AutoCloner

Multiple sequence alignment - TraesCS5D01G347900

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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	TraesCS5D01G347900	chr5D	100.000	2438	0	0	1	2438	433198375	433195938	0.000000e+00	4503.0
1	TraesCS5D01G347900	chr5D	94.130	920	50	3	1521	2438	522358591	522357674	0.000000e+00	1397.0
2	TraesCS5D01G347900	chr5D	84.131	731	93	17	798	1521	433332628	433331914	0.000000e+00	686.0
3	TraesCS5D01G347900	chr5D	76.033	242	50	6	1125	1359	435259060	435258820	4.260000e-23	119.0
4	TraesCS5D01G347900	chr5D	80.000	125	25	0	1125	1249	435255800	435255676	2.580000e-15	93.5
5	TraesCS5D01G347900	chr5D	91.667	48	3	1	746	792	433218909	433218862	5.630000e-07	65.8
6	TraesCS5D01G347900	chr5B	96.313	1519	47	5	10	1521	526669559	526668043	0.000000e+00	2486.0
7	TraesCS5D01G347900	chr5B	87.665	227	18	3	485	711	526675128	526674912	3.110000e-64	255.0
8	TraesCS5D01G347900	chr5B	75.410	244	48	10	1125	1359	528570340	528570100	9.220000e-20	108.0
9	TraesCS5D01G347900	chr7D	96.848	920	27	2	1521	2438	104668490	104667571	0.000000e+00	1537.0
10	TraesCS5D01G347900	chr3A	95.166	931	41	4	1512	2438	696474365	696473435	0.000000e+00	1467.0
11	TraesCS5D01G347900	chr3A	95.440	921	37	4	1522	2438	51573067	51573986	0.000000e+00	1463.0
12	TraesCS5D01G347900	chr6D	94.662	918	46	3	1523	2438	207063047	207063963	0.000000e+00	1421.0
13	TraesCS5D01G347900	chr7A	93.696	920	53	4	1522	2438	672526276	672525359	0.000000e+00	1373.0
14	TraesCS5D01G347900	chr7A	93.254	919	59	3	1522	2438	672648241	672647324	0.000000e+00	1351.0
15	TraesCS5D01G347900	chr7A	92.927	919	56	6	1522	2438	672710819	672709908	0.000000e+00	1328.0
16	TraesCS5D01G347900	chr1D	93.492	922	56	3	1521	2438	102828870	102827949	0.000000e+00	1367.0
17	TraesCS5D01G347900	chr4B	78.529	340	65	7	334	667	623725909	623726246	1.470000e-52	217.0
18	TraesCS5D01G347900	chr5A	77.016	248	44	11	1122	1359	549196328	549196084	1.970000e-26	130.0
19	TraesCS5D01G347900	chr5A	84.211	76	9	3	185	259	547621435	547621362	1.210000e-08	71.3

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	TraesCS5D01G347900	chr5D	433195938	433198375	2437	True	4503	4503	100.000	1	2438	1	chr5D.!!$R1	2437
1	TraesCS5D01G347900	chr5D	522357674	522358591	917	True	1397	1397	94.130	1521	2438	1	chr5D.!!$R4	917
2	TraesCS5D01G347900	chr5D	433331914	433332628	714	True	686	686	84.131	798	1521	1	chr5D.!!$R3	723
3	TraesCS5D01G347900	chr5B	526668043	526669559	1516	True	2486	2486	96.313	10	1521	1	chr5B.!!$R1	1511
4	TraesCS5D01G347900	chr7D	104667571	104668490	919	True	1537	1537	96.848	1521	2438	1	chr7D.!!$R1	917
5	TraesCS5D01G347900	chr3A	696473435	696474365	930	True	1467	1467	95.166	1512	2438	1	chr3A.!!$R1	926
6	TraesCS5D01G347900	chr3A	51573067	51573986	919	False	1463	1463	95.440	1522	2438	1	chr3A.!!$F1	916
7	TraesCS5D01G347900	chr6D	207063047	207063963	916	False	1421	1421	94.662	1523	2438	1	chr6D.!!$F1	915
8	TraesCS5D01G347900	chr7A	672525359	672526276	917	True	1373	1373	93.696	1522	2438	1	chr7A.!!$R1	916
9	TraesCS5D01G347900	chr7A	672647324	672648241	917	True	1351	1351	93.254	1522	2438	1	chr7A.!!$R2	916
10	TraesCS5D01G347900	chr7A	672709908	672710819	911	True	1328	1328	92.927	1522	2438	1	chr7A.!!$R3	916
11	TraesCS5D01G347900	chr1D	102827949	102828870	921	True	1367	1367	93.492	1521	2438	1	chr1D.!!$R1	917

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
936	945	0.304705	CACAAGCGTCTTCACACCAC	59.695	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2349	2369	0.81804	AAACCTGACACAAGGACGGC	60.818	55.0	0.0	0.0	40.02	5.68	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
22	23	5.456548	GAGTTAGAGAAGGTACTATGGCC	57.543	47.826	0.00	0.00	38.49	5.36
23	24	4.880164	AGTTAGAGAAGGTACTATGGCCA	58.120	43.478	8.56	8.56	38.49	5.36
41	42	3.119352	GGCCACTGGATTTTGACTGAATC	60.119	47.826	0.00	0.00	33.71	2.52
51	52	8.786898	TGGATTTTGACTGAATCTAGAAAACAG	58.213	33.333	16.93	16.93	34.65	3.16
133	134	5.586643	GGAGGAAGAAACCATTGATGTAGAC	59.413	44.000	0.00	0.00	0.00	2.59
195	196	3.425162	AGGCAGAAAGTAAGGAAGTGG	57.575	47.619	0.00	0.00	0.00	4.00
206	207	5.937111	AGTAAGGAAGTGGTTAAGAAAGCA	58.063	37.500	0.00	0.00	40.68	3.91
225	226	9.678260	AGAAAGCAAGATAAACACAGATAGAAT	57.322	29.630	0.00	0.00	0.00	2.40
265	266	5.677319	CAGGGAATCTGGTACTAGAAACA	57.323	43.478	13.39	0.00	39.76	2.83
269	270	6.272558	AGGGAATCTGGTACTAGAAACAAAGT	59.727	38.462	13.39	0.00	0.00	2.66
275	276	7.514721	TCTGGTACTAGAAACAAAGTGGATTT	58.485	34.615	6.45	0.00	0.00	2.17
277	278	8.161699	TGGTACTAGAAACAAAGTGGATTTTC	57.838	34.615	0.00	0.00	0.00	2.29
346	354	7.811282	TGGACAAGCCCTCAGATTTATAAATA	58.189	34.615	10.68	0.00	34.97	1.40
373	381	9.878599	CAGTAAAACACTAAGATAAGTTGGTTG	57.121	33.333	0.00	0.00	34.98	3.77
422	430	8.539544	TCACTTTCCTATATCTCACATCAACAA	58.460	33.333	0.00	0.00	0.00	2.83
445	453	8.103305	ACAAGTTGAATTAGCCTAGAGAAATGA	58.897	33.333	10.54	0.00	0.00	2.57
466	474	4.577283	TGACCAAGGCTTTGTACTACAAAC	59.423	41.667	9.86	7.63	42.55	2.93
473	481	6.327154	AGGCTTTGTACTACAAACAAACAAC	58.673	36.000	9.86	0.00	42.55	3.32
487	495	7.548780	ACAAACAAACAACTTGAATTATGCACT	59.451	29.630	0.00	0.00	38.50	4.40
492	500	5.531634	ACAACTTGAATTATGCACTGGTTG	58.468	37.500	9.65	9.65	37.90	3.77
585	593	5.144359	CGTATACAAACAAACAAGCTCACC	58.856	41.667	3.32	0.00	0.00	4.02
630	638	2.489329	AGATTCAGAACCAATGCAACCG	59.511	45.455	0.00	0.00	0.00	4.44
661	669	0.319405	AAAACCAAGCAGCATGAGGC	59.681	50.000	0.00	0.00	39.69	4.70
718	726	4.663334	ACTGGACCAAGAAAAGGATAACC	58.337	43.478	0.00	0.00	0.00	2.85
728	736	3.611766	AAAGGATAACCAGAGTGGACG	57.388	47.619	0.00	0.00	40.96	4.79
936	945	0.304705	CACAAGCGTCTTCACACCAC	59.695	55.000	0.00	0.00	0.00	4.16
1049	1061	0.039708	GCAAAGAAGTGGCAGCAGAC	60.040	55.000	0.00	0.00	0.00	3.51
1147	1159	1.302192	GACAAGGGCCACTGCGTTA	60.302	57.895	6.18	0.00	38.85	3.18
1251	1263	0.826672	AGGACGAGTTCGGGTTCACT	60.827	55.000	6.48	0.00	44.95	3.41
1260	1272	7.335162	CGAGTTCGGGTTCACTAGTGAAGAT	62.335	48.000	33.36	16.11	41.73	2.40
1583	1596	7.359595	GCATCAAGCGGATACAAAACATAATA	58.640	34.615	0.00	0.00	33.95	0.98
1596	1609	3.857157	ACATAATAAGCATCACCCGGT	57.143	42.857	0.00	0.00	0.00	5.28
1602	1615	1.194781	AAGCATCACCCGGTCTCTGT	61.195	55.000	0.00	0.00	0.00	3.41
1714	1727	0.248949	GTCCGCCTATGTCGAAGGAC	60.249	60.000	5.80	4.29	43.71	3.85
1775	1790	1.920325	TGAAGACCTCCCTGGCCAG	60.920	63.158	26.87	26.87	40.22	4.85
2161	2179	3.418913	CCGTGCCAATTGCGACGA	61.419	61.111	22.12	0.00	45.60	4.20
2175	2195	1.184349	CGACGAGCGAGATTGTCTTC	58.816	55.000	7.09	0.00	44.57	2.87
2195	2215	2.158726	TCGGTTAGCACAACTCCCTTTT	60.159	45.455	1.81	0.00	0.00	2.27
2338	2358	2.571653	CCCAGATGTAGTGAGGTTCCAA	59.428	50.000	0.00	0.00	0.00	3.53
2349	2369	4.279169	AGTGAGGTTCCAATGAAACACATG	59.721	41.667	0.00	0.00	40.22	3.21
2415	2435	2.042686	TGCCATGACATAAGACAGGC	57.957	50.000	5.48	5.48	35.79	4.85
2429	2449	0.611618	ACAGGCGCCAATCAAATCCA	60.612	50.000	31.54	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.650131	AGTGGCCATAGTACCTTCTCTAAC	59.350	45.833	9.72	0.00	0.00	2.34
3	4	4.649674	CAGTGGCCATAGTACCTTCTCTAA	59.350	45.833	9.72	0.00	0.00	2.10
4	5	4.215908	CAGTGGCCATAGTACCTTCTCTA	58.784	47.826	9.72	0.00	0.00	2.43
6	7	2.103263	CCAGTGGCCATAGTACCTTCTC	59.897	54.545	9.72	0.00	0.00	2.87
8	9	2.116238	TCCAGTGGCCATAGTACCTTC	58.884	52.381	9.72	0.00	0.00	3.46
22	23	7.912056	TTCTAGATTCAGTCAAAATCCAGTG	57.088	36.000	0.00	0.00	34.34	3.66
23	24	8.787852	GTTTTCTAGATTCAGTCAAAATCCAGT	58.212	33.333	0.00	0.00	34.34	4.00
55	56	9.860898	AGCCATTTATTTAGCTTTCTTTTGTAG	57.139	29.630	0.00	0.00	29.27	2.74
133	134	2.928334	CTTCCTCCAGATTCCATGTGG	58.072	52.381	0.00	0.00	44.60	4.17
169	170	4.207891	TCCTTACTTTCTGCCTTAGCTG	57.792	45.455	0.00	0.00	40.80	4.24
175	176	2.711547	ACCACTTCCTTACTTTCTGCCT	59.288	45.455	0.00	0.00	0.00	4.75
242	243	5.091552	TGTTTCTAGTACCAGATTCCCTGT	58.908	41.667	0.00	0.00	41.33	4.00
269	270	7.016268	ACTCTTCTGTAACTAGTGGAAAATCCA	59.984	37.037	0.00	0.00	45.98	3.41
275	276	5.243283	GGACACTCTTCTGTAACTAGTGGAA	59.757	44.000	0.00	0.00	41.43	3.53
277	278	4.082136	GGGACACTCTTCTGTAACTAGTGG	60.082	50.000	0.00	0.00	41.43	4.00
320	328	4.803329	ATAAATCTGAGGGCTTGTCCAT	57.197	40.909	0.00	0.00	36.21	3.41
346	354	9.623000	AACCAACTTATCTTAGTGTTTTACTGT	57.377	29.630	0.00	0.00	40.65	3.55
364	372	8.840833	AAAAACACTGTTTATTCAACCAACTT	57.159	26.923	7.59	0.00	33.97	2.66
422	430	7.051000	GGTCATTTCTCTAGGCTAATTCAACT	58.949	38.462	0.00	0.00	0.00	3.16
466	474	5.984926	ACCAGTGCATAATTCAAGTTGTTTG	59.015	36.000	2.11	0.00	38.17	2.93
473	481	3.763360	TCCCAACCAGTGCATAATTCAAG	59.237	43.478	0.00	0.00	0.00	3.02
492	500	1.027357	CATGCTAGCACATGGTTCCC	58.973	55.000	22.07	0.00	43.05	3.97
630	638	5.110940	TGCTTGGTTTTACATTCGTAACC	57.889	39.130	0.00	0.00	37.33	2.85
661	669	6.994496	TCTTATTCTTCCATTATGGCAGTCTG	59.006	38.462	10.46	0.00	37.47	3.51
677	685	7.147811	GGTCCAGTCTATGTCAGTCTTATTCTT	60.148	40.741	0.00	0.00	0.00	2.52
718	726	1.528586	CTGCACTTTTCGTCCACTCTG	59.471	52.381	0.00	0.00	0.00	3.35
728	736	6.619801	TTTTCTTCCTAGTCTGCACTTTTC	57.380	37.500	0.00	0.00	33.62	2.29
792	800	4.104102	ACAAAGTCTTGGTGTTATCCTCCA	59.896	41.667	0.00	0.00	36.82	3.86
936	945	5.047188	GTGTTGGTACTTGATGTTTTTGGG	58.953	41.667	0.00	0.00	0.00	4.12
1251	1263	5.068636	GGTACCGTGATCCTATCTTCACTA	58.931	45.833	0.00	0.00	40.05	2.74
1260	1272	1.855295	TGCAAGGTACCGTGATCCTA	58.145	50.000	29.16	8.23	0.00	2.94
1465	1477	6.916360	ACCAAAAAGGGGTGCATATATATG	57.084	37.500	17.01	17.01	43.89	1.78
1489	1501	5.647589	ACACATTGCATCACATGAAGATTC	58.352	37.500	0.00	0.00	0.00	2.52
1583	1596	1.194781	ACAGAGACCGGGTGATGCTT	61.195	55.000	3.30	0.00	0.00	3.91
1596	1609	8.300286	GCTATGTGCATCTTAGTTATACAGAGA	58.700	37.037	0.00	0.00	42.31	3.10
1602	1615	7.990314	TGTTTGGCTATGTGCATCTTAGTTATA	59.010	33.333	0.00	0.00	45.15	0.98
1824	1839	1.741706	ACGTGATCTACACTACACCGG	59.258	52.381	0.00	0.00	46.24	5.28
2161	2179	2.735762	GCTAACCGAAGACAATCTCGCT	60.736	50.000	0.00	0.00	0.00	4.93
2175	2195	1.892209	AAAGGGAGTTGTGCTAACCG	58.108	50.000	1.57	0.00	31.70	4.44
2338	2358	1.541147	CAAGGACGGCATGTGTTTCAT	59.459	47.619	0.00	0.00	37.22	2.57
2349	2369	0.818040	AAACCTGACACAAGGACGGC	60.818	55.000	0.00	0.00	40.02	5.68
2415	2435	1.679139	TAGGCTGGATTTGATTGGCG	58.321	50.000	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.