AutoCloner

Multiple sequence alignment - TraesCS7A01G024200

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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	TraesCS7A01G024200	chr7A	100.000	2669	0	0	1	2669	9624950	9622282	0.000000e+00	4929
1	TraesCS7A01G024200	chr7A	98.764	2669	32	1	1	2669	9609357	9606690	0.000000e+00	4745
2	TraesCS7A01G024200	chr7A	98.277	2670	41	3	1	2669	9525532	9522867	0.000000e+00	4671
3	TraesCS7A01G024200	chr7A	94.331	2011	105	7	663	2669	9633259	9631254	0.000000e+00	3073
4	TraesCS7A01G024200	chr7A	97.866	1687	30	3	983	2669	9545638	9543958	0.000000e+00	2911
5	TraesCS7A01G024200	chr7A	98.448	1482	18	1	1188	2669	9578619	9577143	0.000000e+00	2604
6	TraesCS7A01G024200	chr7A	99.127	1146	9	1	1	1145	9580687	9579542	0.000000e+00	2060
7	TraesCS7A01G024200	chr7A	99.354	1084	6	1	1	1083	9572119	9571036	0.000000e+00	1962
8	TraesCS7A01G024200	chr7A	99.257	1077	7	1	1	1076	9533107	9532031	0.000000e+00	1943
9	TraesCS7A01G024200	chr7A	99.009	1009	9	1	1168	2176	9587288	9586281	0.000000e+00	1807
10	TraesCS7A01G024200	chr7A	98.069	1036	17	1	1634	2669	9539159	9538127	0.000000e+00	1799
11	TraesCS7A01G024200	chr7A	99.196	995	7	1	1	994	9555754	9554760	0.000000e+00	1792
12	TraesCS7A01G024200	chr7A	99.267	818	5	1	1	817	9617256	9616439	0.000000e+00	1476
13	TraesCS7A01G024200	chr7A	98.974	390	4	0	2280	2669	9586102	9585713	0.000000e+00	699
14	TraesCS7A01G024200	chr7A	98.404	376	6	0	2294	2669	9569727	9569352	0.000000e+00	662
15	TraesCS7A01G024200	chr7A	98.547	344	5	0	2326	2669	9614726	9614383	2.270000e-170	608
16	TraesCS7A01G024200	chr7A	90.680	397	29	7	2044	2438	568685061	568684671	3.040000e-144	521
17	TraesCS7A01G024200	chr7A	96.000	200	8	0	1104	1303	9570956	9570757	2.560000e-85	326
18	TraesCS7A01G024200	chr7D	93.062	1427	75	8	1244	2669	8688290	8686887	0.000000e+00	2065
19	TraesCS7A01G024200	chr7D	92.712	1427	80	8	1244	2669	8650908	8649505	0.000000e+00	2037
20	TraesCS7A01G024200	chr7D	95.621	982	42	1	1214	2195	8699534	8698554	0.000000e+00	1574
21	TraesCS7A01G024200	chr7D	94.177	790	44	2	196	983	8707133	8706344	0.000000e+00	1203
22	TraesCS7A01G024200	chr7D	85.235	149	20	2	1059	1206	8711925	8711778	4.600000e-33	152
23	TraesCS7A01G024200	chrUn	99.196	995	7	1	1	994	365254311	365255305	0.000000e+00	1792
24	TraesCS7A01G024200	chrUn	100.000	300	0	0	1	300	350456125	350456424	3.000000e-154	555

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	TraesCS7A01G024200	chr7A	9622282	9624950	2668	True	4929.000000	4929	100.000000	1	2669	1	chr7A.!!$R7	2668
1	TraesCS7A01G024200	chr7A	9606690	9609357	2667	True	4745.000000	4745	98.764000	1	2669	1	chr7A.!!$R6	2668
2	TraesCS7A01G024200	chr7A	9522867	9525532	2665	True	4671.000000	4671	98.277000	1	2669	1	chr7A.!!$R1	2668
3	TraesCS7A01G024200	chr7A	9631254	9633259	2005	True	3073.000000	3073	94.331000	663	2669	1	chr7A.!!$R8	2006
4	TraesCS7A01G024200	chr7A	9543958	9545638	1680	True	2911.000000	2911	97.866000	983	2669	1	chr7A.!!$R4	1686
5	TraesCS7A01G024200	chr7A	9577143	9580687	3544	True	2332.000000	2604	98.787500	1	2669	2	chr7A.!!$R11	2668
6	TraesCS7A01G024200	chr7A	9532031	9533107	1076	True	1943.000000	1943	99.257000	1	1076	1	chr7A.!!$R2	1075
7	TraesCS7A01G024200	chr7A	9538127	9539159	1032	True	1799.000000	1799	98.069000	1634	2669	1	chr7A.!!$R3	1035
8	TraesCS7A01G024200	chr7A	9554760	9555754	994	True	1792.000000	1792	99.196000	1	994	1	chr7A.!!$R5	993
9	TraesCS7A01G024200	chr7A	9585713	9587288	1575	True	1253.000000	1807	98.991500	1168	2669	2	chr7A.!!$R12	1501
10	TraesCS7A01G024200	chr7A	9614383	9617256	2873	True	1042.000000	1476	98.907000	1	2669	2	chr7A.!!$R13	2668
11	TraesCS7A01G024200	chr7A	9569352	9572119	2767	True	983.333333	1962	97.919333	1	2669	3	chr7A.!!$R10	2668
12	TraesCS7A01G024200	chr7D	8686887	8688290	1403	True	2065.000000	2065	93.062000	1244	2669	1	chr7D.!!$R2	1425
13	TraesCS7A01G024200	chr7D	8649505	8650908	1403	True	2037.000000	2037	92.712000	1244	2669	1	chr7D.!!$R1	1425
14	TraesCS7A01G024200	chr7D	8698554	8699534	980	True	1574.000000	1574	95.621000	1214	2195	1	chr7D.!!$R3	981
15	TraesCS7A01G024200	chr7D	8706344	8707133	789	True	1203.000000	1203	94.177000	196	983	1	chr7D.!!$R4	787
16	TraesCS7A01G024200	chrUn	365254311	365255305	994	False	1792.000000	1792	99.196000	1	994	1	chrUn.!!$F2	993

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
964	966	0.042131	ACCGACCCCTGTATCTCCAA	59.958	55.0	0.0	0.0	0.0	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2322	3707	0.688487	CACCCTTTAGTCCCGGTTCA	59.312	55.0	0.0	0.0	0.0	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
360	361	1.915614	GCTCCACGCTTGGTCATGTG	61.916	60.000	9.36	0.00	44.35	3.21
652	654	0.694444	ATCGTCCATACCCTGCCCTT	60.694	55.000	0.00	0.00	0.00	3.95
777	779	4.418328	GCACCCACGCCCATACCA	62.418	66.667	0.00	0.00	0.00	3.25
958	960	3.467226	CGGCACCGACCCCTGTAT	61.467	66.667	2.01	0.00	42.83	2.29
959	961	2.504519	GGCACCGACCCCTGTATC	59.495	66.667	0.00	0.00	0.00	2.24
960	962	2.064581	GGCACCGACCCCTGTATCT	61.065	63.158	0.00	0.00	0.00	1.98
961	963	1.442148	GCACCGACCCCTGTATCTC	59.558	63.158	0.00	0.00	0.00	2.75
962	964	2.029307	GCACCGACCCCTGTATCTCC	62.029	65.000	0.00	0.00	0.00	3.71
963	965	0.686441	CACCGACCCCTGTATCTCCA	60.686	60.000	0.00	0.00	0.00	3.86
964	966	0.042131	ACCGACCCCTGTATCTCCAA	59.958	55.000	0.00	0.00	0.00	3.53
965	967	0.464452	CCGACCCCTGTATCTCCAAC	59.536	60.000	0.00	0.00	0.00	3.77
966	968	0.102481	CGACCCCTGTATCTCCAACG	59.898	60.000	0.00	0.00	0.00	4.10
967	969	0.179081	GACCCCTGTATCTCCAACGC	60.179	60.000	0.00	0.00	0.00	4.84
968	970	1.146263	CCCCTGTATCTCCAACGCC	59.854	63.158	0.00	0.00	0.00	5.68
969	971	1.622607	CCCCTGTATCTCCAACGCCA	61.623	60.000	0.00	0.00	0.00	5.69
970	972	0.251916	CCCTGTATCTCCAACGCCAA	59.748	55.000	0.00	0.00	0.00	4.52
971	973	1.339631	CCCTGTATCTCCAACGCCAAA	60.340	52.381	0.00	0.00	0.00	3.28
972	974	1.737793	CCTGTATCTCCAACGCCAAAC	59.262	52.381	0.00	0.00	0.00	2.93
973	975	1.737793	CTGTATCTCCAACGCCAAACC	59.262	52.381	0.00	0.00	0.00	3.27
974	976	1.092348	GTATCTCCAACGCCAAACCC	58.908	55.000	0.00	0.00	0.00	4.11
975	977	0.391927	TATCTCCAACGCCAAACCCG	60.392	55.000	0.00	0.00	0.00	5.28
976	978	3.361977	CTCCAACGCCAAACCCGG	61.362	66.667	0.00	0.00	0.00	5.73
977	979	4.192453	TCCAACGCCAAACCCGGT	62.192	61.111	0.00	0.00	0.00	5.28
978	980	3.972276	CCAACGCCAAACCCGGTG	61.972	66.667	0.00	0.00	42.68	4.94
979	981	3.972276	CAACGCCAAACCCGGTGG	61.972	66.667	5.21	5.21	39.58	4.61
985	987	4.924187	CAAACCCGGTGGCCCCAA	62.924	66.667	0.00	0.00	33.59	4.12
986	988	4.614036	AAACCCGGTGGCCCCAAG	62.614	66.667	0.00	0.00	33.59	3.61
1206	1208	1.303074	GACCCCCGTTTCTCCAACC	60.303	63.158	0.00	0.00	30.65	3.77
2106	3384	6.292114	CGACATCGTATGCAAAAGTTATAGCA	60.292	38.462	0.00	0.00	36.63	3.49
2322	3707	4.656112	CCCTTTAGTCCCAGTATGAGACAT	59.344	45.833	0.00	0.00	39.69	3.06
2357	3760	1.369625	GGTGTGATGCCCTTTAGTCG	58.630	55.000	0.00	0.00	0.00	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
360	361	4.825085	TGAAATGGTGTACTTTCTTGGTCC	59.175	41.667	6.81	0.00	33.50	4.46
652	654	2.862541	CATGGGAGTTTGTGAAGGTGA	58.137	47.619	0.00	0.00	0.00	4.02
777	779	2.093973	CGATGTTGGAGTTACAGAGGCT	60.094	50.000	0.00	0.00	0.00	4.58
941	943	3.441011	GATACAGGGGTCGGTGCCG	62.441	68.421	3.94	3.94	41.35	5.69
942	944	2.029307	GAGATACAGGGGTCGGTGCC	62.029	65.000	0.00	0.00	0.00	5.01
943	945	1.442148	GAGATACAGGGGTCGGTGC	59.558	63.158	0.00	0.00	0.00	5.01
944	946	0.686441	TGGAGATACAGGGGTCGGTG	60.686	60.000	0.00	0.00	0.00	4.94
945	947	0.042131	TTGGAGATACAGGGGTCGGT	59.958	55.000	0.00	0.00	0.00	4.69
946	948	0.464452	GTTGGAGATACAGGGGTCGG	59.536	60.000	0.00	0.00	0.00	4.79
947	949	0.102481	CGTTGGAGATACAGGGGTCG	59.898	60.000	0.00	0.00	0.00	4.79
948	950	0.179081	GCGTTGGAGATACAGGGGTC	60.179	60.000	0.00	0.00	0.00	4.46
949	951	1.623542	GGCGTTGGAGATACAGGGGT	61.624	60.000	0.00	0.00	0.00	4.95
950	952	1.146263	GGCGTTGGAGATACAGGGG	59.854	63.158	0.00	0.00	0.00	4.79
951	953	0.251916	TTGGCGTTGGAGATACAGGG	59.748	55.000	0.00	0.00	0.00	4.45
952	954	1.737793	GTTTGGCGTTGGAGATACAGG	59.262	52.381	0.00	0.00	0.00	4.00
953	955	1.737793	GGTTTGGCGTTGGAGATACAG	59.262	52.381	0.00	0.00	0.00	2.74
954	956	1.612199	GGGTTTGGCGTTGGAGATACA	60.612	52.381	0.00	0.00	0.00	2.29
955	957	1.092348	GGGTTTGGCGTTGGAGATAC	58.908	55.000	0.00	0.00	0.00	2.24
956	958	0.391927	CGGGTTTGGCGTTGGAGATA	60.392	55.000	0.00	0.00	0.00	1.98
957	959	1.674322	CGGGTTTGGCGTTGGAGAT	60.674	57.895	0.00	0.00	0.00	2.75
958	960	2.281208	CGGGTTTGGCGTTGGAGA	60.281	61.111	0.00	0.00	0.00	3.71
959	961	3.361977	CCGGGTTTGGCGTTGGAG	61.362	66.667	0.00	0.00	0.00	3.86
960	962	4.192453	ACCGGGTTTGGCGTTGGA	62.192	61.111	6.32	0.00	0.00	3.53
961	963	3.972276	CACCGGGTTTGGCGTTGG	61.972	66.667	6.32	0.00	0.00	3.77
962	964	3.972276	CCACCGGGTTTGGCGTTG	61.972	66.667	6.32	0.00	0.00	4.10
968	970	4.924187	TTGGGGCCACCGGGTTTG	62.924	66.667	0.20	0.00	44.64	2.93
969	971	4.614036	CTTGGGGCCACCGGGTTT	62.614	66.667	0.20	0.00	44.64	3.27
974	976	2.325393	GATAGGTCTTGGGGCCACCG	62.325	65.000	0.20	0.00	44.64	4.94
975	977	1.532238	GATAGGTCTTGGGGCCACC	59.468	63.158	0.20	0.56	40.81	4.61
976	978	1.532238	GGATAGGTCTTGGGGCCAC	59.468	63.158	4.39	0.00	0.00	5.01
977	979	1.696314	GGGATAGGTCTTGGGGCCA	60.696	63.158	4.39	0.00	0.00	5.36
978	980	1.386057	AGGGATAGGTCTTGGGGCC	60.386	63.158	0.00	0.00	0.00	5.80
979	981	0.988678	ACAGGGATAGGTCTTGGGGC	60.989	60.000	0.00	0.00	0.00	5.80
980	982	0.839946	CACAGGGATAGGTCTTGGGG	59.160	60.000	0.00	0.00	0.00	4.96
981	983	1.879575	TCACAGGGATAGGTCTTGGG	58.120	55.000	0.00	0.00	0.00	4.12
982	984	2.486191	GCATCACAGGGATAGGTCTTGG	60.486	54.545	0.00	0.00	33.95	3.61
983	985	2.486191	GGCATCACAGGGATAGGTCTTG	60.486	54.545	0.00	0.00	33.95	3.02
984	986	1.771255	GGCATCACAGGGATAGGTCTT	59.229	52.381	0.00	0.00	33.95	3.01
985	987	1.428869	GGCATCACAGGGATAGGTCT	58.571	55.000	0.00	0.00	33.95	3.85
986	988	0.034059	CGGCATCACAGGGATAGGTC	59.966	60.000	0.00	0.00	33.95	3.85
987	989	2.044806	GCGGCATCACAGGGATAGGT	62.045	60.000	0.00	0.00	33.95	3.08
988	990	1.302033	GCGGCATCACAGGGATAGG	60.302	63.158	0.00	0.00	33.95	2.57
1028	1030	1.048724	TGGCGTTGGAGAGATAGGGG	61.049	60.000	0.00	0.00	0.00	4.79
1145	1147	2.203408	TTGGTGTTGGCGGCATCA	60.203	55.556	17.80	17.80	0.00	3.07
1391	1948	2.572095	CTTGCCGGTCGATGTAGCCA	62.572	60.000	1.90	0.00	0.00	4.75
2287	3640	1.622312	ACTAAAGGGGTTCGTGTCTCC	59.378	52.381	0.00	0.00	0.00	3.71
2322	3707	0.688487	CACCCTTTAGTCCCGGTTCA	59.312	55.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.