCTTCTCCCCGTCCGTC	62.066	68.421	0.00	0.00	0.00	4.79
212	214	1.373748	TGTTCTACGCCACTTCGCC	60.374	57.895	0.00	0.00	0.00	5.54
273	275	4.447989	GCAGCCGAGCAGAGCAGA	62.448	66.667	0.00	0.00	0.00	4.26
274	276	2.202770	CAGCCGAGCAGAGCAGAG	60.203	66.667	0.00	0.00	0.00	3.35
275	277	4.146075	AGCCGAGCAGAGCAGAGC	62.146	66.667	0.00	0.00	0.00	4.09
276	278	4.146075	GCCGAGCAGAGCAGAGCT	62.146	66.667	0.00	0.00	45.25	4.09
298	300	1.551452	AGTACACTGCCTCAGGAGAC	58.449	55.000	0.00	0.00	35.51	3.36
328	334	2.652079	CGTGCACAGTCACAGAGCG	61.652	63.158	18.64	0.00	36.80	5.03
447	460	4.168291	CGCCTTCCTCCTCCTGGC	62.168	72.222	0.00	0.00	40.14	4.85
634	662	2.594962	CCACAACCGCTGACGTGAC	61.595	63.158	0.00	0.00	37.70	3.67
639	667	0.386476	AACCGCTGACGTGACTACAA	59.614	50.000	0.00	0.00	37.70	2.41

Showing 1 to 25 of 52 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.305219	TAGGAATGCTTGCCACACGC	61.305	55.000	0.00	0.00	38.31	5.34
39	40	0.447801	GTAGGAATGCTTGCCACACG	59.552	55.000	0.00	0.00	0.00	4.49
40	41	0.811281	GGTAGGAATGCTTGCCACAC	59.189	55.000	0.00	0.00	0.00	3.82
41	42	0.323360	GGGTAGGAATGCTTGCCACA	60.323	55.000	0.00	0.00	0.00	4.17
82	83	1.133025	CGAGGACACAATCATTTGGCC	59.867	52.381	0.00	0.00	37.15	5.36
119	121	0.390124	CTTTATACCGCCGTGCCCTA	59.610	55.000	0.00	0.00	0.00	3.53
120	122	1.145377	CTTTATACCGCCGTGCCCT	59.855	57.895	0.00	0.00	0.00	5.19
121	123	1.890510	CCTTTATACCGCCGTGCCC	60.891	63.158	0.00	0.00	0.00	5.36
122	124	1.890510	CCCTTTATACCGCCGTGCC	60.891	63.158	0.00	0.00	0.00	5.01
123	125	2.540228	GCCCTTTATACCGCCGTGC	61.540	63.158	0.00	0.00	0.00	5.34
124	126	0.463116	AAGCCCTTTATACCGCCGTG	60.463	55.000	0.00	0.00	0.00	4.94
172	174	0.034337	TTTTGACGGACGGGGAGAAG	59.966	55.000	0.00	0.00	0.00	2.85
212	214	3.486584	GAGAGAAAACTTCAGCGCATTG	58.513	45.455	11.47	0.00	0.00	2.82
271	273	2.096248	GAGGCAGTGTACTACAGCTCT	58.904	52.381	10.79	7.59	41.16	4.09
273	275	1.821753	CTGAGGCAGTGTACTACAGCT	59.178	52.381	10.79	0.00	41.16	4.24
274	276	1.134965	CCTGAGGCAGTGTACTACAGC	60.135	57.143	0.00	0.00	40.72	4.40
275	277	2.425312	CTCCTGAGGCAGTGTACTACAG	59.575	54.545	0.00	0.00	0.00	2.74
276	278	2.041216	TCTCCTGAGGCAGTGTACTACA	59.959	50.000	0.00	0.00	0.00	2.74
298	300	0.038801	TGTGCACGAGAGAAGCTGAG	60.039	55.000	13.13	0.00	36.80	3.35
328	334	4.426313	GGGCTGTGGTACCCTGCC	62.426	72.222	28.17	28.17	43.36	4.85
634	662	2.515996	ATCGGGTGGCGGTGTTGTAG	62.516	60.000	0.00	0.00	0.00	2.74
639	667	2.890766	AAGAATCGGGTGGCGGTGT	61.891	57.895	0.00	0.00	0.00	4.16
648	691	1.884926	GAGAGCGCCAAGAATCGGG	60.885	63.158	2.29	0.00	0.00	5.14
676	719	2.758089	GCCACGATCCAAGCAGCAG	61.758	63.158	0.00	0.00	0.00	4.24
717	764	3.838565	TCTTGGGCCTCTGATCTAGTAG	58.161	50.000	4.53	0.00	0.00	2.57

Showing 1 to 25 of 57 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.