AutoCloner

Multiple sequence alignment - TraesCS1D01G228500

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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	TraesCS1D01G228500	chr1D	100.000	2654	0	0	1	2654	316602837	316600184	0.000000e+00	4902.0
1	TraesCS1D01G228500	chr1B	95.666	2238	58	16	438	2650	428638325	428636102	0.000000e+00	3559.0
2	TraesCS1D01G228500	chr1B	84.906	265	23	9	1	265	428640396	428640149	4.390000e-63	252.0
3	TraesCS1D01G228500	chr1B	92.727	165	4	1	398	562	428616731	428616575	5.710000e-57	231.0
4	TraesCS1D01G228500	chr1B	91.971	137	8	3	19	155	428618700	428618567	3.490000e-44	189.0
5	TraesCS1D01G228500	chr1A	95.078	1605	56	17	1058	2654	397669477	397667888	0.000000e+00	2505.0
6	TraesCS1D01G228500	chr1A	91.008	645	31	8	436	1060	397700544	397699907	0.000000e+00	845.0
7	TraesCS1D01G228500	chr1A	94.839	155	7	1	1	155	397700728	397700575	9.490000e-60	241.0
8	TraesCS1D01G228500	chr5D	86.803	1076	105	20	1571	2615	35803894	35804963	0.000000e+00	1166.0
9	TraesCS1D01G228500	chr5A	85.024	1055	107	28	1584	2615	24354082	24355108	0.000000e+00	1026.0
10	TraesCS1D01G228500	chr5A	89.024	410	25	11	1725	2120	23900968	23900565	8.540000e-135	490.0
11	TraesCS1D01G228500	chr5A	86.702	188	25	0	1463	1650	23901275	23901088	2.680000e-50	209.0
12	TraesCS1D01G228500	chr5B	84.630	1067	99	41	1569	2596	26642047	26641007	0.000000e+00	1002.0
13	TraesCS1D01G228500	chr5B	82.873	1086	111	36	1569	2614	26637363	26636313	0.000000e+00	905.0
14	TraesCS1D01G228500	chr5B	78.853	558	109	7	1085	1639	26637914	26637363	4.170000e-98	368.0
15	TraesCS1D01G228500	chr5B	78.853	558	109	7	1085	1639	26642598	26642047	4.170000e-98	368.0
16	TraesCS1D01G228500	chrUn	85.988	521	59	10	2090	2596	389867537	389867017	1.800000e-151	545.0
17	TraesCS1D01G228500	chrUn	78.853	558	109	7	1085	1639	323957054	323956503	4.170000e-98	368.0
18	TraesCS1D01G228500	chrUn	81.948	421	48	19	1569	1969	323956503	323956091	5.480000e-87	331.0
19	TraesCS1D01G228500	chr2D	75.748	635	104	30	1717	2333	127820310	127819708	9.360000e-70	274.0
20	TraesCS1D01G228500	chr2A	75.637	628	103	31	1725	2333	85612443	85611847	1.570000e-67	267.0
21	TraesCS1D01G228500	chr2A	95.238	42	2	0	238	279	100223805	100223846	1.700000e-07	67.6
22	TraesCS1D01G228500	chr4A	100.000	35	0	0	2616	2650	456934428	456934462	6.130000e-07	65.8
23	TraesCS1D01G228500	chr4A	97.143	35	1	0	2616	2650	456844606	456844640	2.850000e-05	60.2
24	TraesCS1D01G228500	chr4D	97.222	36	1	0	2616	2651	14628774	14628809	7.930000e-06	62.1
25	TraesCS1D01G228500	chr7D	100.000	28	0	0	144	171	108400005	108399978	5.000000e-03	52.8

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	TraesCS1D01G228500	chr1D	316600184	316602837	2653	True	4902.00	4902	100.00000	1	2654	1	chr1D.!!$R1	2653
1	TraesCS1D01G228500	chr1B	428636102	428640396	4294	True	1905.50	3559	90.28600	1	2650	2	chr1B.!!$R2	2649
2	TraesCS1D01G228500	chr1B	428616575	428618700	2125	True	210.00	231	92.34900	19	562	2	chr1B.!!$R1	543
3	TraesCS1D01G228500	chr1A	397667888	397669477	1589	True	2505.00	2505	95.07800	1058	2654	1	chr1A.!!$R1	1596
4	TraesCS1D01G228500	chr1A	397699907	397700728	821	True	543.00	845	92.92350	1	1060	2	chr1A.!!$R2	1059
5	TraesCS1D01G228500	chr5D	35803894	35804963	1069	False	1166.00	1166	86.80300	1571	2615	1	chr5D.!!$F1	1044
6	TraesCS1D01G228500	chr5A	24354082	24355108	1026	False	1026.00	1026	85.02400	1584	2615	1	chr5A.!!$F1	1031
7	TraesCS1D01G228500	chr5A	23900565	23901275	710	True	349.50	490	87.86300	1463	2120	2	chr5A.!!$R1	657
8	TraesCS1D01G228500	chr5B	26636313	26642598	6285	True	660.75	1002	81.30225	1085	2614	4	chr5B.!!$R1	1529
9	TraesCS1D01G228500	chrUn	389867017	389867537	520	True	545.00	545	85.98800	2090	2596	1	chrUn.!!$R1	506
10	TraesCS1D01G228500	chrUn	323956091	323957054	963	True	349.50	368	80.40050	1085	1969	2	chrUn.!!$R2	884
11	TraesCS1D01G228500	chr2D	127819708	127820310	602	True	274.00	274	75.74800	1717	2333	1	chr2D.!!$R1	616
12	TraesCS1D01G228500	chr2A	85611847	85612443	596	True	267.00	267	75.63700	1725	2333	1	chr2A.!!$R1	608

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
429	2107	0.036388	TGTCGCCTGAGGATTTGTCC	60.036	55.0	0.65	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2282	5684	0.459078	CACCCACACATGCACACAAA	59.541	50.0	0.0	0.0	0.0	2.83	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
155	157	0.526211	TCAGTGTGTGTAGCGCCTAG	59.474	55.000	2.29	0.00	0.00	3.02
156	158	0.243907	CAGTGTGTGTAGCGCCTAGT	59.756	55.000	2.29	0.00	0.00	2.57
157	159	0.243907	AGTGTGTGTAGCGCCTAGTG	59.756	55.000	2.29	0.00	0.00	2.74
159	161	0.242825	TGTGTGTAGCGCCTAGTGTC	59.757	55.000	2.29	0.00	0.00	3.67
161	163	1.741706	GTGTGTAGCGCCTAGTGTCTA	59.258	52.381	2.29	0.00	0.00	2.59
162	164	2.014857	TGTGTAGCGCCTAGTGTCTAG	58.985	52.381	2.29	0.00	0.00	2.43
163	165	1.334243	GTGTAGCGCCTAGTGTCTAGG	59.666	57.143	15.97	15.97	37.75	3.02
170	172	1.676746	CCTAGTGTCTAGGCGCTACA	58.323	55.000	13.56	4.25	0.00	2.74
171	173	1.604755	CCTAGTGTCTAGGCGCTACAG	59.395	57.143	13.56	7.09	0.00	2.74
172	174	2.290464	CTAGTGTCTAGGCGCTACAGT	58.710	52.381	13.56	12.12	0.00	3.55
173	175	2.414994	AGTGTCTAGGCGCTACAGTA	57.585	50.000	9.08	0.00	0.00	2.74
176	178	3.814283	AGTGTCTAGGCGCTACAGTATAC	59.186	47.826	9.08	0.00	0.00	1.47
187	189	4.547406	CTACAGTATACAGTGTAGCGCA	57.453	45.455	11.47	0.00	46.51	6.09
201	203	3.923614	CGCATAGTGTCTAGGCGC	58.076	61.111	19.29	0.00	40.67	6.53
203	205	0.591659	CGCATAGTGTCTAGGCGCTA	59.408	55.000	19.32	19.32	40.67	4.26
204	206	1.400371	CGCATAGTGTCTAGGCGCTAG	60.400	57.143	21.26	14.41	40.67	3.42
223	225	2.882777	CACTAGTGCAGCGCCTCG	60.883	66.667	10.54	0.00	0.00	4.63
248	250	4.200283	GCGCGCCTAGCTCTCAGT	62.200	66.667	23.24	0.00	45.59	3.41
265	267	2.287644	TCAGTCGTTGCACATTGACTTG	59.712	45.455	6.59	4.31	39.55	3.16
333	376	0.519519	CGTGGCGCTTAATTGTTGGA	59.480	50.000	7.64	0.00	0.00	3.53
335	378	0.519519	TGGCGCTTAATTGTTGGACG	59.480	50.000	7.64	0.00	0.00	4.79
337	1506	1.400494	GGCGCTTAATTGTTGGACGAT	59.600	47.619	7.64	0.00	0.00	3.73
395	2073	8.691727	CACGTATAATCTTGTTACTACATGCTC	58.308	37.037	0.00	0.00	33.44	4.26
396	2074	8.410912	ACGTATAATCTTGTTACTACATGCTCA	58.589	33.333	0.00	0.00	33.44	4.26
415	2093	1.061799	ACACGTCGTACGAATGTCGC	61.062	55.000	23.73	10.14	46.05	5.19
416	2094	1.512734	ACGTCGTACGAATGTCGCC	60.513	57.895	21.39	4.55	46.05	5.54
417	2095	1.226211	CGTCGTACGAATGTCGCCT	60.226	57.895	21.39	0.00	46.05	5.52
420	2098	0.098200	TCGTACGAATGTCGCCTGAG	59.902	55.000	17.11	0.00	45.12	3.35
423	2101	1.067212	GTACGAATGTCGCCTGAGGAT	59.933	52.381	0.65	0.00	45.12	3.24
424	2102	0.537188	ACGAATGTCGCCTGAGGATT	59.463	50.000	0.65	0.00	45.12	3.01
425	2103	1.066143	ACGAATGTCGCCTGAGGATTT	60.066	47.619	0.65	0.00	45.12	2.17
426	2104	1.328680	CGAATGTCGCCTGAGGATTTG	59.671	52.381	0.65	0.00	31.14	2.32
427	2105	2.359900	GAATGTCGCCTGAGGATTTGT	58.640	47.619	0.65	0.00	0.00	2.83
428	2106	2.029838	ATGTCGCCTGAGGATTTGTC	57.970	50.000	0.65	0.00	0.00	3.18
429	2107	0.036388	TGTCGCCTGAGGATTTGTCC	60.036	55.000	0.65	0.00	0.00	4.02
430	2108	0.744771	GTCGCCTGAGGATTTGTCCC	60.745	60.000	0.65	0.00	0.00	4.46
431	2109	0.909610	TCGCCTGAGGATTTGTCCCT	60.910	55.000	0.65	0.00	36.57	4.20
432	2110	0.745845	CGCCTGAGGATTTGTCCCTG	60.746	60.000	0.65	0.00	33.36	4.45
433	2111	0.620556	GCCTGAGGATTTGTCCCTGA	59.379	55.000	0.65	0.00	33.36	3.86
434	2112	1.407989	GCCTGAGGATTTGTCCCTGAG	60.408	57.143	0.65	0.00	35.22	3.35
472	3680	0.109458	GACATGCTCACGTCGTACCA	60.109	55.000	0.00	0.00	0.00	3.25
473	3681	0.315886	ACATGCTCACGTCGTACCAA	59.684	50.000	0.00	0.00	0.00	3.67
474	3682	1.269883	ACATGCTCACGTCGTACCAAA	60.270	47.619	0.00	0.00	0.00	3.28
475	3683	1.126113	CATGCTCACGTCGTACCAAAC	59.874	52.381	0.00	0.00	0.00	2.93
894	4128	3.067461	CAGCTAAGCAACTCGATCTACCT	59.933	47.826	0.00	0.00	0.00	3.08
897	4131	4.515944	GCTAAGCAACTCGATCTACCTCTA	59.484	45.833	0.00	0.00	0.00	2.43
930	4167	4.490743	GTTCTTCTTCTCTCTTCCTTCCG	58.509	47.826	0.00	0.00	0.00	4.30
1061	4298	0.966920	CGCCACCATACCTACCCTAG	59.033	60.000	0.00	0.00	0.00	3.02
1710	5050	7.093509	TGCAAGACTCCATGAAGTGTTAGTATA	60.094	37.037	0.00	0.00	31.56	1.47
2247	5644	3.502595	GGTGTCTTCTTTCAGCTAAACCC	59.497	47.826	0.00	0.00	0.00	4.11
2282	5684	4.070009	GACCGACAAGGGTTATTGAACTT	58.930	43.478	0.00	0.00	46.96	2.66
2385	5805	1.851658	ACGAAACATTGTTGGCTTGC	58.148	45.000	2.13	0.00	0.00	4.01
2392	5812	4.816786	ACATTGTTGGCTTGCATTTTTC	57.183	36.364	0.00	0.00	0.00	2.29
2597	10706	5.124457	ACTCTCACATGGTTTGTTGCATATC	59.876	40.000	0.00	0.00	36.00	1.63
2632	10741	0.034756	TGTGACGGTGTCCTGGATTG	59.965	55.000	0.00	0.00	0.00	2.67
2651	10760	2.228480	GGGGGTGCTAACCTGGTCA	61.228	63.158	0.00	0.00	46.70	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
100	102	3.665675	AACCCGAGGTGCGATGCTC	62.666	63.158	0.00	0.00	44.57	4.26
155	157	3.562973	TGTATACTGTAGCGCCTAGACAC	59.437	47.826	2.29	2.30	0.00	3.67
156	158	3.812262	TGTATACTGTAGCGCCTAGACA	58.188	45.455	2.29	2.49	0.00	3.41
157	159	3.814283	ACTGTATACTGTAGCGCCTAGAC	59.186	47.826	13.19	0.00	0.00	2.59
159	161	3.564644	ACACTGTATACTGTAGCGCCTAG	59.435	47.826	14.25	2.15	0.00	3.02
161	163	2.376109	ACACTGTATACTGTAGCGCCT	58.624	47.619	14.25	0.00	0.00	5.52
162	164	2.865343	ACACTGTATACTGTAGCGCC	57.135	50.000	14.25	0.00	0.00	6.53
166	168	4.547406	TGCGCTACACTGTATACTGTAG	57.453	45.455	20.31	20.31	41.91	2.74
167	169	5.761726	ACTATGCGCTACACTGTATACTGTA	59.238	40.000	14.25	9.37	0.00	2.74
168	170	4.579340	ACTATGCGCTACACTGTATACTGT	59.421	41.667	9.73	9.42	0.00	3.55
169	171	4.912187	CACTATGCGCTACACTGTATACTG	59.088	45.833	9.73	8.11	0.00	2.74
170	172	4.579340	ACACTATGCGCTACACTGTATACT	59.421	41.667	9.73	0.00	0.00	2.12
171	173	4.856664	ACACTATGCGCTACACTGTATAC	58.143	43.478	9.73	0.00	0.00	1.47
172	174	4.820173	AGACACTATGCGCTACACTGTATA	59.180	41.667	9.73	0.00	0.00	1.47
173	175	3.632604	AGACACTATGCGCTACACTGTAT	59.367	43.478	9.73	0.00	0.00	2.29
176	178	2.568696	AGACACTATGCGCTACACTG	57.431	50.000	9.73	0.00	0.00	3.66
187	189	1.249407	GCCTAGCGCCTAGACACTAT	58.751	55.000	2.29	0.00	36.26	2.12
214	216	2.103143	CCTAGTGTCGAGGCGCTG	59.897	66.667	7.64	0.00	0.00	5.18
222	224	3.884350	TAGGCGCGCCTAGTGTCG	61.884	66.667	46.98	0.00	46.14	4.35
232	234	2.025441	GACTGAGAGCTAGGCGCG	59.975	66.667	0.00	0.00	45.59	6.86
237	239	1.068264	TGTGCAACGACTGAGAGCTAG	60.068	52.381	0.00	0.00	42.39	3.42
243	245	2.138320	AGTCAATGTGCAACGACTGAG	58.862	47.619	7.54	0.00	42.39	3.35
244	246	2.238942	AGTCAATGTGCAACGACTGA	57.761	45.000	7.54	0.00	42.39	3.41
248	250	0.310543	GCCAAGTCAATGTGCAACGA	59.689	50.000	0.00	0.00	42.39	3.85
265	267	1.200020	CCGGACTGTCTGAAAATTGCC	59.800	52.381	18.02	0.00	0.00	4.52
314	357	0.519519	TCCAACAATTAAGCGCCACG	59.480	50.000	2.29	0.00	0.00	4.94
328	371	4.989168	AGACTCTTTTGTGTATCGTCCAAC	59.011	41.667	0.00	0.00	0.00	3.77
333	376	4.235360	CGGAAGACTCTTTTGTGTATCGT	58.765	43.478	0.00	0.00	0.00	3.73
335	378	3.933332	CCCGGAAGACTCTTTTGTGTATC	59.067	47.826	0.73	0.00	0.00	2.24
337	1506	2.701951	ACCCGGAAGACTCTTTTGTGTA	59.298	45.455	0.73	0.00	0.00	2.90
368	1537	8.410912	AGCATGTAGTAACAAGATTATACGTGA	58.589	33.333	0.00	0.00	39.58	4.35
369	1538	8.575565	AGCATGTAGTAACAAGATTATACGTG	57.424	34.615	0.00	0.00	39.58	4.49
370	1539	8.410912	TGAGCATGTAGTAACAAGATTATACGT	58.589	33.333	0.00	0.00	39.58	3.57
372	1541	9.529325	TGTGAGCATGTAGTAACAAGATTATAC	57.471	33.333	0.00	0.00	39.58	1.47
395	2073	0.626817	CGACATTCGTACGACGTGTG	59.373	55.000	29.47	21.76	43.14	3.82
396	2074	1.061799	GCGACATTCGTACGACGTGT	61.062	55.000	26.46	26.46	42.81	4.49
415	2093	1.211457	CCTCAGGGACAAATCCTCAGG	59.789	57.143	0.00	0.00	45.46	3.86
416	2094	2.170187	CTCCTCAGGGACAAATCCTCAG	59.830	54.545	0.00	0.00	45.46	3.35
417	2095	2.191400	CTCCTCAGGGACAAATCCTCA	58.809	52.381	0.00	0.00	45.46	3.86
420	2098	1.584724	TCCTCCTCAGGGACAAATCC	58.415	55.000	0.00	0.00	45.42	3.01
423	2101	2.716424	ACAAATCCTCCTCAGGGACAAA	59.284	45.455	0.00	0.00	40.80	2.83
424	2102	2.305927	GACAAATCCTCCTCAGGGACAA	59.694	50.000	0.00	0.00	40.80	3.18
425	2103	1.909302	GACAAATCCTCCTCAGGGACA	59.091	52.381	0.00	0.00	40.80	4.02
426	2104	1.210722	GGACAAATCCTCCTCAGGGAC	59.789	57.143	0.00	0.00	42.45	4.46
427	2105	1.584724	GGACAAATCCTCCTCAGGGA	58.415	55.000	0.00	0.00	42.45	4.20
428	2106	0.548510	GGGACAAATCCTCCTCAGGG	59.451	60.000	0.00	0.00	45.46	4.45
429	2107	1.289160	TGGGACAAATCCTCCTCAGG	58.711	55.000	0.00	0.00	45.46	3.86
545	3762	5.819379	TCAATAGCTAGCTCCATTTCACTTG	59.181	40.000	23.26	11.40	0.00	3.16
894	4128	6.906659	AGAAGAAGAACGACGTATTGTTAGA	58.093	36.000	0.00	0.00	32.12	2.10
897	4131	5.770417	AGAGAAGAAGAACGACGTATTGTT	58.230	37.500	0.00	4.43	34.92	2.83
930	4167	5.363580	AGGAGAAGAAGAACAGAGATGGATC	59.636	44.000	0.00	0.00	0.00	3.36
1341	4578	1.227380	GACGAGCCGATTGCATCCT	60.227	57.895	1.50	0.00	44.83	3.24
1712	5052	8.958506	CATAGTATAGGAAGCGTAGAAAGGTAT	58.041	37.037	0.00	0.00	0.00	2.73
1714	5054	6.294620	GCATAGTATAGGAAGCGTAGAAAGGT	60.295	42.308	0.00	0.00	0.00	3.50
2060	5447	7.466746	AACGGGCGTTTTACCTCTATATATA	57.533	36.000	0.00	0.00	34.22	0.86
2064	5459	4.183101	CAAACGGGCGTTTTACCTCTATA	58.817	43.478	0.00	0.00	44.84	1.31
2282	5684	0.459078	CACCCACACATGCACACAAA	59.541	50.000	0.00	0.00	0.00	2.83
2385	5805	8.369218	AGTAACTCCAAATTTGCAGAAAAATG	57.631	30.769	16.08	0.00	30.21	2.32
2392	5812	8.424274	AAAGAAAAGTAACTCCAAATTTGCAG	57.576	30.769	12.92	10.24	0.00	4.41
2461	5883	3.829948	CAAGATGCACACATTTCTGACC	58.170	45.455	0.00	0.00	36.35	4.02
2551	5984	0.740868	CCACGGTTGTCAGATGCGAT	60.741	55.000	0.00	0.00	0.00	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.