AutoCloner

Multiple sequence alignment - TraesCS4A01G180900

Loading Multiple Alignment...

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	TraesCS4A01G180900	chr4A	100.000	3172	0	0	1	3172	455271258	455274429	0.000000e+00	5858.0
1	TraesCS4A01G180900	chr4A	100.000	124	0	0	3389	3512	455274646	455274769	2.730000e-56	230.0
2	TraesCS4A01G180900	chr4D	93.157	1476	66	13	1247	2706	118374340	118372884	0.000000e+00	2134.0
3	TraesCS4A01G180900	chr4D	95.425	1246	45	7	1	1244	118375672	118374437	0.000000e+00	1975.0
4	TraesCS4A01G180900	chr4D	92.773	595	32	3	1880	2466	114197694	114198285	0.000000e+00	850.0
5	TraesCS4A01G180900	chr4D	88.153	498	35	11	2453	2945	114211610	114212088	3.930000e-159	571.0
6	TraesCS4A01G180900	chr4D	91.498	247	16	3	2701	2945	118339495	118339252	5.620000e-88	335.0
7	TraesCS4A01G180900	chr4D	90.179	224	19	2	2950	3172	118338465	118338244	4.440000e-74	289.0
8	TraesCS4A01G180900	chr4D	94.400	125	6	1	3389	3512	118338207	118338083	1.290000e-44	191.0
9	TraesCS4A01G180900	chr4B	91.623	1158	61	13	1270	2412	180561261	180560125	0.000000e+00	1568.0
10	TraesCS4A01G180900	chr4B	91.529	850	31	19	394	1218	180562095	180561262	0.000000e+00	1133.0
11	TraesCS4A01G180900	chr4B	95.025	402	13	3	2545	2945	180558824	180558429	2.980000e-175	625.0
12	TraesCS4A01G180900	chr4B	90.037	271	12	8	1	271	180562885	180562630	1.560000e-88	337.0
13	TraesCS4A01G180900	chr4B	92.478	226	15	1	2947	3172	180557654	180557431	4.370000e-84	322.0
14	TraesCS4A01G180900	chr4B	99.320	147	1	0	2404	2550	180560000	180559854	2.080000e-67	267.0
15	TraesCS4A01G180900	chr4B	96.800	125	3	1	3389	3512	180557156	180557032	1.280000e-49	207.0
16	TraesCS4A01G180900	chr4B	92.913	127	5	2	259	383	180562306	180562182	7.740000e-42	182.0
17	TraesCS4A01G180900	chr5A	81.250	288	37	9	1103	1373	330199414	330199701	2.120000e-52	217.0
18	TraesCS4A01G180900	chr5A	96.875	32	1	0	1040	1071	330199333	330199364	2.000000e-03	54.7
19	TraesCS4A01G180900	chr5D	80.364	275	39	10	1103	1373	246303362	246303625	9.950000e-46	195.0
20	TraesCS4A01G180900	chr5D	100.000	29	0	0	1043	1071	246303284	246303312	2.000000e-03	54.7
21	TraesCS4A01G180900	chr5B	77.807	374	39	27	1040	1373	280987545	280987914	1.290000e-44	191.0
22	TraesCS4A01G180900	chr5B	82.609	69	8	4	2666	2733	315834697	315834762	1.360000e-04	58.4
23	TraesCS4A01G180900	chr6D	97.778	45	1	0	2817	2861	108191826	108191870	1.050000e-10	78.7
24	TraesCS4A01G180900	chr7D	83.333	66	8	2	2676	2741	386922345	386922407	1.360000e-04	58.4

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	TraesCS4A01G180900	chr4A	455271258	455274769	3511	False	3044.000000	5858	100.000000	1	3512	2	chr4A.!!$F1	3511
1	TraesCS4A01G180900	chr4D	118372884	118375672	2788	True	2054.500000	2134	94.291000	1	2706	2	chr4D.!!$R2	2705
2	TraesCS4A01G180900	chr4D	114197694	114198285	591	False	850.000000	850	92.773000	1880	2466	1	chr4D.!!$F1	586
3	TraesCS4A01G180900	chr4D	118338083	118339495	1412	True	271.666667	335	92.025667	2701	3512	3	chr4D.!!$R1	811
4	TraesCS4A01G180900	chr4B	180557032	180562885	5853	True	580.125000	1568	93.715625	1	3512	8	chr4B.!!$R1	3511

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
374	713	0.539986	TTCTAGGACCCACCGATTGC	59.460	55.000	0.00	0.00	44.74	3.56	F
1310	1847	1.198637	GCAGTTGCAACTCCTAAGCTG	59.801	52.381	28.97	16.72	41.59	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1473	2010	0.911769	ATCTGAAGGCCCATCGTCAA	59.088	50.0	0.0	0.0	0.0	3.18	R
2962	5496	0.396435	TGGCACTCTGGTTGAATCGT	59.604	50.0	0.0	0.0	0.0	3.73	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
44	45	7.535139	CACAACTTTTTCTTGAAACTCAGGTA	58.465	34.615	0.00	0.00	0.00	3.08
102	103	8.213518	AGTGCTAACATATAACATTCAACCAG	57.786	34.615	0.00	0.00	0.00	4.00
195	196	4.679373	ATGATGTCTACCCTGTGATGTC	57.321	45.455	0.00	0.00	0.00	3.06
374	713	0.539986	TTCTAGGACCCACCGATTGC	59.460	55.000	0.00	0.00	44.74	3.56
475	892	6.862711	AGCTGGACTTTTTAGTTAGTGTTC	57.137	37.500	0.00	0.00	0.00	3.18
508	925	6.476378	CCTTAGATCTCTCTTTTCCAAACCA	58.524	40.000	0.00	0.00	32.66	3.67
767	1185	7.469181	GCTTCCTTCCAAAGTCCACATATAATG	60.469	40.741	0.00	0.00	0.00	1.90
768	1186	6.969043	TCCTTCCAAAGTCCACATATAATGT	58.031	36.000	0.00	0.00	46.22	2.71
769	1187	8.096621	TCCTTCCAAAGTCCACATATAATGTA	57.903	34.615	0.00	0.00	42.70	2.29
770	1188	8.210946	TCCTTCCAAAGTCCACATATAATGTAG	58.789	37.037	0.00	0.00	42.70	2.74
771	1189	7.445402	CCTTCCAAAGTCCACATATAATGTAGG	59.555	40.741	0.00	0.00	42.70	3.18
772	1190	7.684317	TCCAAAGTCCACATATAATGTAGGA	57.316	36.000	6.95	6.95	42.70	2.94
801	1219	2.036475	TGAGCTCACTTCTGTTGTCTCC	59.964	50.000	13.74	0.00	0.00	3.71
947	1384	2.624838	ACAACAACAGCCTCAAATCAGG	59.375	45.455	0.00	0.00	36.50	3.86
1125	1562	2.758327	TCGTCAGTGCGCCCCTAT	60.758	61.111	4.18	0.00	0.00	2.57
1226	1669	2.362717	GCCAAGATCGTAAGCCTACTCT	59.637	50.000	0.00	0.00	37.18	3.24
1227	1670	3.551250	GCCAAGATCGTAAGCCTACTCTC	60.551	52.174	0.00	0.00	37.18	3.20
1228	1671	3.632604	CCAAGATCGTAAGCCTACTCTCA	59.367	47.826	0.00	0.00	37.18	3.27
1237	1680	4.640771	AAGCCTACTCTCATTTTCCACA	57.359	40.909	0.00	0.00	0.00	4.17
1244	1687	6.989169	CCTACTCTCATTTTCCACAATCCTAG	59.011	42.308	0.00	0.00	0.00	3.02
1245	1688	5.189180	ACTCTCATTTTCCACAATCCTAGC	58.811	41.667	0.00	0.00	0.00	3.42
1258	1795	6.933521	CCACAATCCTAGCTATATATGCATCC	59.066	42.308	0.19	0.00	0.00	3.51
1261	1798	8.373981	ACAATCCTAGCTATATATGCATCCATC	58.626	37.037	0.19	0.00	32.85	3.51
1284	1821	7.060600	TCGACATGTTAACTTGATGTTCATC	57.939	36.000	23.89	10.77	39.89	2.92
1294	1831	4.581824	ACTTGATGTTCATCTTTGTGCAGT	59.418	37.500	12.94	3.06	0.00	4.40
1310	1847	1.198637	GCAGTTGCAACTCCTAAGCTG	59.801	52.381	28.97	16.72	41.59	4.24
1393	1930	6.757010	CAGGTACGCATCACTTTACTTCTTAT	59.243	38.462	0.00	0.00	0.00	1.73
1426	1963	2.096466	CGTCTTTTGCTGTGCGTTCATA	60.096	45.455	0.00	0.00	0.00	2.15
1452	1989	1.227060	GATTCCCCTTTGCATGCGC	60.227	57.895	14.09	0.00	39.24	6.09
1473	2010	5.176223	GCGCAATGCTAATTCTGCAATTAAT	59.824	36.000	0.30	0.00	44.01	1.40
1517	2054	4.573900	ACAGAAGCAAGAAGATTGACGAT	58.426	39.130	0.00	0.00	0.00	3.73
1541	2078	0.743345	GCCAGGGTATGTCCACGAAC	60.743	60.000	0.00	0.00	38.11	3.95
1544	2081	1.548719	CAGGGTATGTCCACGAACTCA	59.451	52.381	0.00	0.00	38.11	3.41
1561	2098	3.350833	ACTCATGAATTTCACAGCCCTC	58.649	45.455	0.15	0.00	0.00	4.30
1562	2099	2.686915	CTCATGAATTTCACAGCCCTCC	59.313	50.000	0.15	0.00	0.00	4.30
1563	2100	2.309755	TCATGAATTTCACAGCCCTCCT	59.690	45.455	0.15	0.00	0.00	3.69
1594	2145	5.132648	TCAGTATATTTTGCCCTGATCTGGT	59.867	40.000	16.63	0.70	0.00	4.00
1598	2149	0.036388	TTTGCCCTGATCTGGTCGAC	60.036	55.000	16.63	7.13	0.00	4.20
1600	2151	1.323271	TGCCCTGATCTGGTCGACTC	61.323	60.000	16.46	5.51	0.00	3.36
1654	2207	6.684538	ACAGGGAGGACAAGTCTATAACTAT	58.315	40.000	0.00	0.00	37.17	2.12
1749	2302	5.649782	AAATTGCCCTCTACACATTCAAG	57.350	39.130	0.00	0.00	0.00	3.02
1937	2494	2.224161	GCACTAGACCATGTCCTCCATC	60.224	54.545	0.00	0.00	32.18	3.51
1998	2558	4.036971	CACCGTTTACTTGGATCAAAACCA	59.963	41.667	0.00	0.00	35.47	3.67
2133	2693	6.347969	CGAGAAATGATTATCACGCCATGAAT	60.348	38.462	0.00	0.00	41.93	2.57
2179	2739	1.517257	CAAGCTGCTACGACGGAGG	60.517	63.158	9.61	0.00	0.00	4.30
2193	2765	1.135139	ACGGAGGACAACGATGATCAG	59.865	52.381	0.09	0.00	0.00	2.90
2374	2946	6.168389	GCTACTAGACTGTCTCTATCCCTAC	58.832	48.000	14.62	0.00	30.60	3.18
2390	2962	5.109328	TCCCTACTCTCTCCTAGTCCTAT	57.891	47.826	0.00	0.00	0.00	2.57
2518	3223	6.662663	TCTTGATCTCACCATATGATCGATCT	59.337	38.462	25.02	13.51	38.75	2.75
2671	4413	4.651503	CCCTCGGCCTCAGTCATTATATAT	59.348	45.833	0.00	0.00	0.00	0.86
2672	4414	5.129485	CCCTCGGCCTCAGTCATTATATATT	59.871	44.000	0.00	0.00	0.00	1.28
2673	4415	6.276847	CCTCGGCCTCAGTCATTATATATTC	58.723	44.000	0.00	0.00	0.00	1.75
2674	4416	6.222038	TCGGCCTCAGTCATTATATATTCC	57.778	41.667	0.00	0.00	0.00	3.01
2752	4494	5.765182	CACAGTCATTTTTGTTACTCCCTCT	59.235	40.000	0.00	0.00	0.00	3.69
2758	4500	9.232473	GTCATTTTTGTTACTCCCTCTAATTCT	57.768	33.333	0.00	0.00	0.00	2.40
2791	4533	2.837591	TCAGCCTTGTATAGAGGTTGCA	59.162	45.455	11.83	0.00	43.00	4.08
2902	4647	3.013921	GACACACCACCTTCAAACTTGA	58.986	45.455	0.00	0.00	34.92	3.02
2945	4690	0.610232	GTTGCTTGCCCTGACCTCAT	60.610	55.000	0.00	0.00	0.00	2.90
2952	5486	1.040339	GCCCTGACCTCATCGAGTCT	61.040	60.000	4.43	0.00	0.00	3.24
2962	5496	0.749049	CATCGAGTCTGCCATCCTCA	59.251	55.000	0.00	0.00	0.00	3.86
2977	5511	2.248248	TCCTCACGATTCAACCAGAGT	58.752	47.619	0.00	0.00	0.00	3.24
2985	5519	1.691195	TTCAACCAGAGTGCCACCGA	61.691	55.000	0.00	0.00	0.00	4.69
3030	5564	2.202623	CTAGACAGCCACGGTCGC	60.203	66.667	0.00	0.00	40.20	5.19
3093	5628	1.915141	CTTTCTTGATGGCCACCTGT	58.085	50.000	8.16	0.00	0.00	4.00
3094	5629	1.542915	CTTTCTTGATGGCCACCTGTG	59.457	52.381	8.16	0.00	0.00	3.66
3105	5640	1.760527	CACCTGTGTGGGGATGACA	59.239	57.895	0.00	0.00	43.63	3.58
3141	5676	2.070650	GGAGGGGTTGGCGGTAGAT	61.071	63.158	0.00	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	6.412362	TGGTACATTGTGCAATTAAAGGTT	57.588	33.333	7.21	0.00	0.00	3.50
146	147	6.694447	AGGTCAATCGTTTGCTTAGTAGTAA	58.306	36.000	1.18	0.00	32.61	2.24
287	625	1.813513	CAGATCAGTGCCGACCTTTT	58.186	50.000	0.00	0.00	0.00	2.27
288	626	0.674895	GCAGATCAGTGCCGACCTTT	60.675	55.000	0.00	0.00	37.49	3.11
321	660	0.771756	CACAAGCGCACGTTTCATTG	59.228	50.000	11.47	5.06	0.00	2.82
325	664	0.041312	ACATCACAAGCGCACGTTTC	60.041	50.000	11.47	0.00	0.00	2.78
475	892	1.761784	AGAGATCTAAGGCCAGCACTG	59.238	52.381	5.01	0.00	0.00	3.66
508	925	4.816925	GTGTGGCTTTCACTTTCTCTAGTT	59.183	41.667	0.00	0.00	46.20	2.24
624	1041	6.366340	TGTATACCTAAGGAGAGAAGGACAG	58.634	44.000	0.00	0.00	34.34	3.51
690	1108	4.013267	AGTGAGGTGGTGAAAGATTGAG	57.987	45.455	0.00	0.00	0.00	3.02
767	1185	3.320541	AGTGAGCTCATGCATACTCCTAC	59.679	47.826	21.47	1.59	42.74	3.18
768	1186	3.570540	AGTGAGCTCATGCATACTCCTA	58.429	45.455	21.47	0.00	42.74	2.94
769	1187	2.396608	AGTGAGCTCATGCATACTCCT	58.603	47.619	21.47	5.75	42.74	3.69
770	1188	2.906691	AGTGAGCTCATGCATACTCC	57.093	50.000	21.47	3.18	42.74	3.85
771	1189	3.803231	CAGAAGTGAGCTCATGCATACTC	59.197	47.826	21.47	13.83	42.74	2.59
772	1190	3.197333	ACAGAAGTGAGCTCATGCATACT	59.803	43.478	21.47	8.14	42.74	2.12
947	1384	0.249238	ATGATCGAGGCGCTTGAGAC	60.249	55.000	7.64	2.71	0.00	3.36
1113	1550	2.180159	AACGAACATAGGGGCGCACT	62.180	55.000	10.74	9.64	0.00	4.40
1125	1562	1.609580	CGGGGATTCTTGGAACGAACA	60.610	52.381	0.00	0.00	0.00	3.18
1161	1598	1.676384	GAAGCAGTGGTGGAGCTCT	59.324	57.895	14.64	0.00	37.70	4.09
1213	1656	4.567159	GTGGAAAATGAGAGTAGGCTTACG	59.433	45.833	0.00	0.00	34.88	3.18
1228	1671	9.401058	GCATATATAGCTAGGATTGTGGAAAAT	57.599	33.333	0.00	0.00	0.00	1.82
1237	1680	7.452813	TCGATGGATGCATATATAGCTAGGATT	59.547	37.037	0.00	0.00	0.00	3.01
1244	1687	5.987953	ACATGTCGATGGATGCATATATAGC	59.012	40.000	0.00	0.00	33.39	2.97
1245	1688	9.533253	TTAACATGTCGATGGATGCATATATAG	57.467	33.333	0.00	0.00	33.39	1.31
1258	1795	6.830736	TGAACATCAAGTTAACATGTCGATG	58.169	36.000	8.61	13.00	41.51	3.84
1261	1798	7.065216	AGATGAACATCAAGTTAACATGTCG	57.935	36.000	15.63	4.77	41.51	4.35
1294	1831	1.271379	GGACCAGCTTAGGAGTTGCAA	60.271	52.381	0.00	0.00	33.24	4.08
1393	1930	2.786578	GCAAAAGACGACGATGCAAAAA	59.213	40.909	0.00	0.00	37.00	1.94
1426	1963	3.509442	TGCAAAGGGGAATCAGTGAAAT	58.491	40.909	0.00	0.00	0.00	2.17
1452	1989	8.263950	CGTCAATTAATTGCAGAATTAGCATTG	58.736	33.333	21.15	7.34	42.33	2.82
1473	2010	0.911769	ATCTGAAGGCCCATCGTCAA	59.088	50.000	0.00	0.00	0.00	3.18
1517	2054	2.372074	GGACATACCCTGGCCGGAA	61.372	63.158	15.09	0.00	45.37	4.30
1541	2078	2.686915	GGAGGGCTGTGAAATTCATGAG	59.313	50.000	0.00	0.00	0.00	2.90
1544	2081	3.463048	AAGGAGGGCTGTGAAATTCAT	57.537	42.857	0.00	0.00	0.00	2.57
1561	2098	6.324770	AGGGCAAAATATACTGAATCCAAAGG	59.675	38.462	0.00	0.00	0.00	3.11
1562	2099	7.068593	TCAGGGCAAAATATACTGAATCCAAAG	59.931	37.037	0.00	0.00	35.45	2.77
1563	2100	6.894654	TCAGGGCAAAATATACTGAATCCAAA	59.105	34.615	0.00	0.00	35.45	3.28
1594	2145	3.443681	TGATGACTGCACATAAGAGTCGA	59.556	43.478	0.00	0.00	39.23	4.20
1598	2149	5.851720	ACCTATGATGACTGCACATAAGAG	58.148	41.667	0.00	0.00	0.00	2.85
1600	2151	5.464722	GTGACCTATGATGACTGCACATAAG	59.535	44.000	0.00	0.00	0.00	1.73
1654	2207	1.135094	GATGGAAGGGGAGATGAGCA	58.865	55.000	0.00	0.00	0.00	4.26
1937	2494	4.559063	CATGCCAGCTCCCCCTCG	62.559	72.222	0.00	0.00	0.00	4.63
1998	2558	4.936411	GCTGCTGCTGATGATGAATAGTAT	59.064	41.667	10.92	0.00	36.03	2.12
2133	2693	2.098607	CCGTCTTTCATAGTGGTAGCGA	59.901	50.000	0.00	0.00	0.00	4.93
2179	2739	3.744942	CCATGGATCTGATCATCGTTGTC	59.255	47.826	18.64	0.35	0.00	3.18
2193	2765	5.639506	CAGGTTTATATCACGACCATGGATC	59.360	44.000	21.47	11.37	34.60	3.36
2374	2946	7.741785	TCAAGAGTAATAGGACTAGGAGAGAG	58.258	42.308	0.00	0.00	0.00	3.20
2390	2962	4.094476	ACTCCCCTTTCGATCAAGAGTAA	58.906	43.478	0.00	0.00	31.62	2.24
2791	4533	4.141181	TCCCTCCGATCCAAATTCATTGAT	60.141	41.667	0.00	0.00	41.85	2.57
2862	4606	4.081087	GTGTCTTTATTGCCTAGAGGGTGA	60.081	45.833	0.00	0.00	37.43	4.02
2902	4647	5.457197	CCCTGATCAAGACCACCATTATCAT	60.457	44.000	0.00	0.00	0.00	2.45
2945	4690	1.657751	CGTGAGGATGGCAGACTCGA	61.658	60.000	14.14	0.00	34.03	4.04
2952	5486	1.678728	GGTTGAATCGTGAGGATGGCA	60.679	52.381	0.00	0.00	34.93	4.92
2962	5496	0.396435	TGGCACTCTGGTTGAATCGT	59.604	50.000	0.00	0.00	0.00	3.73
2977	5511	3.385384	CTGCTCCTCTCGGTGGCA	61.385	66.667	0.00	0.00	37.61	4.92
2985	5519	2.983930	GCACGACGTCTGCTCCTCT	61.984	63.158	23.86	0.00	0.00	3.69
3093	5628	1.151699	TCCCCTTGTCATCCCCACA	60.152	57.895	0.00	0.00	0.00	4.17
3094	5629	0.914417	TCTCCCCTTGTCATCCCCAC	60.914	60.000	0.00	0.00	0.00	4.61
3105	5640	4.439901	GCCCTCCCCTCTCCCCTT	62.440	72.222	0.00	0.00	0.00	3.95
3137	5672	2.942306	GCGCAAAACCTTACCCCATCTA	60.942	50.000	0.30	0.00	0.00	1.98
3141	5676	1.904378	GGCGCAAAACCTTACCCCA	60.904	57.895	10.83	0.00	0.00	4.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.