AutoCloner

Multiple sequence alignment - TraesCS2B01G011700

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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	TraesCS2B01G011700	chr2B	100.000	2397	0	0	1	2397	6131796	6134192	0.000000e+00	4427.0
1	TraesCS2B01G011700	chr2B	92.162	1429	92	14	1	1421	6111428	6112844	0.000000e+00	2001.0
2	TraesCS2B01G011700	chr2B	94.592	980	50	3	1419	2397	6030286	6031263	0.000000e+00	1513.0
3	TraesCS2B01G011700	chr2B	82.049	1220	157	32	238	1421	5997108	5998301	0.000000e+00	983.0
4	TraesCS2B01G011700	chr2B	96.377	552	19	1	870	1421	6029704	6030254	0.000000e+00	907.0
5	TraesCS2B01G011700	chr2B	74.922	642	93	33	1759	2366	689162468	689161861	5.150000e-57	231.0
6	TraesCS2B01G011700	chr2B	89.349	169	15	2	1559	1725	6113046	6113213	2.410000e-50	209.0
7	TraesCS2B01G011700	chr2B	90.260	154	14	1	1419	1572	6112876	6113028	1.450000e-47	200.0
8	TraesCS2B01G011700	chr2B	84.946	186	25	2	1797	1982	714503972	714503790	4.070000e-43	185.0
9	TraesCS2B01G011700	chr2A	83.766	887	109	16	561	1427	4110225	4109354	0.000000e+00	808.0
10	TraesCS2B01G011700	chr2D	87.078	503	61	3	918	1417	5481355	5481856	1.240000e-157	566.0
11	TraesCS2B01G011700	chr1B	76.847	704	113	28	1732	2397	629801187	629800496	3.790000e-93	351.0
12	TraesCS2B01G011700	chr7B	73.810	672	110	30	1731	2368	227305001	227304362	3.120000e-49	206.0
13	TraesCS2B01G011700	chr4A	80.108	186	36	1	686	870	546957417	546957232	1.160000e-28	137.0
14	TraesCS2B01G011700	chr7A	90.000	60	5	1	1851	1909	88947664	88947723	2.560000e-10	76.8

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	TraesCS2B01G011700	chr2B	6131796	6134192	2396	False	4427.000000	4427	100.000000	1	2397	1	chr2B.!!$F2	2396
1	TraesCS2B01G011700	chr2B	6029704	6031263	1559	False	1210.000000	1513	95.484500	870	2397	2	chr2B.!!$F3	1527
2	TraesCS2B01G011700	chr2B	5997108	5998301	1193	False	983.000000	983	82.049000	238	1421	1	chr2B.!!$F1	1183
3	TraesCS2B01G011700	chr2B	6111428	6113213	1785	False	803.333333	2001	90.590333	1	1725	3	chr2B.!!$F4	1724
4	TraesCS2B01G011700	chr2B	689161861	689162468	607	True	231.000000	231	74.922000	1759	2366	1	chr2B.!!$R1	607
5	TraesCS2B01G011700	chr2A	4109354	4110225	871	True	808.000000	808	83.766000	561	1427	1	chr2A.!!$R1	866
6	TraesCS2B01G011700	chr2D	5481355	5481856	501	False	566.000000	566	87.078000	918	1417	1	chr2D.!!$F1	499
7	TraesCS2B01G011700	chr1B	629800496	629801187	691	True	351.000000	351	76.847000	1732	2397	1	chr1B.!!$R1	665
8	TraesCS2B01G011700	chr7B	227304362	227305001	639	True	206.000000	206	73.810000	1731	2368	1	chr7B.!!$R1	637

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
107	108	1.472662	GCTCAGGATTAGCCGGGCTA	61.473	60.0	24.51	24.51	43.43	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1844	1959	0.32336	TCTTATTGCAAAGGCCCGCT	60.323	50.0	1.71	0.0	40.13	5.52	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
105	106	2.281139	GCTCAGGATTAGCCGGGC	60.281	66.667	12.11	12.11	43.43	6.13
107	108	1.472662	GCTCAGGATTAGCCGGGCTA	61.473	60.000	24.51	24.51	43.43	3.93
112	113	2.093973	CAGGATTAGCCGGGCTATGTAG	60.094	54.545	28.22	14.04	41.01	2.74
132	133	6.665695	TGTAGGTTAGGTCTGGTTTTTCTTT	58.334	36.000	0.00	0.00	0.00	2.52
136	137	6.321435	AGGTTAGGTCTGGTTTTTCTTTTCTG	59.679	38.462	0.00	0.00	0.00	3.02
137	138	6.096423	GGTTAGGTCTGGTTTTTCTTTTCTGT	59.904	38.462	0.00	0.00	0.00	3.41
138	139	7.363530	GGTTAGGTCTGGTTTTTCTTTTCTGTT	60.364	37.037	0.00	0.00	0.00	3.16
139	140	6.605471	AGGTCTGGTTTTTCTTTTCTGTTT	57.395	33.333	0.00	0.00	0.00	2.83
140	141	7.004555	AGGTCTGGTTTTTCTTTTCTGTTTT	57.995	32.000	0.00	0.00	0.00	2.43
141	142	7.097192	AGGTCTGGTTTTTCTTTTCTGTTTTC	58.903	34.615	0.00	0.00	0.00	2.29
296	298	9.722056	GTGTGAGTTCTATTTTGGCAATATAAG	57.278	33.333	0.00	1.47	0.00	1.73
323	325	7.519032	TTGTCCGAAGATGATTTTAAGGTTT	57.481	32.000	0.00	0.00	0.00	3.27
447	461	8.424274	AAGAAATTCACATTCCAAACTTTGAC	57.576	30.769	2.87	0.00	0.00	3.18
472	486	2.700722	TTATGTGGCGGTTATGCTCA	57.299	45.000	0.00	0.00	34.52	4.26
504	518	8.864024	CGCATGAGTATATCGAATTTATTGTCT	58.136	33.333	0.00	0.00	0.00	3.41
1071	1115	0.030235	TCGTCATTCCTACGGATGCG	59.970	55.000	4.58	4.58	40.68	4.73
1190	1238	6.547141	TGATGGTATCTTGACAAATGGATTCC	59.453	38.462	0.00	0.00	0.00	3.01
1222	1270	0.958876	CTGCAGATTGCCTGTCAGCA	60.959	55.000	8.42	0.00	44.23	4.41
1454	1536	6.494893	TCTCATTTTCATTTACTTGTCCCG	57.505	37.500	0.00	0.00	0.00	5.14
1567	1680	6.614694	ACAGTACAACTATCAACCATGGTA	57.385	37.500	20.12	3.19	0.00	3.25
1704	1819	5.044558	GCTGGTAACTATGCTCTTGTCTAC	58.955	45.833	0.00	0.00	37.61	2.59
1780	1895	6.263617	GGCCGGGTGATGTTTAGAAAATATTA	59.736	38.462	2.18	0.00	0.00	0.98
1785	1900	8.860088	GGGTGATGTTTAGAAAATATTAGCCAT	58.140	33.333	13.48	0.00	0.00	4.40
1814	1929	1.377202	GTTGGATGGCAAGCTCGGA	60.377	57.895	0.00	0.00	0.00	4.55
1844	1959	3.840078	TGATCTTCTTCCCATGAGTGTGA	59.160	43.478	0.00	0.00	0.00	3.58
1859	1974	2.283101	TGAGCGGGCCTTTGCAAT	60.283	55.556	15.67	0.00	40.13	3.56
1874	1989	1.472082	TGCAATAAGACCCATGTTGCG	59.528	47.619	9.52	0.00	45.94	4.85
1920	2035	4.778143	GCGCTCCCACCGAACCAT	62.778	66.667	0.00	0.00	0.00	3.55
1921	2036	2.897207	CGCTCCCACCGAACCATA	59.103	61.111	0.00	0.00	0.00	2.74
1972	2088	1.734465	GAAACAAGACTCCCTGATGCG	59.266	52.381	0.00	0.00	0.00	4.73
1979	2095	1.740025	GACTCCCTGATGCGGAAAAAG	59.260	52.381	0.00	0.00	0.00	2.27
1983	2099	1.885887	CCCTGATGCGGAAAAAGAACA	59.114	47.619	0.00	0.00	0.00	3.18
1990	2106	6.507900	TGATGCGGAAAAAGAACATTTGTTA	58.492	32.000	0.00	0.00	38.56	2.41
2060	2176	8.409358	AACAAGAGGCTTGTTGTAGAAAATAT	57.591	30.769	20.88	0.00	39.63	1.28
2078	2194	8.053355	AGAAAATATAATCCCCTTTGTCGTTCT	58.947	33.333	0.00	0.00	0.00	3.01
2172	2303	1.380112	GAGGCGTAGAGGAGGGTGT	60.380	63.158	0.00	0.00	0.00	4.16
2197	2328	0.258774	ACATTACTGGTGGCCATCCC	59.741	55.000	15.03	9.82	30.82	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	4.760047	CCTAGCCCACGTGCGCTT	62.760	66.667	30.65	15.88	36.53	4.68
63	64	0.611714	ACAACTAACCCTAGCCCACG	59.388	55.000	0.00	0.00	0.00	4.94
73	74	0.250727	TGAGCAGCCCACAACTAACC	60.251	55.000	0.00	0.00	0.00	2.85
74	75	1.160137	CTGAGCAGCCCACAACTAAC	58.840	55.000	0.00	0.00	0.00	2.34
101	102	2.296471	CAGACCTAACCTACATAGCCCG	59.704	54.545	0.00	0.00	0.00	6.13
105	106	7.621796	AGAAAAACCAGACCTAACCTACATAG	58.378	38.462	0.00	0.00	0.00	2.23
107	108	6.449830	AGAAAAACCAGACCTAACCTACAT	57.550	37.500	0.00	0.00	0.00	2.29
112	113	6.096423	ACAGAAAAGAAAAACCAGACCTAACC	59.904	38.462	0.00	0.00	0.00	2.85
296	298	8.209917	ACCTTAAAATCATCTTCGGACAATAC	57.790	34.615	0.00	0.00	0.00	1.89
345	347	0.539438	TAGGTTGCTTTGGGGCACAG	60.539	55.000	0.00	0.00	42.27	3.66
379	393	3.920231	TCTTGTGATGCTTGAGCCTAT	57.080	42.857	0.00	0.00	41.18	2.57
472	486	8.932945	AAATTCGATATACTCATGCGATATGT	57.067	30.769	0.00	0.00	0.00	2.29
504	518	5.012458	ACCTATATAAGCTTGCTGCAGATCA	59.988	40.000	20.43	3.45	45.94	2.92
597	619	8.627403	AGGCTAATCATGTAATGTCTGATTTTG	58.373	33.333	2.71	0.00	46.80	2.44
785	808	8.681486	TCTCAACATATTTAGCATGCAGTTAT	57.319	30.769	21.98	9.87	0.00	1.89
808	831	7.222872	CCTAGATTGCTCCAATGATAAACTCT	58.777	38.462	0.00	0.00	33.90	3.24
913	955	6.610830	TGATGTGTCACCCTATATCTACTCA	58.389	40.000	0.00	0.00	0.00	3.41
919	963	5.478679	AGCTACTGATGTGTCACCCTATATC	59.521	44.000	0.00	0.00	0.00	1.63
981	1025	3.538591	CATGGATGCAGCTTAAGAGACA	58.461	45.455	6.67	0.21	0.00	3.41
1071	1115	2.158900	ACCTATATGTGGTGTCTGCTGC	60.159	50.000	0.00	0.00	36.30	5.25
1076	1120	3.641906	GTGCCTACCTATATGTGGTGTCT	59.358	47.826	11.15	0.00	38.42	3.41
1086	1130	4.103013	TGTACCGATGTGCCTACCTATA	57.897	45.455	0.00	0.00	0.00	1.31
1190	1238	4.377124	GCAATCTGCAGATCATACGACATG	60.377	45.833	28.83	19.70	44.26	3.21
1454	1536	4.943705	TGGCAAGAGAGATTATTGAACACC	59.056	41.667	0.00	0.00	29.34	4.16
1704	1819	8.594881	AAGAAAGACATATAGTATCCGCTTTG	57.405	34.615	0.00	0.00	0.00	2.77
1814	1929	4.647564	TGGGAAGAAGATCAGAAAGCTT	57.352	40.909	0.00	0.00	0.00	3.74
1844	1959	0.323360	TCTTATTGCAAAGGCCCGCT	60.323	50.000	1.71	0.00	40.13	5.52
1859	1974	0.739462	CGAGCGCAACATGGGTCTTA	60.739	55.000	11.47	0.00	32.36	2.10
1874	1989	0.376852	TGTGTTGCAAAGTGTCGAGC	59.623	50.000	0.00	0.00	0.00	5.03
1965	2081	4.984161	ACAAATGTTCTTTTTCCGCATCAG	59.016	37.500	0.00	0.00	0.00	2.90
1972	2088	6.072728	GGGGCAATAACAAATGTTCTTTTTCC	60.073	38.462	1.37	0.56	39.31	3.13
1979	2095	4.551702	AAGGGGGCAATAACAAATGTTC	57.448	40.909	1.37	0.00	39.31	3.18
1983	2099	2.641815	TGCAAAGGGGGCAATAACAAAT	59.358	40.909	0.00	0.00	38.54	2.32
2060	2176	2.907696	TGGAGAACGACAAAGGGGATTA	59.092	45.455	0.00	0.00	0.00	1.75
2152	2283	2.907917	CCCTCCTCTACGCCTCCG	60.908	72.222	0.00	0.00	41.14	4.63
2172	2303	1.342819	GGCCACCAGTAATGTTTGCAA	59.657	47.619	0.00	0.00	0.00	4.08
2197	2328	0.179137	TCAGCGACCTACATGCTTCG	60.179	55.000	0.00	0.00	36.69	3.79
2306	2456	1.102809	TGAATCATGCCGGCCATCAC	61.103	55.000	26.77	11.65	29.71	3.06
2318	2468	3.819337	GCATCTAGCACACCATGAATCAT	59.181	43.478	0.00	0.00	44.79	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.