AutoCloner

Multiple sequence alignment - TraesCS5B01G421400

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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	TraesCS5B01G421400	chr5B	100.000	2141	0	0	1	2141	596941828	596939688	0.000000e+00	3954.0
1	TraesCS5B01G421400	chr5D	92.333	2152	132	15	1	2141	485830173	485828044	0.000000e+00	3029.0
2	TraesCS5B01G421400	chr5D	91.282	2168	151	14	1	2141	485619171	485617015	0.000000e+00	2922.0
3	TraesCS5B01G421400	chr5D	92.170	1737	100	9	432	2141	485386468	485384741	0.000000e+00	2422.0
4	TraesCS5B01G421400	chr5D	84.615	1300	156	25	1	1282	485750118	485748845	0.000000e+00	1253.0
5	TraesCS5B01G421400	chr5D	85.223	1164	133	24	42	1189	440716128	440717268	0.000000e+00	1160.0
6	TraesCS5B01G421400	chr5D	86.683	826	105	3	1315	2140	485748760	485747940	0.000000e+00	911.0
7	TraesCS5B01G421400	chr5D	86.562	826	99	4	1318	2135	440717413	440718234	0.000000e+00	900.0
8	TraesCS5B01G421400	chr5D	93.750	64	4	0	4	67	485386533	485386470	1.750000e-16	97.1
9	TraesCS5B01G421400	chr5A	89.430	2176	154	30	4	2141	606635390	606633253	0.000000e+00	2675.0
10	TraesCS5B01G421400	chr5A	89.123	2179	161	28	1	2141	606552011	606549871	0.000000e+00	2641.0
11	TraesCS5B01G421400	chr3D	79.876	646	117	9	1315	1956	564655728	564656364	5.380000e-126	460.0
12	TraesCS5B01G421400	chr3D	82.077	491	65	11	655	1142	486548555	486549025	4.280000e-107	398.0
13	TraesCS5B01G421400	chr6D	79.795	584	102	12	1402	1980	21063876	21063304	5.500000e-111	411.0
14	TraesCS5B01G421400	chr7A	83.105	219	31	3	917	1130	40436027	40435810	6.030000e-46	195.0
15	TraesCS5B01G421400	chr3A	83.962	212	19	11	933	1142	696886093	696886291	2.800000e-44	189.0
16	TraesCS5B01G421400	chr3A	83.962	212	19	11	933	1142	696897167	696897365	2.800000e-44	189.0
17	TraesCS5B01G421400	chr7B	93.478	46	3	0	38	83	639058399	639058444	3.810000e-08	69.4

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	TraesCS5B01G421400	chr5B	596939688	596941828	2140	True	3954.00	3954	100.0000	1	2141	1	chr5B.!!$R1	2140
1	TraesCS5B01G421400	chr5D	485828044	485830173	2129	True	3029.00	3029	92.3330	1	2141	1	chr5D.!!$R2	2140
2	TraesCS5B01G421400	chr5D	485617015	485619171	2156	True	2922.00	2922	91.2820	1	2141	1	chr5D.!!$R1	2140
3	TraesCS5B01G421400	chr5D	485384741	485386533	1792	True	1259.55	2422	92.9600	4	2141	2	chr5D.!!$R3	2137
4	TraesCS5B01G421400	chr5D	485747940	485750118	2178	True	1082.00	1253	85.6490	1	2140	2	chr5D.!!$R4	2139
5	TraesCS5B01G421400	chr5D	440716128	440718234	2106	False	1030.00	1160	85.8925	42	2135	2	chr5D.!!$F1	2093
6	TraesCS5B01G421400	chr5A	606633253	606635390	2137	True	2675.00	2675	89.4300	4	2141	1	chr5A.!!$R2	2137
7	TraesCS5B01G421400	chr5A	606549871	606552011	2140	True	2641.00	2641	89.1230	1	2141	1	chr5A.!!$R1	2140
8	TraesCS5B01G421400	chr3D	564655728	564656364	636	False	460.00	460	79.8760	1315	1956	1	chr3D.!!$F2	641
9	TraesCS5B01G421400	chr6D	21063304	21063876	572	True	411.00	411	79.7950	1402	1980	1	chr6D.!!$R1	578

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
304	312	0.10741	GGGGACATGCGACATGGTTA	60.107	55.0	19.3	0.0	0.0	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2000	2123	0.179034	GTGGTGGATGATGCCTCTCC	60.179	60.0	0.0	0.0	0.0	3.71	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
119	124	2.746277	GGCGCACCAAAGACGGAT	60.746	61.111	10.83	0.00	35.26	4.18
128	133	0.721718	CAAAGACGGATTGGTCGCTC	59.278	55.000	0.00	0.00	41.81	5.03
129	134	0.736325	AAAGACGGATTGGTCGCTCG	60.736	55.000	0.00	0.00	41.81	5.03
130	135	1.592400	AAGACGGATTGGTCGCTCGA	61.592	55.000	0.00	0.00	41.81	4.04
131	136	1.872679	GACGGATTGGTCGCTCGAC	60.873	63.158	13.45	13.45	43.87	4.20
132	137	2.180769	CGGATTGGTCGCTCGACA	59.819	61.111	21.71	4.99	46.20	4.35
133	138	1.445410	CGGATTGGTCGCTCGACAA	60.445	57.895	21.71	9.95	46.20	3.18
159	164	4.261801	CAACCAATCCACTAGTCGGAAAT	58.738	43.478	15.22	7.36	35.77	2.17
174	179	1.474330	GAAATGGAAATGTCGGCCCT	58.526	50.000	0.00	0.00	0.00	5.19
192	197	0.758685	CTTGGTTGGGAGGGCAACAA	60.759	55.000	0.00	0.00	39.74	2.83
259	267	3.319972	AGCAGCTGATGAACATGTGTTTT	59.680	39.130	20.43	0.00	38.56	2.43
304	312	0.107410	GGGGACATGCGACATGGTTA	60.107	55.000	19.30	0.00	0.00	2.85
321	329	3.073209	TGGTTAACCAGACCATGCTAACA	59.927	43.478	23.69	0.00	42.06	2.41
429	438	3.327757	ACTTTGTTGTGAGGGATGAGCTA	59.672	43.478	0.00	0.00	0.00	3.32
563	572	2.740826	GCTCGTTTGGCGGTGCTA	60.741	61.111	0.00	0.00	41.72	3.49
577	586	3.943381	GCGGTGCTAATTAAGGTTAAGGT	59.057	43.478	0.00	0.00	0.00	3.50
592	601	1.718280	AAGGTTCCCTTCAGTCGTCT	58.282	50.000	0.00	0.00	40.17	4.18
625	634	2.283388	CATGCAGGTGGCTTGGGT	60.283	61.111	0.00	0.00	45.15	4.51
626	635	1.001020	CATGCAGGTGGCTTGGGTA	60.001	57.895	0.00	0.00	45.15	3.69
640	655	3.119955	GCTTGGGTAAAGGACGTCAAATC	60.120	47.826	18.91	0.00	36.30	2.17
762	782	9.769677	ATGCTATGGTAATTGAGGAGTATACTA	57.230	33.333	5.09	0.00	0.00	1.82
807	827	0.394352	ATGTGTTTGGGCTCGGATCC	60.394	55.000	0.00	0.00	0.00	3.36
915	953	5.072741	AGCTAAATGGCGTTGAATATGGAT	58.927	37.500	0.00	0.00	37.29	3.41
928	966	8.233868	CGTTGAATATGGATGTTTGTTTGAGTA	58.766	33.333	0.00	0.00	0.00	2.59
994	1042	5.724854	AGGGAATGTTGAGCTAGGTAAACTA	59.275	40.000	20.36	9.45	0.00	2.24
1049	1097	2.756755	GCATTTTTGCGCAAATTACGG	58.243	42.857	33.94	21.79	0.00	4.02
1066	1114	2.006888	ACGGTAAGATTGGCGATGTTG	58.993	47.619	7.35	0.00	0.00	3.33
1071	1119	2.048444	AGATTGGCGATGTTGCAGAT	57.952	45.000	0.00	0.00	36.28	2.90
1081	1129	2.583024	TGTTGCAGATCAATGTGGGA	57.417	45.000	0.00	0.00	36.99	4.37
1133	1181	7.335673	TCAGTTTAGCGATTTTATGATGGTTCA	59.664	33.333	0.00	0.00	36.00	3.18
1160	1208	6.373774	ACCTAGAAATGAGTTCATTGCTCAAG	59.626	38.462	16.73	10.78	46.64	3.02
1241	1298	1.710809	AGGGTAAGTTGGGCATGACTT	59.289	47.619	0.00	0.16	39.32	3.01
1252	1310	0.729116	GCATGACTTGACCCGATGTG	59.271	55.000	0.00	0.00	0.00	3.21
1273	1332	9.922305	GATGTGTAAGGAGAAAGATTATTTTCG	57.078	33.333	0.00	0.00	40.99	3.46
1279	1338	6.301687	GGAGAAAGATTATTTTCGCCCTAC	57.698	41.667	9.28	0.00	45.60	3.18
1280	1339	5.050295	GGAGAAAGATTATTTTCGCCCTACG	60.050	44.000	9.28	0.00	45.60	3.51
1292	1358	1.378531	GCCCTACGATGTCAATGCAA	58.621	50.000	0.00	0.00	0.00	4.08
1293	1359	1.742831	GCCCTACGATGTCAATGCAAA	59.257	47.619	0.00	0.00	0.00	3.68
1295	1361	2.223021	CCCTACGATGTCAATGCAAACG	60.223	50.000	0.00	0.00	0.00	3.60
1301	1367	2.592796	TGTCAATGCAAACGATGTCG	57.407	45.000	0.11	0.11	46.33	4.35
1378	1489	0.321653	CAGGGGGAAGGAAAGTGTCG	60.322	60.000	0.00	0.00	0.00	4.35
1394	1505	7.550196	GGAAAGTGTCGGGTCTTATAAAATACA	59.450	37.037	0.00	0.00	0.00	2.29
1431	1542	0.319900	GCGAGCAACTCAACTCAGGA	60.320	55.000	0.00	0.00	32.98	3.86
1459	1578	6.455360	TCTTTGCAAGTTCAAGTGAAGAAT	57.545	33.333	0.00	0.00	34.27	2.40
1460	1579	6.267817	TCTTTGCAAGTTCAAGTGAAGAATG	58.732	36.000	0.00	0.00	34.27	2.67
1480	1599	1.343681	GGGTAGAGGATGGTGGGTGTA	60.344	57.143	0.00	0.00	0.00	2.90
1519	1641	1.207089	CATCGCTTCCTTGTACCTCCA	59.793	52.381	0.00	0.00	0.00	3.86
1554	1676	2.191400	TCCTGCTAATCTGGCTTGTCT	58.809	47.619	0.00	0.00	34.13	3.41
1569	1691	3.317993	GCTTGTCTTCCTTGCCTTGTTTA	59.682	43.478	0.00	0.00	0.00	2.01
1605	1727	2.872245	CGTACTTGATTCCGCATTCCAT	59.128	45.455	0.00	0.00	0.00	3.41
1676	1798	2.114638	GGCACTTTGTGTCCTTGCA	58.885	52.632	0.00	0.00	35.75	4.08
1823	1945	3.797039	TCATAGACAGGAAAAGGATGCG	58.203	45.455	0.00	0.00	0.00	4.73
1977	2100	1.681486	GGGAAGCGAGGAAGAGGGAG	61.681	65.000	0.00	0.00	0.00	4.30
2089	2212	5.598830	ACATGTGAATCTACTACTCGGGATT	59.401	40.000	0.00	0.00	0.00	3.01
2125	2248	2.125350	GGAGTGAGGCGCCAGAAG	60.125	66.667	31.54	0.00	37.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	2.738147	GGTCATCAACGACCGACAG	58.262	57.895	0.00	0.00	45.77	3.51
28	29	0.949105	ACGCTTGGGTCATCAACGAC	60.949	55.000	0.00	0.00	35.03	4.34
84	89	1.227497	CGGGATCTCAAGCCAGCTC	60.227	63.158	0.00	0.00	30.22	4.09
85	90	2.739996	CCGGGATCTCAAGCCAGCT	61.740	63.158	0.00	0.00	30.22	4.24
119	124	2.723116	TCGTTGTCGAGCGACCAA	59.277	55.556	18.98	11.03	43.97	3.67
124	129	1.484227	TTGGTTGTCGTTGTCGAGCG	61.484	55.000	0.00	0.00	46.96	5.03
128	133	1.070175	GTGGATTGGTTGTCGTTGTCG	60.070	52.381	0.00	0.00	38.55	4.35
129	134	2.218603	AGTGGATTGGTTGTCGTTGTC	58.781	47.619	0.00	0.00	0.00	3.18
130	135	2.341846	AGTGGATTGGTTGTCGTTGT	57.658	45.000	0.00	0.00	0.00	3.32
131	136	3.399330	ACTAGTGGATTGGTTGTCGTTG	58.601	45.455	0.00	0.00	0.00	4.10
132	137	3.660865	GACTAGTGGATTGGTTGTCGTT	58.339	45.455	0.00	0.00	0.00	3.85
133	138	2.352421	CGACTAGTGGATTGGTTGTCGT	60.352	50.000	0.00	0.00	40.24	4.34
159	164	1.304052	CCAAGGGCCGACATTTCCA	60.304	57.895	0.00	0.00	0.00	3.53
174	179	0.105246	ATTGTTGCCCTCCCAACCAA	60.105	50.000	2.97	0.00	43.36	3.67
192	197	0.674895	GCTCGCCTCTTTGGTGTCAT	60.675	55.000	0.00	0.00	46.10	3.06
230	235	1.260538	TTCATCAGCTGCTCCTCGGT	61.261	55.000	9.47	0.00	0.00	4.69
259	267	1.229177	TAGTGCCCCTGAGACTGCA	60.229	57.895	0.00	0.00	0.00	4.41
304	312	3.758554	GTCATTGTTAGCATGGTCTGGTT	59.241	43.478	0.00	0.00	36.79	3.67
429	438	1.608590	CGTGTGTTCTTCATGGGCTTT	59.391	47.619	0.00	0.00	0.00	3.51
553	562	2.500392	AACCTTAATTAGCACCGCCA	57.500	45.000	0.00	0.00	0.00	5.69
577	586	1.048601	AGCAAGACGACTGAAGGGAA	58.951	50.000	0.00	0.00	0.00	3.97
592	601	1.604185	GCATGGCGGTGTAAAAAGCAA	60.604	47.619	0.00	0.00	0.00	3.91
625	634	5.046159	AGTGGTATGGATTTGACGTCCTTTA	60.046	40.000	14.12	0.00	36.68	1.85
626	635	4.007659	GTGGTATGGATTTGACGTCCTTT	58.992	43.478	14.12	0.00	36.68	3.11
669	685	4.252570	TCCCCAAAACACTTAAACTCCA	57.747	40.909	0.00	0.00	0.00	3.86
762	782	5.336531	CGGAGTTATAAGGGCGACATATTCT	60.337	44.000	0.00	0.00	0.00	2.40
807	827	1.519455	GCAAGTCCGATCGACCCAG	60.519	63.158	18.66	4.57	43.08	4.45
915	953	6.993786	TCTTGACATGTACTCAAACAAACA	57.006	33.333	0.00	0.00	32.02	2.83
928	966	6.349944	GCTTCTCCAATTTGATCTTGACATGT	60.350	38.462	0.00	0.00	0.00	3.21
994	1042	0.534203	AGCACACGGAACATTTCGGT	60.534	50.000	0.00	0.00	42.97	4.69
997	1045	5.753438	TCTCATATAGCACACGGAACATTTC	59.247	40.000	0.00	0.00	0.00	2.17
1049	1097	2.677836	TCTGCAACATCGCCAATCTTAC	59.322	45.455	0.00	0.00	0.00	2.34
1066	1114	1.684983	CCCATTCCCACATTGATCTGC	59.315	52.381	0.00	0.00	0.00	4.26
1071	1119	1.430853	TGAACCCCATTCCCACATTGA	59.569	47.619	0.00	0.00	36.36	2.57
1081	1129	4.335735	TCTTTGGATCATGAACCCCATT	57.664	40.909	18.52	0.00	31.94	3.16
1133	1181	6.716628	TGAGCAATGAACTCATTTCTAGGTTT	59.283	34.615	4.84	0.00	43.48	3.27
1160	1208	2.932614	CACAAGTAGTGCTACCATGAGC	59.067	50.000	15.23	0.00	42.15	4.26
1241	1298	2.225382	TCTCCTTACACATCGGGTCA	57.775	50.000	0.00	0.00	0.00	4.02
1252	1310	6.542735	AGGGCGAAAATAATCTTTCTCCTTAC	59.457	38.462	5.38	0.00	39.26	2.34
1273	1332	1.378531	TTGCATTGACATCGTAGGGC	58.621	50.000	0.00	0.00	0.00	5.19
1278	1337	2.483877	ACATCGTTTGCATTGACATCGT	59.516	40.909	0.00	0.00	0.00	3.73
1279	1338	3.093574	GACATCGTTTGCATTGACATCG	58.906	45.455	0.00	0.00	0.00	3.84
1280	1339	3.093574	CGACATCGTTTGCATTGACATC	58.906	45.455	0.00	0.00	34.11	3.06
1283	1349	2.873170	TCGACATCGTTTGCATTGAC	57.127	45.000	0.54	0.00	40.80	3.18
1284	1350	2.476018	GCATCGACATCGTTTGCATTGA	60.476	45.455	19.59	0.00	43.46	2.57
1289	1355	1.643810	GTTTGCATCGACATCGTTTGC	59.356	47.619	18.45	18.45	43.88	3.68
1292	1358	0.442310	CCGTTTGCATCGACATCGTT	59.558	50.000	12.28	0.00	40.80	3.85
1293	1359	0.389296	TCCGTTTGCATCGACATCGT	60.389	50.000	12.28	0.00	40.80	3.73
1295	1361	1.061131	CACTCCGTTTGCATCGACATC	59.939	52.381	12.28	0.00	0.00	3.06
1301	1367	1.900237	GCAATCACTCCGTTTGCATC	58.100	50.000	2.25	0.00	45.68	3.91
1378	1489	7.523415	TCCCCTCATTGTATTTTATAAGACCC	58.477	38.462	0.00	0.00	0.00	4.46
1394	1505	0.252239	GCCCCAGTTTTCCCCTCATT	60.252	55.000	0.00	0.00	0.00	2.57
1459	1578	0.620410	CACCCACCATCCTCTACCCA	60.620	60.000	0.00	0.00	0.00	4.51
1460	1579	0.620700	ACACCCACCATCCTCTACCC	60.621	60.000	0.00	0.00	0.00	3.69
1480	1599	4.504858	GATGAAAACACTATCAGGACGGT	58.495	43.478	0.00	0.00	0.00	4.83
1519	1641	4.273148	AGCAGGAAACGAAGAGTGTAAT	57.727	40.909	0.00	0.00	0.00	1.89
1554	1676	1.133730	ACCCGTAAACAAGGCAAGGAA	60.134	47.619	0.00	0.00	0.00	3.36
1569	1691	0.528249	GTACGTGTCACACAACCCGT	60.528	55.000	9.06	1.91	33.80	5.28
1676	1798	0.731417	CGACACCGTCTCCGTCTTAT	59.269	55.000	0.00	0.00	0.00	1.73
1693	1815	3.303135	AAGAGCACGGGCAGTCGA	61.303	61.111	14.57	0.00	44.61	4.20
1823	1945	2.939103	CACTACCTGCTAGTCCAATTGC	59.061	50.000	0.00	0.00	32.90	3.56
1905	2028	4.250305	AACAAGGCGGCTGACGGT	62.250	61.111	14.21	6.12	44.51	4.83
1941	2064	2.348998	CCTATCGCCATCCCCTGC	59.651	66.667	0.00	0.00	0.00	4.85
1977	2100	0.468648	CCCGGAACCCTCTTATGTCC	59.531	60.000	0.73	0.00	0.00	4.02
2000	2123	0.179034	GTGGTGGATGATGCCTCTCC	60.179	60.000	0.00	0.00	0.00	3.71
2089	2212	1.525765	ACAACAGCCACGTCATGCA	60.526	52.632	0.00	0.00	0.00	3.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.