AutoCloner

Multiple sequence alignment - TraesCS7A01G289100

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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	TraesCS7A01G289100	chr7A	100.000	1735	0	0	1	1735	352129608	352127874	0.000000e+00	3205.0
1	TraesCS7A01G289100	chr7A	100.000	402	0	0	2030	2431	352127579	352127178	0.000000e+00	743.0
2	TraesCS7A01G289100	chr5D	94.891	1742	80	7	1	1735	503243820	503245559	0.000000e+00	2715.0
3	TraesCS7A01G289100	chr5D	94.828	1740	83	7	1	1735	503266755	503265018	0.000000e+00	2708.0
4	TraesCS7A01G289100	chr5D	94.365	1739	91	7	1	1735	432433807	432435542	0.000000e+00	2662.0
5	TraesCS7A01G289100	chr3D	94.937	1738	80	8	1	1733	589264975	589263241	0.000000e+00	2715.0
6	TraesCS7A01G289100	chr3D	95.025	402	20	0	2030	2431	589263150	589262749	1.230000e-177	632.0
7	TraesCS7A01G289100	chr7B	94.834	1742	81	7	1	1735	663100877	663099138	0.000000e+00	2710.0
8	TraesCS7A01G289100	chr7B	95.025	402	20	0	2030	2431	663099049	663098648	1.230000e-177	632.0
9	TraesCS7A01G289100	chr7B	95.000	400	20	0	2030	2429	662726780	662727179	1.590000e-176	628.0
10	TraesCS7A01G289100	chr6D	94.834	1742	81	7	1	1735	389247274	389245535	0.000000e+00	2710.0
11	TraesCS7A01G289100	chr6D	94.776	402	21	0	2030	2431	389245446	389245045	5.710000e-176	627.0
12	TraesCS7A01G289100	chr1D	94.716	1741	84	7	1	1735	254383473	254381735	0.000000e+00	2699.0
13	TraesCS7A01G289100	chr1D	94.776	402	21	0	2030	2431	254381625	254381224	5.710000e-176	627.0
14	TraesCS7A01G289100	chr3A	94.658	1741	85	7	1	1735	66006584	66004846	0.000000e+00	2693.0
15	TraesCS7A01G289100	chr2A	94.661	1742	84	7	1	1735	726907907	726906168	0.000000e+00	2693.0
16	TraesCS7A01G289100	chr2D	95.025	402	20	0	2030	2431	591984985	591985386	1.230000e-177	632.0
17	TraesCS7A01G289100	chr2D	100.000	30	0	0	1706	1735	159590855	159590826	3.380000e-04	56.5
18	TraesCS7A01G289100	chr1B	95.025	402	20	0	2030	2431	638729014	638729415	1.230000e-177	632.0
19	TraesCS7A01G289100	chr7D	94.776	402	21	0	2030	2431	231554050	231553649	5.710000e-176	627.0
20	TraesCS7A01G289100	chr5B	94.776	402	21	0	2030	2431	127808809	127809210	5.710000e-176	627.0

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	TraesCS7A01G289100	chr7A	352127178	352129608	2430	True	1974.0	3205	100.0000	1	2431	2	chr7A.!!$R1	2430
1	TraesCS7A01G289100	chr5D	503243820	503245559	1739	False	2715.0	2715	94.8910	1	1735	1	chr5D.!!$F2	1734
2	TraesCS7A01G289100	chr5D	503265018	503266755	1737	True	2708.0	2708	94.8280	1	1735	1	chr5D.!!$R1	1734
3	TraesCS7A01G289100	chr5D	432433807	432435542	1735	False	2662.0	2662	94.3650	1	1735	1	chr5D.!!$F1	1734
4	TraesCS7A01G289100	chr3D	589262749	589264975	2226	True	1673.5	2715	94.9810	1	2431	2	chr3D.!!$R1	2430
5	TraesCS7A01G289100	chr7B	663098648	663100877	2229	True	1671.0	2710	94.9295	1	2431	2	chr7B.!!$R1	2430
6	TraesCS7A01G289100	chr6D	389245045	389247274	2229	True	1668.5	2710	94.8050	1	2431	2	chr6D.!!$R1	2430
7	TraesCS7A01G289100	chr1D	254381224	254383473	2249	True	1663.0	2699	94.7460	1	2431	2	chr1D.!!$R1	2430
8	TraesCS7A01G289100	chr3A	66004846	66006584	1738	True	2693.0	2693	94.6580	1	1735	1	chr3A.!!$R1	1734
9	TraesCS7A01G289100	chr2A	726906168	726907907	1739	True	2693.0	2693	94.6610	1	1735	1	chr2A.!!$R1	1734

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
273	274	0.034896	ACAAAGGGTTGCGATCTCGT	59.965	50.0	1.14	0.0	42.22	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2205	2214	0.25316	AACTGCCCATCCTACCTCCA	60.253	55.0	0.0	0.0	0.0	3.86	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
46	47	2.843545	GGGTTGCCCTCAGGAACA	59.156	61.111	0.00	0.00	41.34	3.18
58	59	0.677288	CAGGAACACGGACACAGGTA	59.323	55.000	0.00	0.00	0.00	3.08
76	77	0.389817	TAGTGCATGGCTGTCGTCAC	60.390	55.000	0.00	0.00	0.00	3.67
85	86	3.207547	CTGTCGTCACCTCGTGCCA	62.208	63.158	0.00	0.00	32.98	4.92
93	94	1.078426	ACCTCGTGCCATAAGGTGC	60.078	57.895	0.60	0.00	41.83	5.01
111	112	1.003118	TGCTGGGTTAAGTCTCGCAAT	59.997	47.619	0.00	0.00	0.00	3.56
130	131	2.954753	GAGCGCAACCCTCGTGTTG	61.955	63.158	11.47	9.72	46.59	3.33
203	204	1.433121	GAAGGAGAGGATGAGGCCAT	58.567	55.000	5.01	0.00	35.29	4.40
228	229	1.632018	CGTTCCCCTTATGCCCTGGA	61.632	60.000	0.00	0.00	0.00	3.86
263	264	2.380571	AATGGGCGGGACAAAGGGTT	62.381	55.000	0.00	0.00	0.00	4.11
273	274	0.034896	ACAAAGGGTTGCGATCTCGT	59.965	50.000	1.14	0.00	42.22	4.18
297	298	3.138468	AGGGTGAGCTAACTCCAAAAACT	59.862	43.478	0.00	0.00	42.74	2.66
306	307	3.553828	ACTCCAAAAACTCGTCCTCAA	57.446	42.857	0.00	0.00	0.00	3.02
323	324	0.101759	CAATTCGGATTGCAGGCTGG	59.898	55.000	17.64	0.00	36.54	4.85
329	330	0.322816	GGATTGCAGGCTGGAACTCA	60.323	55.000	24.08	5.58	28.29	3.41
369	370	1.209128	CTAGTAATTGCCGGTCAGCG	58.791	55.000	1.90	0.00	34.65	5.18
373	374	2.037251	AGTAATTGCCGGTCAGCGATAT	59.963	45.455	1.90	0.00	35.75	1.63
426	427	1.389609	CCGCCCGTCACACTATAGGT	61.390	60.000	4.43	0.00	0.00	3.08
446	447	2.076100	TGCTAGCCATGTTTGAAGTCG	58.924	47.619	13.29	0.00	0.00	4.18
505	506	1.871080	CTTGCGACTGGAGTGAAGTT	58.129	50.000	0.00	0.00	0.00	2.66
520	521	4.131596	GTGAAGTTGTAACAAGGTAGCCA	58.868	43.478	0.00	0.00	0.00	4.75
534	535	1.486726	GTAGCCATACTGGAAGGTGCT	59.513	52.381	0.00	0.00	40.96	4.40
816	818	5.860648	AGGAAAGGGATGGAGTTTTTCTA	57.139	39.130	0.00	0.00	0.00	2.10
826	828	3.957497	TGGAGTTTTTCTAGCTTTTGGCA	59.043	39.130	0.00	0.00	44.79	4.92
841	843	2.597340	GCATAGCAGGCCTCCCAA	59.403	61.111	0.00	0.00	0.00	4.12
842	844	1.076777	GCATAGCAGGCCTCCCAAA	60.077	57.895	0.00	0.00	0.00	3.28
844	846	0.257039	CATAGCAGGCCTCCCAAAGT	59.743	55.000	0.00	0.00	0.00	2.66
903	905	0.813610	CGCCCCTGATAATTGCGTCA	60.814	55.000	0.00	0.00	40.33	4.35
912	914	3.443329	TGATAATTGCGTCATTGTGCCTT	59.557	39.130	0.00	0.06	0.00	4.35
917	919	1.305219	GCGTCATTGTGCCTTGGCTA	61.305	55.000	13.18	0.00	0.00	3.93
1055	1057	5.656416	TGAAACCAAACAAACTTCTCCTCAT	59.344	36.000	0.00	0.00	0.00	2.90
1073	1075	1.066573	CATGAGGATAGATGGGGCGAC	60.067	57.143	0.00	0.00	0.00	5.19
1126	1128	3.075005	CACTCGTGGGATCCGGGT	61.075	66.667	5.45	0.00	40.23	5.28
1146	1152	4.731853	TCCGAGGGGCCACCATGA	62.732	66.667	0.00	0.00	43.89	3.07
1197	1203	5.717178	TCCCTTATCAGTGTATGGATAGCTC	59.283	44.000	0.00	0.00	0.00	4.09
1240	1246	2.091541	TCGTCCTCAATGGGAAAATGC	58.908	47.619	0.00	0.00	37.10	3.56
1262	1268	1.130561	GCACCTAACAACGCATCTTCC	59.869	52.381	0.00	0.00	0.00	3.46
1287	1293	3.162666	ACCAAGAACTACGAGATCACCA	58.837	45.455	0.00	0.00	0.00	4.17
1305	1311	2.176798	ACCACTTTCATTCTGGGGTGAA	59.823	45.455	0.00	0.00	32.86	3.18
1451	1458	1.729586	TGGGAGTAGAGCAGGTTTGT	58.270	50.000	0.00	0.00	0.00	2.83
1482	1489	0.117340	AGAGTGTCTAGGGTTGGGCT	59.883	55.000	0.00	0.00	0.00	5.19
1498	1505	2.250273	TGGGCTAGGAGGGTCTCTTAAT	59.750	50.000	0.00	0.00	0.00	1.40
1508	1515	3.201045	AGGGTCTCTTAATGCCTTCCTTC	59.799	47.826	0.00	0.00	0.00	3.46
1521	1528	1.208052	CTTCCTTCTTCTGCCCATCGA	59.792	52.381	0.00	0.00	0.00	3.59
1530	1537	5.984725	TCTTCTGCCCATCGAAGTTATTTA	58.015	37.500	0.00	0.00	38.20	1.40
1537	1544	4.578928	CCCATCGAAGTTATTTACCAAGGG	59.421	45.833	0.00	0.00	0.00	3.95
1593	1601	2.738846	CACTTGAAGAGCGCAGTACAAT	59.261	45.455	11.47	0.00	0.00	2.71
1611	1619	0.625316	ATGGGGAGTTGTATGCTGCA	59.375	50.000	4.13	4.13	0.00	4.41
1695	1704	3.576078	TGGGGCGATGATTTACTTCAT	57.424	42.857	0.00	0.00	39.04	2.57
1704	1713	1.604278	GATTTACTTCATGGGCGAGGC	59.396	52.381	0.00	0.00	0.00	4.70
1719	1728	0.980423	GAGGCCTCTGGTTCAAGTCT	59.020	55.000	26.25	0.00	0.00	3.24
2057	2066	2.223479	GCAATTGGGTCGTTGCGATTAT	60.223	45.455	7.72	0.00	40.95	1.28
2058	2067	3.002862	GCAATTGGGTCGTTGCGATTATA	59.997	43.478	7.72	0.00	40.95	0.98
2082	2091	1.985159	TGGCTGTCTAATTGTCCAGGT	59.015	47.619	0.00	0.00	0.00	4.00
2103	2112	8.307483	CCAGGTGGTAATGATAGTATCTTGTAG	58.693	40.741	11.40	0.00	0.00	2.74
2121	2130	2.425592	CTGAACCGGTGGCTCACA	59.574	61.111	8.52	1.22	35.86	3.58
2146	2155	7.525158	TTTTCTAAGTAATGGGGAAGAGGAT	57.475	36.000	0.00	0.00	0.00	3.24
2159	2168	3.703052	GGAAGAGGATTGAAACATGCCAT	59.297	43.478	0.00	0.00	0.00	4.40
2205	2214	3.074538	AGATGGGCTGTCAAAAAGGTAGT	59.925	43.478	0.00	0.00	0.00	2.73
2233	2242	1.490490	GGATGGGCAGTTGGTCAGATA	59.510	52.381	0.00	0.00	0.00	1.98
2238	2247	3.780294	TGGGCAGTTGGTCAGATATAGTT	59.220	43.478	0.00	0.00	0.00	2.24
2255	2264	3.973206	AGTTTGGATCGTACATGGACA	57.027	42.857	9.21	0.00	0.00	4.02
2267	2276	5.046878	TCGTACATGGACAATAGTTGGAGTT	60.047	40.000	9.21	0.00	34.12	3.01
2270	2279	4.042809	ACATGGACAATAGTTGGAGTTGGA	59.957	41.667	0.00	0.00	34.12	3.53
2295	2304	2.248686	TCTCCTAGGCTTCCCTCATCTT	59.751	50.000	2.96	0.00	41.75	2.40
2360	2369	5.104193	ACTTGATGCACTATCTCCCTTCAAT	60.104	40.000	0.00	0.00	36.71	2.57
2361	2370	4.711399	TGATGCACTATCTCCCTTCAATG	58.289	43.478	0.00	0.00	36.71	2.82
2424	2433	2.237965	CCCCATTGTCTCCACCCCA	61.238	63.158	0.00	0.00	0.00	4.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.881074	CTCTTTCAAGAGGATTCGCGA	58.119	47.619	3.71	3.71	46.88	5.87
32	33	2.144078	TCCGTGTTCCTGAGGGCAA	61.144	57.895	0.00	0.00	0.00	4.52
40	41	0.966920	CTACCTGTGTCCGTGTTCCT	59.033	55.000	0.00	0.00	0.00	3.36
58	59	1.669115	GTGACGACAGCCATGCACT	60.669	57.895	0.00	0.00	0.00	4.40
76	77	1.091771	CAGCACCTTATGGCACGAGG	61.092	60.000	14.57	14.57	36.63	4.63
85	86	3.118738	CGAGACTTAACCCAGCACCTTAT	60.119	47.826	0.00	0.00	0.00	1.73
93	94	2.932614	CTCATTGCGAGACTTAACCCAG	59.067	50.000	0.00	0.00	45.45	4.45
111	112	3.454587	AACACGAGGGTTGCGCTCA	62.455	57.895	9.73	0.00	42.44	4.26
130	131	2.027192	TCCAAACTCATAGTGGCACCTC	60.027	50.000	15.27	0.00	32.10	3.85
133	134	2.488153	GGTTCCAAACTCATAGTGGCAC	59.512	50.000	10.29	10.29	32.10	5.01
203	204	1.134220	GGCATAAGGGGAACGATGACA	60.134	52.381	0.00	0.00	0.00	3.58
210	211	0.106669	GTCCAGGGCATAAGGGGAAC	60.107	60.000	0.00	0.00	0.00	3.62
263	264	1.657751	CTCACCCTCACGAGATCGCA	61.658	60.000	1.39	0.00	44.43	5.10
273	274	2.024176	TTGGAGTTAGCTCACCCTCA	57.976	50.000	8.96	0.00	43.37	3.86
297	298	1.066502	TGCAATCCGAATTGAGGACGA	60.067	47.619	0.00	0.00	44.25	4.20
306	307	0.034186	TTCCAGCCTGCAATCCGAAT	60.034	50.000	0.00	0.00	0.00	3.34
358	359	2.421314	CCATATCGCTGACCGGCA	59.579	61.111	0.00	0.00	37.59	5.69
426	427	2.076100	CGACTTCAAACATGGCTAGCA	58.924	47.619	18.24	2.97	0.00	3.49
520	521	0.254178	CCAGCAGCACCTTCCAGTAT	59.746	55.000	0.00	0.00	0.00	2.12
575	576	6.728632	AGTGTCAAACCAAAATACCCCAATAT	59.271	34.615	0.00	0.00	0.00	1.28
580	581	4.587262	AGAAGTGTCAAACCAAAATACCCC	59.413	41.667	0.00	0.00	0.00	4.95
662	664	5.617252	CTTGGTCTTACTTCACCCTAAACA	58.383	41.667	0.00	0.00	0.00	2.83
816	818	2.196319	GCCTGCTATGCCAAAAGCT	58.804	52.632	4.34	0.00	44.23	3.74
826	828	0.257039	CACTTTGGGAGGCCTGCTAT	59.743	55.000	24.77	0.00	0.00	2.97
903	905	1.410648	CCCTCATAGCCAAGGCACAAT	60.411	52.381	14.40	0.88	44.88	2.71
1055	1057	0.188587	AGTCGCCCCATCTATCCTCA	59.811	55.000	0.00	0.00	0.00	3.86
1073	1075	3.570540	TCTACATGGGATCTCACCTGAG	58.429	50.000	0.00	0.00	43.36	3.35
1100	1102	4.501571	CGGATCCCACGAGTGAATAGAAAT	60.502	45.833	6.06	0.00	0.00	2.17
1133	1135	3.017581	GGAGTCATGGTGGCCCCT	61.018	66.667	0.00	0.00	0.00	4.79
1240	1246	1.442769	AGATGCGTTGTTAGGTGCTG	58.557	50.000	0.00	0.00	0.00	4.41
1262	1268	3.444034	TGATCTCGTAGTTCTTGGTCTGG	59.556	47.826	0.00	0.00	0.00	3.86
1287	1293	2.716424	TCCTTCACCCCAGAATGAAAGT	59.284	45.455	0.00	0.00	39.69	2.66
1305	1311	3.169099	CTCGAATGGTATGATCCCTCCT	58.831	50.000	0.00	0.00	0.00	3.69
1346	1353	0.532573	CTGCTTTCTCCAGACCGCTA	59.467	55.000	0.00	0.00	32.03	4.26
1347	1354	1.294780	CTGCTTTCTCCAGACCGCT	59.705	57.895	0.00	0.00	32.03	5.52
1419	1426	7.182060	TGCTCTACTCCCATTTAAGGAAAAAT	58.818	34.615	0.00	0.00	31.49	1.82
1438	1445	6.374417	AGATCCTTTTACAAACCTGCTCTA	57.626	37.500	0.00	0.00	0.00	2.43
1451	1458	7.420029	ACCCTAGACACTCTAAGATCCTTTTA	58.580	38.462	0.00	0.00	0.00	1.52
1482	1489	3.708236	AGGCATTAAGAGACCCTCCTA	57.292	47.619	0.00	0.00	0.00	2.94
1498	1505	1.380302	GGGCAGAAGAAGGAAGGCA	59.620	57.895	0.00	0.00	0.00	4.75
1508	1515	5.007724	GGTAAATAACTTCGATGGGCAGAAG	59.992	44.000	3.12	3.93	46.66	2.85
1521	1528	3.513912	GGCAAGCCCTTGGTAAATAACTT	59.486	43.478	9.81	0.00	40.74	2.66
1537	1544	0.255890	TCCCTCTTACCATGGCAAGC	59.744	55.000	18.63	0.00	0.00	4.01
1593	1601	0.625316	ATGCAGCATACAACTCCCCA	59.375	50.000	5.94	0.00	0.00	4.96
1611	1619	1.417890	AGCGATTCATCCTTCCCGAAT	59.582	47.619	0.00	0.00	32.15	3.34
1674	1682	3.576078	TGAAGTAAATCATCGCCCCAT	57.424	42.857	0.00	0.00	0.00	4.00
1704	1713	3.133721	CCATCCTAGACTTGAACCAGAGG	59.866	52.174	0.00	0.00	0.00	3.69
2057	2066	3.585289	TGGACAATTAGACAGCCAACCTA	59.415	43.478	0.00	0.00	0.00	3.08
2058	2067	2.375174	TGGACAATTAGACAGCCAACCT	59.625	45.455	0.00	0.00	0.00	3.50
2082	2091	8.706322	TCAGCTACAAGATACTATCATTACCA	57.294	34.615	0.00	0.00	0.00	3.25
2103	2112	3.050275	GTGAGCCACCGGTTCAGC	61.050	66.667	2.97	8.91	43.22	4.26
2121	2130	7.525158	TCCTCTTCCCCATTACTTAGAAAAT	57.475	36.000	0.00	0.00	0.00	1.82
2146	2155	5.302568	AGAGTCTTTCAATGGCATGTTTCAA	59.697	36.000	0.00	0.00	0.00	2.69
2205	2214	0.253160	AACTGCCCATCCTACCTCCA	60.253	55.000	0.00	0.00	0.00	3.86
2233	2242	5.607939	TGTCCATGTACGATCCAAACTAT	57.392	39.130	0.00	0.00	0.00	2.12
2238	2247	5.607939	ACTATTGTCCATGTACGATCCAA	57.392	39.130	0.00	0.00	0.00	3.53
2255	2264	3.185455	AGAGCCTCCAACTCCAACTATT	58.815	45.455	0.00	0.00	34.56	1.73
2295	2304	3.597071	CCTATTCCCCAGGGATCCA	57.403	57.895	15.23	0.00	44.74	3.41
2360	2369	2.150390	TGCTACATTTCGCTCAAAGCA	58.850	42.857	0.00	0.00	42.58	3.91
2361	2370	2.900122	TGCTACATTTCGCTCAAAGC	57.100	45.000	0.00	0.00	38.02	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.