AutoCloner

Multiple sequence alignment - TraesCS6B01G187300

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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	TraesCS6B01G187300	chr6B	100.000	2216	0	0	1	2216	213468293	213466078	0.000000e+00	4093.0
1	TraesCS6B01G187300	chr6B	82.601	569	85	5	264	825	567612317	567611756	7.110000e-135	490.0
2	TraesCS6B01G187300	chr6B	86.071	280	35	3	990	1266	567611687	567611409	4.630000e-77	298.0
3	TraesCS6B01G187300	chr6B	79.208	202	35	7	1021	1217	567711706	567711905	1.380000e-27	134.0
4	TraesCS6B01G187300	chr6A	89.940	2008	116	30	1	1958	162309309	162311280	0.000000e+00	2510.0
5	TraesCS6B01G187300	chr6A	82.778	871	108	13	1	852	177697853	177697006	0.000000e+00	739.0
6	TraesCS6B01G187300	chr6A	82.777	569	84	5	264	825	521649560	521648999	1.530000e-136	496.0
7	TraesCS6B01G187300	chr6A	86.429	280	34	2	990	1266	521648930	521648652	9.940000e-79	303.0
8	TraesCS6B01G187300	chr6A	78.151	238	39	10	1021	1250	521881431	521881663	2.970000e-29	139.0
9	TraesCS6B01G187300	chr6A	79.130	230	11	12	1989	2216	162311473	162311667	8.310000e-25	124.0
10	TraesCS6B01G187300	chr6A	84.058	138	13	7	1	129	521649790	521649653	8.310000e-25	124.0
11	TraesCS6B01G187300	chr6D	89.961	1295	86	19	1	1280	136390469	136389204	0.000000e+00	1631.0
12	TraesCS6B01G187300	chr6D	94.325	934	32	11	1	913	121344919	121345852	0.000000e+00	1411.0
13	TraesCS6B01G187300	chr6D	90.138	578	27	9	1639	2205	121346573	121347131	0.000000e+00	725.0
14	TraesCS6B01G187300	chr6D	84.882	721	63	22	971	1668	121345869	121346566	0.000000e+00	686.0
15	TraesCS6B01G187300	chr6D	84.023	532	73	3	264	789	379338458	379338983	3.280000e-138	501.0
16	TraesCS6B01G187300	chr6D	87.500	280	31	3	990	1266	379339096	379339374	9.870000e-84	320.0
17	TraesCS6B01G187300	chr6D	79.310	203	35	6	1021	1218	379333727	379333527	3.840000e-28	135.0
18	TraesCS6B01G187300	chr7A	78.481	237	42	6	1021	1251	173638635	173638868	1.770000e-31	147.0
19	TraesCS6B01G187300	chr7B	78.333	240	37	11	1021	1251	137026833	137027066	8.250000e-30	141.0
20	TraesCS6B01G187300	chr7D	87.500	80	10	0	2	81	170729792	170729871	2.340000e-15	93.5

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	TraesCS6B01G187300	chr6B	213466078	213468293	2215	True	4093.000000	4093	100.000000	1	2216	1	chr6B.!!$R1	2215
1	TraesCS6B01G187300	chr6B	567611409	567612317	908	True	394.000000	490	84.336000	264	1266	2	chr6B.!!$R2	1002
2	TraesCS6B01G187300	chr6A	162309309	162311667	2358	False	1317.000000	2510	84.535000	1	2216	2	chr6A.!!$F2	2215
3	TraesCS6B01G187300	chr6A	177697006	177697853	847	True	739.000000	739	82.778000	1	852	1	chr6A.!!$R1	851
4	TraesCS6B01G187300	chr6A	521648652	521649790	1138	True	307.666667	496	84.421333	1	1266	3	chr6A.!!$R2	1265
5	TraesCS6B01G187300	chr6D	136389204	136390469	1265	True	1631.000000	1631	89.961000	1	1280	1	chr6D.!!$R1	1279
6	TraesCS6B01G187300	chr6D	121344919	121347131	2212	False	940.666667	1411	89.781667	1	2205	3	chr6D.!!$F1	2204
7	TraesCS6B01G187300	chr6D	379338458	379339374	916	False	410.500000	501	85.761500	264	1266	2	chr6D.!!$F2	1002

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
921	990	0.600255	GCTATTCCCGTCATCCCGTG	60.6	60.0	0.0	0.0	0.0	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2076	2409	0.03309	TGAGTCACTGACTGCAGCAG	59.967	55.0	26.43	26.43	43.53	4.24	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
148	158	3.977244	GCACGCACACCCCAAAGG	61.977	66.667	0.00	0.00	43.78	3.11
161	171	0.680618	CCAAAGGCAAACCATCAGCA	59.319	50.000	0.00	0.00	39.06	4.41
162	172	1.337447	CCAAAGGCAAACCATCAGCAG	60.337	52.381	0.00	0.00	39.06	4.24
501	558	2.126071	CTCCGTCGCGTTGTGGAT	60.126	61.111	5.77	0.00	0.00	3.41
913	982	1.222115	GCGGACATGCTATTCCCGTC	61.222	60.000	0.00	0.00	41.95	4.79
915	984	1.270305	CGGACATGCTATTCCCGTCAT	60.270	52.381	0.00	0.00	35.83	3.06
917	986	2.417719	GACATGCTATTCCCGTCATCC	58.582	52.381	0.00	0.00	0.00	3.51
920	989	1.046472	TGCTATTCCCGTCATCCCGT	61.046	55.000	0.00	0.00	0.00	5.28
921	990	0.600255	GCTATTCCCGTCATCCCGTG	60.600	60.000	0.00	0.00	0.00	4.94
922	991	0.600255	CTATTCCCGTCATCCCGTGC	60.600	60.000	0.00	0.00	0.00	5.34
923	992	2.035237	TATTCCCGTCATCCCGTGCC	62.035	60.000	0.00	0.00	0.00	5.01
938	1007	2.747855	GCCCTCGAGTTGCCAAGG	60.748	66.667	12.31	4.43	0.00	3.61
940	1009	2.750350	CCTCGAGTTGCCAAGGGT	59.250	61.111	12.31	0.00	0.00	4.34
1060	1150	2.511600	CGACGAAGGCCATGGACC	60.512	66.667	16.13	15.57	0.00	4.46
1220	1316	1.536766	CGTCAGGTTGGTGTAGTACGA	59.463	52.381	0.00	0.00	0.00	3.43
1221	1317	2.163010	CGTCAGGTTGGTGTAGTACGAT	59.837	50.000	0.00	0.00	0.00	3.73
1257	1359	2.124901	CATTGGCCCCGCGTAAGA	60.125	61.111	4.92	0.00	43.02	2.10
1271	1373	1.449789	CGTAAGATCGCATGCTTCGAG	59.550	52.381	17.13	0.00	39.47	4.04
1275	1383	4.838152	TCGCATGCTTCGAGGGCC	62.838	66.667	17.13	0.00	0.00	5.80
1299	1407	3.878519	GGAGACGCCGACGAGGAG	61.879	72.222	0.00	5.04	45.00	3.69
1304	1412	3.185155	CGCCGACGAGGAGTAGTT	58.815	61.111	0.00	0.00	45.00	2.24
1305	1413	1.226323	CGCCGACGAGGAGTAGTTG	60.226	63.158	0.00	0.00	45.00	3.16
1306	1414	1.642037	CGCCGACGAGGAGTAGTTGA	61.642	60.000	0.00	0.00	45.00	3.18
1307	1415	0.179169	GCCGACGAGGAGTAGTTGAC	60.179	60.000	0.00	0.00	45.00	3.18
1308	1416	0.450983	CCGACGAGGAGTAGTTGACC	59.549	60.000	0.00	0.00	45.00	4.02
1309	1417	1.162698	CGACGAGGAGTAGTTGACCA	58.837	55.000	0.00	0.00	0.00	4.02
1310	1418	1.130749	CGACGAGGAGTAGTTGACCAG	59.869	57.143	0.00	0.00	0.00	4.00
1311	1419	1.473278	GACGAGGAGTAGTTGACCAGG	59.527	57.143	0.00	0.00	0.00	4.45
1316	1424	0.108756	GAGTAGTTGACCAGGGACGC	60.109	60.000	0.00	0.00	0.00	5.19
1317	1425	1.079336	GTAGTTGACCAGGGACGCC	60.079	63.158	0.00	0.00	0.00	5.68
1320	1428	3.235481	TTGACCAGGGACGCCGAA	61.235	61.111	0.00	0.00	0.00	4.30
1367	1475	0.997196	GGCGAAGTTGACGATGGTAC	59.003	55.000	0.00	0.00	0.00	3.34
1449	1569	0.931662	CGCGGCGTATGTACTGGTAC	60.932	60.000	15.36	4.15	36.63	3.34
1450	1570	0.595825	GCGGCGTATGTACTGGTACC	60.596	60.000	9.37	4.43	35.26	3.34
1563	1686	3.971702	GGGCTGCTCTTGTGGGGT	61.972	66.667	0.00	0.00	0.00	4.95
1629	1752	2.435059	GAAGGTGACGGGCAGAGC	60.435	66.667	0.00	0.00	0.00	4.09
1660	1793	6.426633	GTGGAAGAAGAAGAAGAAGAAGAAGG	59.573	42.308	0.00	0.00	0.00	3.46
1705	1865	1.853319	GCGTGTCGTGTTCTTGAGG	59.147	57.895	0.00	0.00	0.00	3.86
1709	1869	2.059541	GTGTCGTGTTCTTGAGGTAGC	58.940	52.381	0.00	0.00	0.00	3.58
1816	1987	3.487544	GCATTTGCCTCGTTCCATAGTTC	60.488	47.826	0.00	0.00	34.31	3.01
1828	1999	5.656480	GTTCCATAGTTCAAGACTCTCTCC	58.344	45.833	0.00	0.00	39.86	3.71
1887	2058	3.569701	TCTTTCTGAATTCTGGTGGTTGC	59.430	43.478	11.89	0.00	0.00	4.17
2009	2342	5.329035	CCAAACTTGGTATTGCTAGCATT	57.671	39.130	20.13	17.66	43.43	3.56
2010	2343	5.723295	CCAAACTTGGTATTGCTAGCATTT	58.277	37.500	20.13	10.45	43.43	2.32
2011	2344	6.165577	CCAAACTTGGTATTGCTAGCATTTT	58.834	36.000	20.13	9.32	43.43	1.82
2012	2345	6.311200	CCAAACTTGGTATTGCTAGCATTTTC	59.689	38.462	20.13	11.25	43.43	2.29
2013	2346	5.235305	ACTTGGTATTGCTAGCATTTTCG	57.765	39.130	20.13	6.81	35.40	3.46
2014	2347	4.700213	ACTTGGTATTGCTAGCATTTTCGT	59.300	37.500	20.13	7.44	35.40	3.85
2076	2409	1.828832	GTCGACGTCACCTGATGATC	58.171	55.000	17.16	0.00	40.28	2.92
2091	2424	0.971386	TGATCTGCTGCAGTCAGTGA	59.029	50.000	27.24	15.79	42.29	3.41
2092	2425	1.337541	TGATCTGCTGCAGTCAGTGAC	60.338	52.381	27.24	15.78	42.29	3.67
2093	2426	0.975135	ATCTGCTGCAGTCAGTGACT	59.025	50.000	27.24	20.34	44.44	3.41
2094	2427	0.316522	TCTGCTGCAGTCAGTGACTC	59.683	55.000	27.24	17.03	41.37	3.36
2095	2428	0.033090	CTGCTGCAGTCAGTGACTCA	59.967	55.000	23.08	20.18	41.37	3.41
2096	2429	0.033090	TGCTGCAGTCAGTGACTCAG	59.967	55.000	29.37	29.37	41.37	3.35
2097	2430	0.033228	GCTGCAGTCAGTGACTCAGT	59.967	55.000	31.27	13.22	41.37	3.41
2098	2431	1.780806	CTGCAGTCAGTGACTCAGTG	58.219	55.000	27.39	18.91	41.37	3.66
2109	2442	1.096416	GACTCAGTGTACCGCTAGCT	58.904	55.000	13.93	0.00	0.00	3.32
2135	2468	2.287368	CGTGGGTTTTCTGCTTGGTTAC	60.287	50.000	0.00	0.00	0.00	2.50
2185	2518	4.880120	TCTGTATCCAACGTTCGATCTACT	59.120	41.667	11.83	0.00	0.00	2.57
2186	2519	6.018425	GTCTGTATCCAACGTTCGATCTACTA	60.018	42.308	11.83	0.00	0.00	1.82
2187	2520	6.018425	TCTGTATCCAACGTTCGATCTACTAC	60.018	42.308	11.83	5.39	0.00	2.73
2205	2538	5.259832	ACTACCACGGATTAGCTTTCTAC	57.740	43.478	0.00	0.00	0.00	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	122	2.049156	CAGGTTGACGCGCTGAGA	60.049	61.111	5.73	0.00	0.00	3.27
140	150	0.609662	CTGATGGTTTGCCTTTGGGG	59.390	55.000	0.00	0.00	35.27	4.96
148	158	1.503542	CGGTCTGCTGATGGTTTGC	59.496	57.895	0.00	0.00	0.00	3.68
161	171	3.735029	GGAGACGTGACGCGGTCT	61.735	66.667	12.47	13.61	46.52	3.85
542	599	2.803479	CCCCTCGGTGTACTACGC	59.197	66.667	5.13	0.00	0.00	4.42
634	691	2.733593	GACGTGCACCTCGACACC	60.734	66.667	12.15	0.00	33.09	4.16
855	921	1.871676	CGATCGTCCACTTCTATCCGA	59.128	52.381	7.03	0.00	0.00	4.55
859	925	0.311165	CGCCGATCGTCCACTTCTAT	59.689	55.000	15.09	0.00	0.00	1.98
913	982	3.019003	AACTCGAGGGCACGGGATG	62.019	63.158	18.41	0.00	37.20	3.51
915	984	3.691342	CAACTCGAGGGCACGGGA	61.691	66.667	18.41	0.00	37.20	5.14
920	989	2.032528	CTTGGCAACTCGAGGGCA	59.967	61.111	25.99	19.97	37.85	5.36
921	990	2.747855	CCTTGGCAACTCGAGGGC	60.748	66.667	18.41	19.04	37.61	5.19
922	991	2.045926	CCCTTGGCAACTCGAGGG	60.046	66.667	18.41	6.81	42.65	4.30
923	992	0.323629	TTACCCTTGGCAACTCGAGG	59.676	55.000	18.41	0.17	37.61	4.63
962	1031	1.308069	ACGGCACATCTCATGTTGCC	61.308	55.000	14.90	14.90	45.55	4.52
1005	1095	0.753262	ACCACGTCAAGTCTCTGCTT	59.247	50.000	0.00	0.00	0.00	3.91
1242	1344	2.188469	GATCTTACGCGGGGCCAA	59.812	61.111	12.47	0.00	0.00	4.52
1296	1404	0.531200	CGTCCCTGGTCAACTACTCC	59.469	60.000	0.00	0.00	0.00	3.85
1298	1406	1.542187	GGCGTCCCTGGTCAACTACT	61.542	60.000	0.00	0.00	0.00	2.57
1299	1407	1.079336	GGCGTCCCTGGTCAACTAC	60.079	63.158	0.00	0.00	0.00	2.73
1300	1408	2.642254	CGGCGTCCCTGGTCAACTA	61.642	63.158	0.00	0.00	0.00	2.24
1301	1409	4.003788	CGGCGTCCCTGGTCAACT	62.004	66.667	0.00	0.00	0.00	3.16
1302	1410	3.524648	TTCGGCGTCCCTGGTCAAC	62.525	63.158	6.85	0.00	0.00	3.18
1303	1411	3.234630	CTTCGGCGTCCCTGGTCAA	62.235	63.158	6.85	0.00	0.00	3.18
1304	1412	3.691342	CTTCGGCGTCCCTGGTCA	61.691	66.667	6.85	0.00	0.00	4.02
1305	1413	3.379445	TCTTCGGCGTCCCTGGTC	61.379	66.667	6.85	0.00	0.00	4.02
1306	1414	3.692406	GTCTTCGGCGTCCCTGGT	61.692	66.667	6.85	0.00	0.00	4.00
1307	1415	4.796231	CGTCTTCGGCGTCCCTGG	62.796	72.222	6.85	0.00	0.00	4.45
1308	1416	3.685214	CTCGTCTTCGGCGTCCCTG	62.685	68.421	6.85	0.00	37.69	4.45
1309	1417	3.441290	CTCGTCTTCGGCGTCCCT	61.441	66.667	6.85	0.00	37.69	4.20
1310	1418	4.493747	CCTCGTCTTCGGCGTCCC	62.494	72.222	6.85	0.00	37.69	4.46
1311	1419	3.398353	CTCCTCGTCTTCGGCGTCC	62.398	68.421	6.85	0.00	37.69	4.79
1316	1424	0.171455	CAACTCCTCCTCGTCTTCGG	59.829	60.000	0.00	0.00	37.69	4.30
1317	1425	0.171455	CCAACTCCTCCTCGTCTTCG	59.829	60.000	0.00	0.00	38.55	3.79
1320	1428	1.985116	GGCCAACTCCTCCTCGTCT	60.985	63.158	0.00	0.00	0.00	4.18
1349	1457	1.654105	CAGTACCATCGTCAACTTCGC	59.346	52.381	0.00	0.00	0.00	4.70
1353	1461	1.402456	GCGACAGTACCATCGTCAACT	60.402	52.381	15.47	0.00	40.49	3.16
1355	1463	0.108992	GGCGACAGTACCATCGTCAA	60.109	55.000	14.23	0.00	42.43	3.18
1414	1531	1.524482	GCGCCTCCTCTTCATCCTT	59.476	57.895	0.00	0.00	0.00	3.36
1450	1570	1.136611	CGACTTCAACTTCGCCGAAAG	60.137	52.381	0.00	0.00	0.00	2.62
1563	1686	2.119484	AACGCCCCTCGACCATGAAA	62.119	55.000	0.00	0.00	41.67	2.69
1588	1711	4.257510	TCCTGATCTCGAGCGCGC	62.258	66.667	26.66	26.66	37.46	6.86
1593	1716	2.649190	TCCTCAACTCCTGATCTCGAG	58.351	52.381	5.93	5.93	32.14	4.04
1629	1752	2.099141	TCTTCTTCTTCCACATGCGG	57.901	50.000	0.00	0.00	0.00	5.69
1705	1865	3.075866	ACGAGTAATTACGCCAGCTAC	57.924	47.619	12.94	0.00	0.00	3.58
1709	1869	4.030134	AGAGAACGAGTAATTACGCCAG	57.970	45.455	12.94	7.27	0.00	4.85
1816	1987	1.466697	GCTTCGTCGGAGAGAGTCTTG	60.467	57.143	4.21	0.00	36.95	3.02
1828	1999	0.807667	CCCAGGAGAATGCTTCGTCG	60.808	60.000	0.00	0.00	29.87	5.12
1887	2058	1.421485	GTGCTTCGTCAGAATGCCG	59.579	57.895	0.00	0.00	35.56	5.69
2009	2342	5.905181	GCTTACGATCTGTTTTGAAACGAAA	59.095	36.000	0.00	0.00	41.74	3.46
2010	2343	5.006844	TGCTTACGATCTGTTTTGAAACGAA	59.993	36.000	0.00	0.00	41.74	3.85
2011	2344	4.508492	TGCTTACGATCTGTTTTGAAACGA	59.492	37.500	0.00	3.66	41.74	3.85
2012	2345	4.768145	TGCTTACGATCTGTTTTGAAACG	58.232	39.130	0.00	0.00	41.74	3.60
2013	2346	5.049680	TCCTGCTTACGATCTGTTTTGAAAC	60.050	40.000	0.00	0.00	39.33	2.78
2014	2347	5.049680	GTCCTGCTTACGATCTGTTTTGAAA	60.050	40.000	0.00	0.00	0.00	2.69
2056	2389	0.098905	ATCATCAGGTGACGTCGACG	59.901	55.000	34.58	34.58	40.28	5.12
2057	2390	1.402259	AGATCATCAGGTGACGTCGAC	59.598	52.381	11.62	5.18	40.28	4.20
2067	2400	1.134491	TGACTGCAGCAGATCATCAGG	60.134	52.381	29.70	0.00	35.18	3.86
2076	2409	0.033090	TGAGTCACTGACTGCAGCAG	59.967	55.000	26.43	26.43	43.53	4.24
2091	2424	1.546961	AAGCTAGCGGTACACTGAGT	58.453	50.000	9.55	0.00	0.00	3.41
2092	2425	2.656560	AAAGCTAGCGGTACACTGAG	57.343	50.000	9.55	0.00	0.00	3.35
2093	2426	2.353406	GGAAAAGCTAGCGGTACACTGA	60.353	50.000	9.55	0.00	0.00	3.41
2094	2427	2.000447	GGAAAAGCTAGCGGTACACTG	59.000	52.381	9.55	0.00	0.00	3.66
2095	2428	1.403780	CGGAAAAGCTAGCGGTACACT	60.404	52.381	9.55	0.00	0.00	3.55
2096	2429	0.997196	CGGAAAAGCTAGCGGTACAC	59.003	55.000	9.55	0.34	0.00	2.90
2097	2430	0.604578	ACGGAAAAGCTAGCGGTACA	59.395	50.000	9.55	0.00	0.00	2.90
2098	2431	0.997196	CACGGAAAAGCTAGCGGTAC	59.003	55.000	9.55	2.88	0.00	3.34
2109	2442	1.770294	AGCAGAAAACCCACGGAAAA	58.230	45.000	0.00	0.00	0.00	2.29
2135	2468	1.270625	TGCTGTTTCCAGTCCTAACCG	60.271	52.381	0.00	0.00	41.02	4.44
2185	2518	4.463539	TGTGTAGAAAGCTAATCCGTGGTA	59.536	41.667	0.00	0.00	0.00	3.25
2186	2519	3.259876	TGTGTAGAAAGCTAATCCGTGGT	59.740	43.478	0.00	0.00	0.00	4.16
2187	2520	3.857052	TGTGTAGAAAGCTAATCCGTGG	58.143	45.455	0.00	0.00	0.00	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.