AutoCloner

Multiple sequence alignment - TraesCS2D01G510700

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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	TraesCS2D01G510700	chr2D	100.000	2423	0	0	1	2423	602551198	602553620	0.000000e+00	4475.0
1	TraesCS2D01G510700	chr2D	95.822	1125	45	2	1299	2423	303077919	303079041	0.000000e+00	1816.0
2	TraesCS2D01G510700	chr2D	91.822	269	20	2	1299	1566	411786123	411785856	8.180000e-100	374.0
3	TraesCS2D01G510700	chr3D	95.822	1125	44	3	1299	2423	322705371	322704250	0.000000e+00	1814.0
4	TraesCS2D01G510700	chr3D	95.401	1109	39	7	1325	2423	126250815	126251921	0.000000e+00	1755.0
5	TraesCS2D01G510700	chr1D	94.305	1159	41	8	1288	2423	448455881	448454725	0.000000e+00	1751.0
6	TraesCS2D01G510700	chr1D	79.735	1283	174	44	26	1243	483981336	483980075	0.000000e+00	850.0
7	TraesCS2D01G510700	chr1D	77.744	1312	202	44	55	1296	126609576	126608285	0.000000e+00	723.0
8	TraesCS2D01G510700	chr1D	78.524	1057	156	40	281	1298	229040776	229039752	1.580000e-176	628.0
9	TraesCS2D01G510700	chr7D	94.164	1148	42	5	1299	2423	137778714	137777569	0.000000e+00	1725.0
10	TraesCS2D01G510700	chr7D	93.766	1155	41	10	1299	2423	414313079	414314232	0.000000e+00	1705.0
11	TraesCS2D01G510700	chr7D	84.366	1324	145	32	26	1298	573439034	573437722	0.000000e+00	1242.0
12	TraesCS2D01G510700	chr7D	77.179	872	125	48	26	831	421332398	421331535	7.950000e-120	440.0
13	TraesCS2D01G510700	chr7D	79.035	663	90	24	26	649	548266399	548265747	2.240000e-110	409.0
14	TraesCS2D01G510700	chr6D	93.915	1134	61	4	1296	2423	76990542	76991673	0.000000e+00	1705.0
15	TraesCS2D01G510700	chr6D	82.299	1209	156	37	139	1298	6323450	6324649	0.000000e+00	994.0
16	TraesCS2D01G510700	chr6D	79.955	1327	202	38	26	1298	263157540	263158856	0.000000e+00	918.0
17	TraesCS2D01G510700	chr4B	93.624	1145	52	3	1298	2423	415585318	415584176	0.000000e+00	1690.0
18	TraesCS2D01G510700	chr7A	93.391	1150	48	10	1299	2423	204909660	204908514	0.000000e+00	1677.0
19	TraesCS2D01G510700	chr7A	93.369	1131	67	4	1299	2423	639187399	639188527	0.000000e+00	1666.0
20	TraesCS2D01G510700	chr7A	79.299	599	82	18	281	842	663383916	663383323	4.890000e-102	381.0
21	TraesCS2D01G510700	chr2A	83.504	1267	129	31	104	1298	104390153	104388895	0.000000e+00	1109.0
22	TraesCS2D01G510700	chr2A	78.215	941	148	31	357	1258	20037555	20038477	1.270000e-152	549.0
23	TraesCS2D01G510700	chr2A	91.837	49	1	1	284	329	613360575	613360527	5.590000e-07	65.8
24	TraesCS2D01G510700	chr7B	81.136	1320	180	41	26	1294	632198701	632197400	0.000000e+00	994.0
25	TraesCS2D01G510700	chr7B	79.864	1321	203	39	22	1295	437373502	437372198	0.000000e+00	907.0
26	TraesCS2D01G510700	chr7B	80.966	1035	142	32	283	1298	525086831	525085833	0.000000e+00	769.0
27	TraesCS2D01G510700	chr7B	85.586	555	72	6	748	1298	6792485	6791935	2.090000e-160	575.0
28	TraesCS2D01G510700	chr7B	83.887	391	42	13	1299	1682	682048925	682048549	1.070000e-93	353.0
29	TraesCS2D01G510700	chr5D	90.884	735	53	8	1296	2018	441283881	441284613	0.000000e+00	974.0
30	TraesCS2D01G510700	chr6A	79.860	1286	191	55	58	1298	129751355	129750093	0.000000e+00	878.0
31	TraesCS2D01G510700	chr4D	85.207	845	99	9	477	1298	85583765	85584606	0.000000e+00	845.0
32	TraesCS2D01G510700	chr4D	80.394	1168	176	34	173	1298	293667676	293666520	0.000000e+00	839.0
33	TraesCS2D01G510700	chr4D	76.194	1214	201	59	26	1173	505533256	505532065	5.850000e-156	560.0
34	TraesCS2D01G510700	chr1B	78.808	1359	191	53	22	1296	573140389	573139044	0.000000e+00	824.0
35	TraesCS2D01G510700	chr1B	96.875	32	1	0	26	57	146775282	146775251	1.000000e-03	54.7
36	TraesCS2D01G510700	chrUn	78.108	941	149	31	360	1261	236197927	236197005	5.890000e-151	544.0

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	TraesCS2D01G510700	chr2D	602551198	602553620	2422	False	4475	4475	100.000	1	2423	1	chr2D.!!$F2	2422
1	TraesCS2D01G510700	chr2D	303077919	303079041	1122	False	1816	1816	95.822	1299	2423	1	chr2D.!!$F1	1124
2	TraesCS2D01G510700	chr3D	322704250	322705371	1121	True	1814	1814	95.822	1299	2423	1	chr3D.!!$R1	1124
3	TraesCS2D01G510700	chr3D	126250815	126251921	1106	False	1755	1755	95.401	1325	2423	1	chr3D.!!$F1	1098
4	TraesCS2D01G510700	chr1D	448454725	448455881	1156	True	1751	1751	94.305	1288	2423	1	chr1D.!!$R3	1135
5	TraesCS2D01G510700	chr1D	483980075	483981336	1261	True	850	850	79.735	26	1243	1	chr1D.!!$R4	1217
6	TraesCS2D01G510700	chr1D	126608285	126609576	1291	True	723	723	77.744	55	1296	1	chr1D.!!$R1	1241
7	TraesCS2D01G510700	chr1D	229039752	229040776	1024	True	628	628	78.524	281	1298	1	chr1D.!!$R2	1017
8	TraesCS2D01G510700	chr7D	137777569	137778714	1145	True	1725	1725	94.164	1299	2423	1	chr7D.!!$R1	1124
9	TraesCS2D01G510700	chr7D	414313079	414314232	1153	False	1705	1705	93.766	1299	2423	1	chr7D.!!$F1	1124
10	TraesCS2D01G510700	chr7D	573437722	573439034	1312	True	1242	1242	84.366	26	1298	1	chr7D.!!$R4	1272
11	TraesCS2D01G510700	chr7D	421331535	421332398	863	True	440	440	77.179	26	831	1	chr7D.!!$R2	805
12	TraesCS2D01G510700	chr7D	548265747	548266399	652	True	409	409	79.035	26	649	1	chr7D.!!$R3	623
13	TraesCS2D01G510700	chr6D	76990542	76991673	1131	False	1705	1705	93.915	1296	2423	1	chr6D.!!$F2	1127
14	TraesCS2D01G510700	chr6D	6323450	6324649	1199	False	994	994	82.299	139	1298	1	chr6D.!!$F1	1159
15	TraesCS2D01G510700	chr6D	263157540	263158856	1316	False	918	918	79.955	26	1298	1	chr6D.!!$F3	1272
16	TraesCS2D01G510700	chr4B	415584176	415585318	1142	True	1690	1690	93.624	1298	2423	1	chr4B.!!$R1	1125
17	TraesCS2D01G510700	chr7A	204908514	204909660	1146	True	1677	1677	93.391	1299	2423	1	chr7A.!!$R1	1124
18	TraesCS2D01G510700	chr7A	639187399	639188527	1128	False	1666	1666	93.369	1299	2423	1	chr7A.!!$F1	1124
19	TraesCS2D01G510700	chr7A	663383323	663383916	593	True	381	381	79.299	281	842	1	chr7A.!!$R2	561
20	TraesCS2D01G510700	chr2A	104388895	104390153	1258	True	1109	1109	83.504	104	1298	1	chr2A.!!$R1	1194
21	TraesCS2D01G510700	chr2A	20037555	20038477	922	False	549	549	78.215	357	1258	1	chr2A.!!$F1	901
22	TraesCS2D01G510700	chr7B	632197400	632198701	1301	True	994	994	81.136	26	1294	1	chr7B.!!$R4	1268
23	TraesCS2D01G510700	chr7B	437372198	437373502	1304	True	907	907	79.864	22	1295	1	chr7B.!!$R2	1273
24	TraesCS2D01G510700	chr7B	525085833	525086831	998	True	769	769	80.966	283	1298	1	chr7B.!!$R3	1015
25	TraesCS2D01G510700	chr7B	6791935	6792485	550	True	575	575	85.586	748	1298	1	chr7B.!!$R1	550
26	TraesCS2D01G510700	chr5D	441283881	441284613	732	False	974	974	90.884	1296	2018	1	chr5D.!!$F1	722
27	TraesCS2D01G510700	chr6A	129750093	129751355	1262	True	878	878	79.860	58	1298	1	chr6A.!!$R1	1240
28	TraesCS2D01G510700	chr4D	85583765	85584606	841	False	845	845	85.207	477	1298	1	chr4D.!!$F1	821
29	TraesCS2D01G510700	chr4D	293666520	293667676	1156	True	839	839	80.394	173	1298	1	chr4D.!!$R1	1125
30	TraesCS2D01G510700	chr4D	505532065	505533256	1191	True	560	560	76.194	26	1173	1	chr4D.!!$R2	1147
31	TraesCS2D01G510700	chr1B	573139044	573140389	1345	True	824	824	78.808	22	1296	1	chr1B.!!$R2	1274
32	TraesCS2D01G510700	chrUn	236197005	236197927	922	True	544	544	78.108	360	1261	1	chrUn.!!$R1	901

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
464	567	0.247736	ATCGCCGCAGAAACTCTCTT	59.752	50.0	0.0	0.0	29.07	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1882	2165	1.192803	AGAGGAGGAACCGGGTGAAC	61.193	60.0	6.32	0.0	44.74	3.18	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
20	21	4.819761	GCATCGAGCGGCAGTGGA	62.820	66.667	1.45	0.00	0.00	4.02
21	22	2.887568	CATCGAGCGGCAGTGGAC	60.888	66.667	1.45	0.00	0.00	4.02
22	23	3.071206	ATCGAGCGGCAGTGGACT	61.071	61.111	1.45	0.00	0.00	3.85
23	24	2.650116	ATCGAGCGGCAGTGGACTT	61.650	57.895	1.45	0.00	0.00	3.01
24	25	2.842394	ATCGAGCGGCAGTGGACTTG	62.842	60.000	1.45	0.00	0.00	3.16
43	44	2.581354	GAGCATCTCCAGCCACGT	59.419	61.111	0.00	0.00	0.00	4.49
45	46	1.954362	GAGCATCTCCAGCCACGTCT	61.954	60.000	0.00	0.00	0.00	4.18
52	53	1.003355	CCAGCCACGTCTCCAACAT	60.003	57.895	0.00	0.00	0.00	2.71
111	117	1.674057	CCAGTCGCTTCCCAGAAGT	59.326	57.895	6.24	0.00	0.00	3.01
129	135	8.085909	CCCAGAAGTTTAATTTTCGTTGGTTAT	58.914	33.333	0.00	0.00	0.00	1.89
264	300	4.933064	CGTCCTCATCGCCTCGGC	62.933	72.222	0.00	0.00	37.85	5.54
269	305	4.841617	TCATCGCCTCGGCTCCCT	62.842	66.667	6.35	0.00	39.32	4.20
464	567	0.247736	ATCGCCGCAGAAACTCTCTT	59.752	50.000	0.00	0.00	29.07	2.85
473	597	3.169099	CAGAAACTCTCTTCCCCTCTCA	58.831	50.000	0.00	0.00	29.07	3.27
475	599	3.580895	AGAAACTCTCTTCCCCTCTCAAC	59.419	47.826	0.00	0.00	0.00	3.18
507	642	1.398234	CTTTCCTCCCCCTCTCCCT	59.602	63.158	0.00	0.00	0.00	4.20
594	729	1.170290	TCAACTGCACGAGGACGAGA	61.170	55.000	0.00	0.00	42.66	4.04
632	767	4.091939	GACTACCCGGCACCACCC	62.092	72.222	0.00	0.00	33.26	4.61
735	881	3.268965	GAGATAGCGCGCATCCGGA	62.269	63.158	35.10	6.61	34.32	5.14
1074	1258	4.681978	ACGCTCTGCCCCGTCAAC	62.682	66.667	0.00	0.00	31.00	3.18
1265	1463	1.076777	CCATCAAATGGGCGAGGGT	60.077	57.895	0.00	0.00	46.86	4.34
1602	1843	6.157211	GTGCGCCACTACTATGAATATTAGT	58.843	40.000	4.18	0.00	31.40	2.24
1660	1935	5.074791	GGTTACAAAATACGTTACAGCACG	58.925	41.667	0.00	0.00	46.04	5.34
1696	1971	9.665264	CATCACACAATAGAATTCATCATCTTG	57.335	33.333	8.44	4.56	0.00	3.02
1747	2022	6.447162	AGTTCAAACATTAGCCAAGTTTAGC	58.553	36.000	0.00	0.00	34.03	3.09
1791	2074	5.912892	TCATCATATTAGCCGAGTTTGTCA	58.087	37.500	0.00	0.00	0.00	3.58
1882	2165	1.358877	TCATCGCGATGAAACTGGTG	58.641	50.000	41.21	20.16	44.14	4.17
1887	2170	1.398451	CGCGATGAAACTGGTGTTCAC	60.398	52.381	0.00	0.00	34.96	3.18
1918	2201	0.923729	TCTGCTCCCTCCTCTCTCCT	60.924	60.000	0.00	0.00	0.00	3.69
2021	2304	2.680352	TCCGACACTCCTCCCAGC	60.680	66.667	0.00	0.00	0.00	4.85
2183	2466	7.086376	AGAAAAGCAACACATTAATAGCACAG	58.914	34.615	0.00	0.00	0.00	3.66
2352	2635	3.083997	AGGGACCGGAGCATGGAC	61.084	66.667	9.46	0.00	0.00	4.02
2358	2641	2.185350	CGGAGCATGGACGAAGCT	59.815	61.111	0.00	0.00	42.17	3.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	3.303135	AAGTCCACTGCCGCTCGA	61.303	61.111	0.00	0.00	0.00	4.04
7	8	3.114616	CAAGTCCACTGCCGCTCG	61.115	66.667	0.00	0.00	0.00	5.03
8	9	1.739562	CTCAAGTCCACTGCCGCTC	60.740	63.158	0.00	0.00	0.00	5.03
9	10	2.164865	CTCTCAAGTCCACTGCCGCT	62.165	60.000	0.00	0.00	0.00	5.52
10	11	1.739562	CTCTCAAGTCCACTGCCGC	60.740	63.158	0.00	0.00	0.00	6.53
11	12	1.739562	GCTCTCAAGTCCACTGCCG	60.740	63.158	0.00	0.00	0.00	5.69
12	13	0.035630	ATGCTCTCAAGTCCACTGCC	60.036	55.000	0.00	0.00	0.00	4.85
13	14	1.066286	AGATGCTCTCAAGTCCACTGC	60.066	52.381	0.00	0.00	0.00	4.40
14	15	2.418471	GGAGATGCTCTCAAGTCCACTG	60.418	54.545	13.06	0.00	45.12	3.66
15	16	1.830477	GGAGATGCTCTCAAGTCCACT	59.170	52.381	13.06	0.00	45.12	4.00
16	17	1.552337	TGGAGATGCTCTCAAGTCCAC	59.448	52.381	13.06	0.00	45.12	4.02
17	18	1.829849	CTGGAGATGCTCTCAAGTCCA	59.170	52.381	13.06	6.05	45.12	4.02
18	19	1.473080	GCTGGAGATGCTCTCAAGTCC	60.473	57.143	15.03	4.09	44.62	3.85
19	20	1.473080	GGCTGGAGATGCTCTCAAGTC	60.473	57.143	15.03	11.06	44.62	3.01
20	21	0.540923	GGCTGGAGATGCTCTCAAGT	59.459	55.000	15.03	0.00	44.62	3.16
21	22	0.540454	TGGCTGGAGATGCTCTCAAG	59.460	55.000	11.28	11.28	45.39	3.02
22	23	0.251354	GTGGCTGGAGATGCTCTCAA	59.749	55.000	13.06	3.61	45.12	3.02
23	24	1.903294	GTGGCTGGAGATGCTCTCA	59.097	57.895	13.06	0.00	45.12	3.27
24	25	1.227205	CGTGGCTGGAGATGCTCTC	60.227	63.158	5.01	5.01	42.66	3.20
43	44	0.038166	GTCTTGGGGCATGTTGGAGA	59.962	55.000	0.00	0.00	0.00	3.71
45	46	1.076549	GGTCTTGGGGCATGTTGGA	59.923	57.895	0.00	0.00	0.00	3.53
111	117	7.375106	TCGGCTATAACCAACGAAAATTAAA	57.625	32.000	0.00	0.00	0.00	1.52
177	183	3.879180	AAATGCTTCCCCGGGCGTT	62.879	57.895	17.73	8.68	39.04	4.84
178	184	3.879180	AAAATGCTTCCCCGGGCGT	62.879	57.895	17.73	1.17	0.00	5.68
183	210	0.670239	GTGCCAAAAATGCTTCCCCG	60.670	55.000	0.00	0.00	0.00	5.73
264	300	1.406539	CGGCATTGATTTCCAAGGGAG	59.593	52.381	0.00	0.00	38.31	4.30
269	305	1.153862	GCGCGGCATTGATTTCCAA	60.154	52.632	8.83	0.00	39.41	3.53
273	310	4.191950	CCGGCGCGGCATTGATTT	62.192	61.111	32.60	0.00	41.17	2.17
439	529	0.459585	GTTTCTGCGGCGATGGAGTA	60.460	55.000	12.98	0.00	0.00	2.59
464	567	3.068691	CGCTCGGTTGAGAGGGGA	61.069	66.667	3.54	0.00	45.57	4.81
507	642	4.776322	CATTGCTCACCGGCGGGA	62.776	66.667	31.78	22.21	36.97	5.14
578	713	2.955402	GTCTCGTCCTCGTGCAGT	59.045	61.111	0.00	0.00	38.33	4.40
614	749	4.091939	GGTGGTGCCGGGTAGTCC	62.092	72.222	2.18	0.00	0.00	3.85
844	1021	3.636231	CCCCTCGGAGTTGTGCCA	61.636	66.667	4.02	0.00	0.00	4.92
1074	1258	1.153289	CATCTCCTGTTGCTCCGGG	60.153	63.158	0.00	0.00	0.00	5.73
1082	1266	2.185350	CGAGCGGCATCTCCTGTT	59.815	61.111	1.45	0.00	0.00	3.16
1203	1400	0.674581	CCGCATGCTCCTTCTTCACA	60.675	55.000	17.13	0.00	0.00	3.58
1279	1477	2.124819	CTGGCGCTCCATCTGCTT	60.125	61.111	7.64	0.00	42.51	3.91
1364	1562	6.072008	TGTTACTAGTGGCGTGTTAATAGTGA	60.072	38.462	5.39	0.00	31.17	3.41
1693	1968	6.538742	TCGCTATTTAGAATTTGGAGACCAAG	59.461	38.462	3.49	0.00	44.84	3.61
1696	1971	6.315393	TGTTCGCTATTTAGAATTTGGAGACC	59.685	38.462	0.00	0.00	0.00	3.85
1747	2022	5.164233	TGAACTTTGCTAATGTCTCGAGAG	58.836	41.667	17.22	4.67	0.00	3.20
1882	2165	1.192803	AGAGGAGGAACCGGGTGAAC	61.193	60.000	6.32	0.00	44.74	3.18
1887	2170	2.685380	AGCAGAGGAGGAACCGGG	60.685	66.667	6.32	0.00	44.74	5.73
2021	2304	1.746615	TTCCCGGAGTCTACGACGG	60.747	63.158	5.89	0.00	45.57	4.79
2230	2513	5.607939	TGTCTCTTTAGTTTGGACAGTCA	57.392	39.130	2.17	0.00	33.74	3.41
2352	2635	2.772189	CGAAAGACGGCAGCTTCG	59.228	61.111	5.88	5.88	38.46	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.