AutoCloner

Multiple sequence alignment - TraesCS3B01G058300

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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	TraesCS3B01G058300	chr3B	100.000	2549	0	0	1	2549	30406157	30403609	0.000000e+00	4708.0
1	TraesCS3B01G058300	chr3B	93.803	355	12	3	228	572	30099543	30099897	2.250000e-145	525.0
2	TraesCS3B01G058300	chr3B	90.308	227	21	1	346	572	29638276	29638051	1.920000e-76	296.0
3	TraesCS3B01G058300	chr3B	93.421	152	10	0	210	361	29639986	29639835	2.550000e-55	226.0
4	TraesCS3B01G058300	chr3B	96.970	132	4	0	2	133	30098950	30099081	3.300000e-54	222.0
5	TraesCS3B01G058300	chr3B	98.947	95	1	0	39	133	29604608	29604702	1.210000e-38	171.0
6	TraesCS3B01G058300	chr3B	94.737	76	4	0	5	80	29640058	29639983	4.450000e-23	119.0
7	TraesCS3B01G058300	chr6B	99.644	1966	5	2	584	2549	713444661	713446624	0.000000e+00	3591.0
8	TraesCS3B01G058300	chr6B	88.119	101	10	2	121	219	551188211	551188311	4.450000e-23	119.0
9	TraesCS3B01G058300	chr6B	88.119	101	10	2	121	219	551443229	551443329	4.450000e-23	119.0
10	TraesCS3B01G058300	chr2B	99.039	1977	15	3	572	2548	53421420	53423392	0.000000e+00	3542.0
11	TraesCS3B01G058300	chr2B	98.887	1977	20	2	572	2548	776222961	776224935	0.000000e+00	3528.0
12	TraesCS3B01G058300	chr2B	98.837	1977	21	2	572	2548	781094240	781096214	0.000000e+00	3522.0
13	TraesCS3B01G058300	chr2B	90.526	95	7	2	120	214	206711372	206711464	9.580000e-25	124.0
14	TraesCS3B01G058300	chr6A	98.887	1976	21	1	573	2548	507719445	507721419	0.000000e+00	3526.0
15	TraesCS3B01G058300	chr6A	98.786	1977	22	2	572	2548	616131295	616133269	0.000000e+00	3517.0
16	TraesCS3B01G058300	chr7A	98.787	1978	22	2	571	2548	39015366	39017341	0.000000e+00	3518.0
17	TraesCS3B01G058300	chr3A	98.787	1978	21	1	571	2548	54951916	54953890	0.000000e+00	3517.0
18	TraesCS3B01G058300	chr3A	87.968	374	27	8	210	571	26192324	26191957	2.340000e-115	425.0
19	TraesCS3B01G058300	chr3A	91.262	103	9	0	25	127	26193446	26193344	9.510000e-30	141.0
20	TraesCS3B01G058300	chr3A	86.567	67	8	1	238	304	26189680	26189615	3.520000e-09	73.1
21	TraesCS3B01G058300	chr3A	84.507	71	10	1	234	304	26169460	26169391	4.550000e-08	69.4
22	TraesCS3B01G058300	chr5B	98.736	1978	24	1	571	2548	641128781	641126805	0.000000e+00	3513.0
23	TraesCS3B01G058300	chr3D	91.420	338	26	3	210	547	18653802	18653468	6.430000e-126	460.0
24	TraesCS3B01G058300	chr3D	94.253	87	5	0	130	216	24062696	24062610	1.590000e-27	134.0
25	TraesCS3B01G058300	chrUn	90.526	95	9	0	128	222	17148597	17148691	2.660000e-25	126.0
26	TraesCS3B01G058300	chr7D	92.135	89	7	0	128	216	49828774	49828862	2.660000e-25	126.0
27	TraesCS3B01G058300	chr7D	92.222	90	6	1	128	217	565123565	565123477	2.660000e-25	126.0
28	TraesCS3B01G058300	chr1A	92.222	90	6	1	129	217	507880714	507880803	2.660000e-25	126.0
29	TraesCS3B01G058300	chr6D	89.691	97	8	2	121	216	450890401	450890496	3.440000e-24	122.0

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	TraesCS3B01G058300	chr3B	30403609	30406157	2548	True	4708.000000	4708	100.0000	1	2549	1	chr3B.!!$R1	2548
1	TraesCS3B01G058300	chr3B	30098950	30099897	947	False	373.500000	525	95.3865	2	572	2	chr3B.!!$F2	570
2	TraesCS3B01G058300	chr3B	29638051	29640058	2007	True	213.666667	296	92.8220	5	572	3	chr3B.!!$R2	567
3	TraesCS3B01G058300	chr6B	713444661	713446624	1963	False	3591.000000	3591	99.6440	584	2549	1	chr6B.!!$F3	1965
4	TraesCS3B01G058300	chr2B	53421420	53423392	1972	False	3542.000000	3542	99.0390	572	2548	1	chr2B.!!$F1	1976
5	TraesCS3B01G058300	chr2B	776222961	776224935	1974	False	3528.000000	3528	98.8870	572	2548	1	chr2B.!!$F3	1976
6	TraesCS3B01G058300	chr2B	781094240	781096214	1974	False	3522.000000	3522	98.8370	572	2548	1	chr2B.!!$F4	1976
7	TraesCS3B01G058300	chr6A	507719445	507721419	1974	False	3526.000000	3526	98.8870	573	2548	1	chr6A.!!$F1	1975
8	TraesCS3B01G058300	chr6A	616131295	616133269	1974	False	3517.000000	3517	98.7860	572	2548	1	chr6A.!!$F2	1976
9	TraesCS3B01G058300	chr7A	39015366	39017341	1975	False	3518.000000	3518	98.7870	571	2548	1	chr7A.!!$F1	1977
10	TraesCS3B01G058300	chr3A	54951916	54953890	1974	False	3517.000000	3517	98.7870	571	2548	1	chr3A.!!$F1	1977
11	TraesCS3B01G058300	chr3A	26189615	26193446	3831	True	213.033333	425	88.5990	25	571	3	chr3A.!!$R2	546
12	TraesCS3B01G058300	chr5B	641126805	641128781	1976	True	3513.000000	3513	98.7360	571	2548	1	chr5B.!!$R1	1977

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
430	3490	0.617413	CTGGAACATGAGGCTCAGGT	59.383	55.0	27.5	27.5	43.89	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1835	6244	5.163499	ACAGAAAAATACGCAAGAAAACCCA	60.163	36.0	0.0	0.0	43.62	4.51	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
30	31	4.521256	TGTTAAAACCTTCTTGGGAATCCG	59.479	41.667	0.00	0.00	41.11	4.18
126	1147	7.161773	TCTTGGCTTTCTTCATCCAATAAAG	57.838	36.000	0.00	0.00	37.87	1.85
127	1148	6.947733	TCTTGGCTTTCTTCATCCAATAAAGA	59.052	34.615	0.00	0.00	37.87	2.52
128	1149	6.764308	TGGCTTTCTTCATCCAATAAAGAG	57.236	37.500	0.00	0.00	32.37	2.85
129	1150	6.248433	TGGCTTTCTTCATCCAATAAAGAGT	58.752	36.000	0.00	0.00	32.37	3.24
130	1151	7.402054	TGGCTTTCTTCATCCAATAAAGAGTA	58.598	34.615	0.00	0.00	32.37	2.59
131	1152	7.336931	TGGCTTTCTTCATCCAATAAAGAGTAC	59.663	37.037	0.00	0.00	32.37	2.73
132	1153	7.554476	GGCTTTCTTCATCCAATAAAGAGTACT	59.446	37.037	0.00	0.00	32.37	2.73
133	1154	8.608317	GCTTTCTTCATCCAATAAAGAGTACTC	58.392	37.037	15.41	15.41	32.37	2.59
134	1155	9.103861	CTTTCTTCATCCAATAAAGAGTACTCC	57.896	37.037	19.38	1.81	32.37	3.85
135	1156	7.979786	TCTTCATCCAATAAAGAGTACTCCT	57.020	36.000	19.38	9.59	0.00	3.69
136	1157	8.380742	TCTTCATCCAATAAAGAGTACTCCTT	57.619	34.615	19.38	15.14	0.00	3.36
137	1158	8.826765	TCTTCATCCAATAAAGAGTACTCCTTT	58.173	33.333	19.38	18.64	37.57	3.11
138	1159	9.103861	CTTCATCCAATAAAGAGTACTCCTTTC	57.896	37.037	19.38	0.00	35.65	2.62
139	1160	7.265673	TCATCCAATAAAGAGTACTCCTTTCG	58.734	38.462	19.38	10.43	35.65	3.46
140	1161	6.600882	TCCAATAAAGAGTACTCCTTTCGT	57.399	37.500	19.38	8.78	35.65	3.85
141	1162	7.001099	TCCAATAAAGAGTACTCCTTTCGTT	57.999	36.000	19.38	13.05	35.65	3.85
142	1163	7.447594	TCCAATAAAGAGTACTCCTTTCGTTT	58.552	34.615	19.38	13.69	35.65	3.60
143	1164	8.587608	TCCAATAAAGAGTACTCCTTTCGTTTA	58.412	33.333	19.38	15.26	35.65	2.01
144	1165	9.211485	CCAATAAAGAGTACTCCTTTCGTTTAA	57.789	33.333	19.38	4.29	35.65	1.52
150	1171	9.939802	AAGAGTACTCCTTTCGTTTAATAATGT	57.060	29.630	19.38	0.00	0.00	2.71
156	1177	9.715121	ACTCCTTTCGTTTAATAATGTAAGACA	57.285	29.630	0.00	0.00	32.45	3.41
206	1227	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
207	1228	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
208	1229	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
267	1738	2.806745	CGGGATCAGTGTCAAACAGTGT	60.807	50.000	13.11	0.00	46.73	3.55
269	1743	3.632145	GGGATCAGTGTCAAACAGTGTTT	59.368	43.478	15.58	15.58	46.73	2.83
331	1805	3.181468	GGTACTCCAGGTTGTAGGCATAC	60.181	52.174	0.53	0.53	0.00	2.39
381	3441	1.450312	GAGAACCATCCCGTGCAGG	60.450	63.158	0.00	0.00	40.63	4.85
430	3490	0.617413	CTGGAACATGAGGCTCAGGT	59.383	55.000	27.50	27.50	43.89	4.00
504	3571	0.746659	AAACTGGAACACAAGCTGGC	59.253	50.000	0.00	0.00	0.00	4.85
1152	4668	0.318445	GTCCGTTCTACGTGTGCAGT	60.318	55.000	0.00	0.00	40.58	4.40
1835	6244	2.901839	GCATCCAATTAGGCCCATTCAT	59.098	45.455	0.00	0.00	37.29	2.57
1862	6271	7.116819	GGTTTTCTTGCGTATTTTTCTGTTTG	58.883	34.615	0.00	0.00	0.00	2.93
2289	6698	9.601217	GGTATACATAGTGAGACTGTGAATTTT	57.399	33.333	5.01	0.00	39.34	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.771749	TCCCAAGAAGGTTTTAACATTTACGA	59.228	34.615	0.00	0.00	32.47	3.43
1	2	6.972722	TCCCAAGAAGGTTTTAACATTTACG	58.027	36.000	0.00	0.00	32.47	3.18
2	3	9.419297	GATTCCCAAGAAGGTTTTAACATTTAC	57.581	33.333	0.00	0.00	34.86	2.01
3	4	8.590204	GGATTCCCAAGAAGGTTTTAACATTTA	58.410	33.333	0.00	0.00	34.86	1.40
23	24	3.637229	TCAGTTACCAGAGATCGGATTCC	59.363	47.826	0.00	0.00	0.00	3.01
30	31	5.239744	TCGAGCTAATCAGTTACCAGAGATC	59.760	44.000	0.00	0.00	0.00	2.75
130	1151	9.715121	TGTCTTACATTATTAAACGAAAGGAGT	57.285	29.630	0.00	0.00	0.00	3.85
181	1202	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
182	1203	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
183	1204	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
184	1205	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
185	1206	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
187	1208	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
188	1209	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
189	1210	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
190	1211	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
191	1212	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
192	1213	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
193	1214	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
194	1215	2.179424	AGTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
195	1216	1.572415	AGTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
196	1217	1.229131	AGTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
197	1218	0.338814	AAGTACTCCCTCCGTCCCAT	59.661	55.000	0.00	0.00	0.00	4.00
198	1219	0.115745	AAAGTACTCCCTCCGTCCCA	59.884	55.000	0.00	0.00	0.00	4.37
199	1220	1.066358	CAAAAGTACTCCCTCCGTCCC	60.066	57.143	0.00	0.00	0.00	4.46
200	1221	1.897802	TCAAAAGTACTCCCTCCGTCC	59.102	52.381	0.00	0.00	0.00	4.79
201	1222	3.006644	ACTTCAAAAGTACTCCCTCCGTC	59.993	47.826	0.00	0.00	40.69	4.79
202	1223	2.970640	ACTTCAAAAGTACTCCCTCCGT	59.029	45.455	0.00	0.00	40.69	4.69
203	1224	3.679824	ACTTCAAAAGTACTCCCTCCG	57.320	47.619	0.00	0.00	40.69	4.63
204	1225	4.715713	ACAACTTCAAAAGTACTCCCTCC	58.284	43.478	0.00	0.00	41.91	4.30
205	1226	5.932883	CCTACAACTTCAAAAGTACTCCCTC	59.067	44.000	0.00	0.00	41.91	4.30
206	1227	5.745181	GCCTACAACTTCAAAAGTACTCCCT	60.745	44.000	0.00	0.00	41.91	4.20
207	1228	4.454847	GCCTACAACTTCAAAAGTACTCCC	59.545	45.833	0.00	0.00	41.91	4.30
208	1229	5.306394	AGCCTACAACTTCAAAAGTACTCC	58.694	41.667	0.00	0.00	41.91	3.85
267	1738	2.621407	GCTCATGGTGATCTCCCCAAAA	60.621	50.000	11.24	0.00	33.66	2.44
269	1743	0.548031	GCTCATGGTGATCTCCCCAA	59.452	55.000	11.24	0.00	33.66	4.12
331	1805	1.732259	GACATGAGTTGTAGTTGGCCG	59.268	52.381	0.00	0.00	39.18	6.13
381	3441	5.482908	ACGTATTATCCCTCAATGATGCTC	58.517	41.667	0.00	0.00	0.00	4.26
430	3490	6.607600	AGCTGTGACACTAATCTACCTATCAA	59.392	38.462	7.20	0.00	0.00	2.57
504	3571	1.364626	GACGAGCATGGCAGGTCTTG	61.365	60.000	0.00	5.25	32.84	3.02
545	3612	1.618876	TTCGATCCAGCGGGGCTAAA	61.619	55.000	2.05	0.00	36.40	1.85
1152	4668	2.438021	CCCGATTCTTACCCCATTCTCA	59.562	50.000	0.00	0.00	0.00	3.27
1835	6244	5.163499	ACAGAAAAATACGCAAGAAAACCCA	60.163	36.000	0.00	0.00	43.62	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.