AutoCloner

Multiple sequence alignment - TraesCS7A01G149600

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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	TraesCS7A01G149600	chr7A	100.000	2348	0	0	1	2348	102547759	102545412	0.000000e+00	4337.0
1	TraesCS7A01G149600	chr7A	88.575	849	77	8	5	841	70191428	70192268	0.000000e+00	1013.0
2	TraesCS7A01G149600	chr7A	95.745	47	2	0	838	884	70192220	70192266	2.500000e-10	76.8
3	TraesCS7A01G149600	chr7B	95.384	1408	50	7	952	2348	55862454	55861051	0.000000e+00	2226.0
4	TraesCS7A01G149600	chr3B	97.855	839	17	1	1	839	765300890	765300053	0.000000e+00	1448.0
5	TraesCS7A01G149600	chr3B	100.000	46	0	0	840	885	765300097	765300052	4.160000e-13	86.1
6	TraesCS7A01G149600	chr2B	97.622	841	19	1	1	841	572183047	572183886	0.000000e+00	1441.0
7	TraesCS7A01G149600	chr2B	93.623	737	43	3	109	843	114433255	114433989	0.000000e+00	1098.0
8	TraesCS7A01G149600	chr2B	100.000	45	0	0	840	884	572183840	572183884	1.500000e-12	84.2
9	TraesCS7A01G149600	chr2B	97.778	45	1	0	843	887	114433944	114433988	6.960000e-11	78.7
10	TraesCS7A01G149600	chr7D	96.246	879	32	1	1470	2348	100302532	100301655	0.000000e+00	1439.0
11	TraesCS7A01G149600	chr7D	93.798	516	20	4	952	1464	100303600	100303094	0.000000e+00	765.0
12	TraesCS7A01G149600	chr1B	94.893	842	42	1	1	841	582169205	582170046	0.000000e+00	1315.0
13	TraesCS7A01G149600	chr4A	93.632	848	42	4	1	841	705589189	705588347	0.000000e+00	1256.0
14	TraesCS7A01G149600	chr4A	100.000	41	0	0	842	882	705588391	705588351	2.500000e-10	76.8
15	TraesCS7A01G149600	chr2D	90.106	849	68	7	1	839	166809464	166810306	0.000000e+00	1088.0
16	TraesCS7A01G149600	chr1A	88.457	849	77	9	5	840	189708883	189709723	0.000000e+00	1005.0
17	TraesCS7A01G149600	chr2A	87.294	850	86	9	5	840	734085715	734086556	0.000000e+00	952.0
18	TraesCS7A01G149600	chr3A	90.476	63	4	2	837	899	477000013	476999953	5.380000e-12	82.4
19	TraesCS7A01G149600	chr3A	97.727	44	1	0	842	885	85380265	85380222	2.500000e-10	76.8
20	TraesCS7A01G149600	chrUn	95.652	46	0	2	842	886	433954236	433954280	3.240000e-09	73.1
21	TraesCS7A01G149600	chr6A	93.750	48	3	0	837	884	98258282	98258235	3.240000e-09	73.1

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	TraesCS7A01G149600	chr7A	102545412	102547759	2347	True	4337.00	4337	100.0000	1	2348	1	chr7A.!!$R1	2347
1	TraesCS7A01G149600	chr7A	70191428	70192268	840	False	544.90	1013	92.1600	5	884	2	chr7A.!!$F1	879
2	TraesCS7A01G149600	chr7B	55861051	55862454	1403	True	2226.00	2226	95.3840	952	2348	1	chr7B.!!$R1	1396
3	TraesCS7A01G149600	chr3B	765300052	765300890	838	True	767.05	1448	98.9275	1	885	2	chr3B.!!$R1	884
4	TraesCS7A01G149600	chr2B	572183047	572183886	839	False	762.60	1441	98.8110	1	884	2	chr2B.!!$F2	883
5	TraesCS7A01G149600	chr2B	114433255	114433989	734	False	588.35	1098	95.7005	109	887	2	chr2B.!!$F1	778
6	TraesCS7A01G149600	chr7D	100301655	100303600	1945	True	1102.00	1439	95.0220	952	2348	2	chr7D.!!$R1	1396
7	TraesCS7A01G149600	chr1B	582169205	582170046	841	False	1315.00	1315	94.8930	1	841	1	chr1B.!!$F1	840
8	TraesCS7A01G149600	chr4A	705588347	705589189	842	True	666.40	1256	96.8160	1	882	2	chr4A.!!$R1	881
9	TraesCS7A01G149600	chr2D	166809464	166810306	842	False	1088.00	1088	90.1060	1	839	1	chr2D.!!$F1	838
10	TraesCS7A01G149600	chr1A	189708883	189709723	840	False	1005.00	1005	88.4570	5	840	1	chr1A.!!$F1	835
11	TraesCS7A01G149600	chr2A	734085715	734086556	841	False	952.00	952	87.2940	5	840	1	chr2A.!!$F1	835

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
926	1069	0.035458	CTCCACCGGAGTTCTGCTTT	59.965	55.0	9.46	0.0	44.25	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2270	2983	0.389426	CGTAGGTGAACTCGTTGGGG	60.389	60.0	0.0	0.0	0.0	4.96	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
492	571	1.961394	TCCTAATAGGATGCGCTCGTT	59.039	47.619	9.73	3.07	40.06	3.85
730	872	4.412060	ACAGATTAGGATAGGGCTAGCT	57.588	45.455	15.72	0.00	0.00	3.32
771	913	4.262721	GGGACTAATCATGCGGTGGTAATA	60.263	45.833	0.00	0.00	0.00	0.98
796	938	3.450457	TCCGTGTACGTTTTATGGGGTAT	59.550	43.478	0.00	0.00	37.74	2.73
797	939	4.646945	TCCGTGTACGTTTTATGGGGTATA	59.353	41.667	0.00	0.00	37.74	1.47
798	940	4.744631	CCGTGTACGTTTTATGGGGTATAC	59.255	45.833	0.00	0.00	37.74	1.47
799	941	5.451798	CCGTGTACGTTTTATGGGGTATACT	60.452	44.000	2.25	0.00	37.74	2.12
800	942	6.042143	CGTGTACGTTTTATGGGGTATACTT	58.958	40.000	2.25	0.00	34.11	2.24
801	943	7.199766	CGTGTACGTTTTATGGGGTATACTTA	58.800	38.462	2.25	0.00	34.11	2.24
802	944	7.379529	CGTGTACGTTTTATGGGGTATACTTAG	59.620	40.741	2.25	0.00	34.11	2.18
803	945	7.653311	GTGTACGTTTTATGGGGTATACTTAGG	59.347	40.741	2.25	0.00	0.00	2.69
804	946	6.178607	ACGTTTTATGGGGTATACTTAGGG	57.821	41.667	2.25	0.00	0.00	3.53
805	947	5.904750	ACGTTTTATGGGGTATACTTAGGGA	59.095	40.000	2.25	0.00	0.00	4.20
806	948	6.386635	ACGTTTTATGGGGTATACTTAGGGAA	59.613	38.462	2.25	0.00	0.00	3.97
807	949	6.932960	CGTTTTATGGGGTATACTTAGGGAAG	59.067	42.308	2.25	0.00	38.76	3.46
808	950	7.202029	CGTTTTATGGGGTATACTTAGGGAAGA	60.202	40.741	2.25	0.00	36.45	2.87
809	951	8.666821	GTTTTATGGGGTATACTTAGGGAAGAT	58.333	37.037	2.25	0.00	36.45	2.40
810	952	9.917118	TTTTATGGGGTATACTTAGGGAAGATA	57.083	33.333	2.25	0.00	36.45	1.98
811	953	9.917118	TTTATGGGGTATACTTAGGGAAGATAA	57.083	33.333	2.25	0.00	36.45	1.75
813	955	7.808279	TGGGGTATACTTAGGGAAGATAATG	57.192	40.000	2.25	0.00	36.45	1.90
814	956	7.318401	TGGGGTATACTTAGGGAAGATAATGT	58.682	38.462	2.25	0.00	36.45	2.71
815	957	7.797617	TGGGGTATACTTAGGGAAGATAATGTT	59.202	37.037	2.25	0.00	36.45	2.71
816	958	8.666821	GGGGTATACTTAGGGAAGATAATGTTT	58.333	37.037	2.25	0.00	36.45	2.83
900	1043	9.956720	GTAGTATAGAAACGTATGGTTATGTGT	57.043	33.333	0.00	0.00	38.08	3.72
905	1048	7.011828	AGAAACGTATGGTTATGTGTAATGC	57.988	36.000	0.00	0.00	38.08	3.56
906	1049	6.596106	AGAAACGTATGGTTATGTGTAATGCA	59.404	34.615	0.00	0.00	38.08	3.96
907	1050	6.114221	AACGTATGGTTATGTGTAATGCAC	57.886	37.500	0.00	0.00	41.94	4.57
908	1051	5.878116	AACGTATGGTTATGTGTAATGCACT	59.122	36.000	2.75	0.00	42.03	4.40
909	1052	6.036735	AACGTATGGTTATGTGTAATGCACTC	59.963	38.462	2.75	0.00	42.03	3.51
910	1053	8.798147	AACGTATGGTTATGTGTAATGCACTCC	61.798	40.741	2.75	1.72	42.03	3.85
915	1058	2.466867	GTGTAATGCACTCCACCGG	58.533	57.895	0.00	0.00	44.41	5.28
916	1059	0.036765	GTGTAATGCACTCCACCGGA	60.037	55.000	9.46	0.00	44.41	5.14
924	1067	3.382111	CTCCACCGGAGTTCTGCT	58.618	61.111	9.46	0.00	44.25	4.24
925	1068	1.674057	CTCCACCGGAGTTCTGCTT	59.326	57.895	9.46	0.00	44.25	3.91
926	1069	0.035458	CTCCACCGGAGTTCTGCTTT	59.965	55.000	9.46	0.00	44.25	3.51
927	1070	0.250295	TCCACCGGAGTTCTGCTTTG	60.250	55.000	9.46	0.00	0.00	2.77
928	1071	0.535102	CCACCGGAGTTCTGCTTTGT	60.535	55.000	9.46	0.00	0.00	2.83
929	1072	1.270625	CCACCGGAGTTCTGCTTTGTA	60.271	52.381	9.46	0.00	0.00	2.41
930	1073	2.615493	CCACCGGAGTTCTGCTTTGTAT	60.615	50.000	9.46	0.00	0.00	2.29
931	1074	3.369052	CCACCGGAGTTCTGCTTTGTATA	60.369	47.826	9.46	0.00	0.00	1.47
932	1075	4.250464	CACCGGAGTTCTGCTTTGTATAA	58.750	43.478	9.46	0.00	0.00	0.98
933	1076	4.330074	CACCGGAGTTCTGCTTTGTATAAG	59.670	45.833	9.46	0.00	0.00	1.73
934	1077	3.309954	CCGGAGTTCTGCTTTGTATAAGC	59.690	47.826	0.00	2.67	43.29	3.09
947	1090	5.539582	TTGTATAAGCACTAACAAAGGCG	57.460	39.130	0.00	0.00	0.00	5.52
948	1091	3.936453	TGTATAAGCACTAACAAAGGCGG	59.064	43.478	0.00	0.00	0.00	6.13
949	1092	2.843401	TAAGCACTAACAAAGGCGGA	57.157	45.000	0.00	0.00	0.00	5.54
950	1093	1.523758	AAGCACTAACAAAGGCGGAG	58.476	50.000	0.00	0.00	0.00	4.63
951	1094	0.685097	AGCACTAACAAAGGCGGAGA	59.315	50.000	0.00	0.00	0.00	3.71
952	1095	1.079503	GCACTAACAAAGGCGGAGAG	58.920	55.000	0.00	0.00	0.00	3.20
953	1096	1.337823	GCACTAACAAAGGCGGAGAGA	60.338	52.381	0.00	0.00	0.00	3.10
954	1097	2.611518	CACTAACAAAGGCGGAGAGAG	58.388	52.381	0.00	0.00	0.00	3.20
955	1098	2.231478	CACTAACAAAGGCGGAGAGAGA	59.769	50.000	0.00	0.00	0.00	3.10
956	1099	2.897969	ACTAACAAAGGCGGAGAGAGAA	59.102	45.455	0.00	0.00	0.00	2.87
1358	1504	4.019858	TCCATGGTCTGAGTAAGTCTGAG	58.980	47.826	12.58	0.00	34.05	3.35
1359	1505	3.766591	CCATGGTCTGAGTAAGTCTGAGT	59.233	47.826	2.57	0.00	34.05	3.41
1584	2297	0.253327	CCTAAAGCCTCACCACCTCC	59.747	60.000	0.00	0.00	0.00	4.30
1602	2315	2.266055	GCACCACCTCTTCCTCCG	59.734	66.667	0.00	0.00	0.00	4.63
2129	2842	3.064987	CTACCTCCACGCCGTCAGG	62.065	68.421	9.71	9.71	41.62	3.86
2204	2917	2.604046	ACCTCATCATCAAGGCGTAC	57.396	50.000	0.00	0.00	36.01	3.67
2246	2959	3.056328	GCCCTCAAGGTGTTCCGC	61.056	66.667	0.00	0.00	38.26	5.54
2270	2983	4.208686	CCCCTCTACGGCTGCGAC	62.209	72.222	0.00	0.00	0.00	5.19
2273	2986	4.208686	CTCTACGGCTGCGACCCC	62.209	72.222	0.00	0.00	0.00	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
730	872	6.681729	AGTCCCACTAAACTCAATCTAACA	57.318	37.500	0.00	0.00	0.00	2.41
771	913	4.101430	ACCCCATAAAACGTACACGGATAT	59.899	41.667	6.72	0.00	44.95	1.63
837	979	9.937175	GCAAACATTATCTTTCCTAAGTGTATC	57.063	33.333	0.00	0.00	32.98	2.24
838	980	9.686683	AGCAAACATTATCTTTCCTAAGTGTAT	57.313	29.630	0.00	0.00	32.98	2.29
839	981	9.162764	GAGCAAACATTATCTTTCCTAAGTGTA	57.837	33.333	0.00	0.00	32.98	2.90
840	982	7.885399	AGAGCAAACATTATCTTTCCTAAGTGT	59.115	33.333	0.00	0.00	32.98	3.55
898	1041	0.249120	CTCCGGTGGAGTGCATTACA	59.751	55.000	0.00	0.00	44.25	2.41
899	1042	3.065575	CTCCGGTGGAGTGCATTAC	57.934	57.895	0.00	0.00	44.25	1.89
908	1051	0.250295	CAAAGCAGAACTCCGGTGGA	60.250	55.000	8.63	0.00	0.00	4.02
909	1052	0.535102	ACAAAGCAGAACTCCGGTGG	60.535	55.000	8.63	2.00	0.00	4.61
910	1053	2.163818	TACAAAGCAGAACTCCGGTG	57.836	50.000	0.00	0.00	0.00	4.94
911	1054	4.504858	CTTATACAAAGCAGAACTCCGGT	58.495	43.478	0.00	0.00	0.00	5.28
912	1055	3.309954	GCTTATACAAAGCAGAACTCCGG	59.690	47.826	0.00	0.00	42.56	5.14
913	1056	4.522297	GCTTATACAAAGCAGAACTCCG	57.478	45.455	4.91	0.00	42.56	4.63
924	1067	5.106475	CCGCCTTTGTTAGTGCTTATACAAA	60.106	40.000	0.00	0.00	37.95	2.83
925	1068	4.393680	CCGCCTTTGTTAGTGCTTATACAA	59.606	41.667	0.00	0.00	0.00	2.41
926	1069	3.936453	CCGCCTTTGTTAGTGCTTATACA	59.064	43.478	0.00	0.00	0.00	2.29
927	1070	4.186159	TCCGCCTTTGTTAGTGCTTATAC	58.814	43.478	0.00	0.00	0.00	1.47
928	1071	4.160814	TCTCCGCCTTTGTTAGTGCTTATA	59.839	41.667	0.00	0.00	0.00	0.98
929	1072	3.055385	TCTCCGCCTTTGTTAGTGCTTAT	60.055	43.478	0.00	0.00	0.00	1.73
930	1073	2.300723	TCTCCGCCTTTGTTAGTGCTTA	59.699	45.455	0.00	0.00	0.00	3.09
931	1074	1.071699	TCTCCGCCTTTGTTAGTGCTT	59.928	47.619	0.00	0.00	0.00	3.91
932	1075	0.685097	TCTCCGCCTTTGTTAGTGCT	59.315	50.000	0.00	0.00	0.00	4.40
933	1076	1.079503	CTCTCCGCCTTTGTTAGTGC	58.920	55.000	0.00	0.00	0.00	4.40
934	1077	2.231478	TCTCTCTCCGCCTTTGTTAGTG	59.769	50.000	0.00	0.00	0.00	2.74
935	1078	2.526432	TCTCTCTCCGCCTTTGTTAGT	58.474	47.619	0.00	0.00	0.00	2.24
936	1079	3.193691	TCTTCTCTCTCCGCCTTTGTTAG	59.806	47.826	0.00	0.00	0.00	2.34
937	1080	3.056749	GTCTTCTCTCTCCGCCTTTGTTA	60.057	47.826	0.00	0.00	0.00	2.41
938	1081	1.971357	TCTTCTCTCTCCGCCTTTGTT	59.029	47.619	0.00	0.00	0.00	2.83
939	1082	1.273886	GTCTTCTCTCTCCGCCTTTGT	59.726	52.381	0.00	0.00	0.00	2.83
940	1083	1.273606	TGTCTTCTCTCTCCGCCTTTG	59.726	52.381	0.00	0.00	0.00	2.77
941	1084	1.633774	TGTCTTCTCTCTCCGCCTTT	58.366	50.000	0.00	0.00	0.00	3.11
942	1085	1.859302	ATGTCTTCTCTCTCCGCCTT	58.141	50.000	0.00	0.00	0.00	4.35
943	1086	1.754226	GAATGTCTTCTCTCTCCGCCT	59.246	52.381	0.00	0.00	0.00	5.52
944	1087	1.202475	GGAATGTCTTCTCTCTCCGCC	60.202	57.143	0.00	0.00	0.00	6.13
945	1088	1.478510	TGGAATGTCTTCTCTCTCCGC	59.521	52.381	0.00	0.00	0.00	5.54
946	1089	2.757868	AGTGGAATGTCTTCTCTCTCCG	59.242	50.000	0.00	0.00	0.00	4.63
947	1090	3.678529	GCAGTGGAATGTCTTCTCTCTCC	60.679	52.174	0.00	0.00	0.00	3.71
948	1091	3.056250	TGCAGTGGAATGTCTTCTCTCTC	60.056	47.826	0.00	0.00	0.00	3.20
949	1092	2.902486	TGCAGTGGAATGTCTTCTCTCT	59.098	45.455	0.00	0.00	0.00	3.10
950	1093	3.325293	TGCAGTGGAATGTCTTCTCTC	57.675	47.619	0.00	0.00	0.00	3.20
951	1094	3.678252	CGATGCAGTGGAATGTCTTCTCT	60.678	47.826	0.00	0.00	0.00	3.10
952	1095	2.606725	CGATGCAGTGGAATGTCTTCTC	59.393	50.000	0.00	0.00	0.00	2.87
953	1096	2.234661	TCGATGCAGTGGAATGTCTTCT	59.765	45.455	0.00	0.00	0.00	2.85
954	1097	2.349886	GTCGATGCAGTGGAATGTCTTC	59.650	50.000	0.00	0.00	0.00	2.87
955	1098	2.289631	TGTCGATGCAGTGGAATGTCTT	60.290	45.455	0.00	0.00	0.00	3.01
956	1099	1.276138	TGTCGATGCAGTGGAATGTCT	59.724	47.619	0.00	0.00	0.00	3.41
993	1136	3.049080	GCCCCACTCCATCAGGGAC	62.049	68.421	0.00	0.00	45.80	4.46
995	1138	4.181010	CGCCCCACTCCATCAGGG	62.181	72.222	0.00	0.00	42.94	4.45
996	1139	3.083349	TCGCCCCACTCCATCAGG	61.083	66.667	0.00	0.00	0.00	3.86
1262	1405	3.855853	GGGCGAGGGAGAAGAGGC	61.856	72.222	0.00	0.00	0.00	4.70
1305	1448	1.008767	CGTATCGTCGGCCTTCTCC	60.009	63.158	0.00	0.00	0.00	3.71
1358	1504	3.074412	CCAGTGACCCATTTGACAGTAC	58.926	50.000	0.00	0.00	0.00	2.73
1359	1505	2.039746	CCCAGTGACCCATTTGACAGTA	59.960	50.000	0.00	0.00	0.00	2.74
1435	1592	4.072088	GTGGAAAGGTCACGCGCG	62.072	66.667	30.96	30.96	0.00	6.86
1584	2297	2.266055	GGAGGAAGAGGTGGTGCG	59.734	66.667	0.00	0.00	0.00	5.34
1592	2305	0.179124	CGAAGAAGGCGGAGGAAGAG	60.179	60.000	0.00	0.00	0.00	2.85
1816	2529	4.647615	CGATGTAGGAGGCCGGCG	62.648	72.222	22.54	0.00	0.00	6.46
1817	2530	4.971125	GCGATGTAGGAGGCCGGC	62.971	72.222	21.18	21.18	0.00	6.13
1820	2533	4.971125	GCGGCGATGTAGGAGGCC	62.971	72.222	12.98	0.00	42.14	5.19
1874	2587	1.596934	GTGGATGAGGTTCTCCGCA	59.403	57.895	0.00	0.00	46.64	5.69
1985	2698	3.363970	GCATCTTGTTGAACACGTCGAAT	60.364	43.478	0.00	0.00	0.00	3.34
1992	2705	1.330080	GCGCGCATCTTGTTGAACAC	61.330	55.000	29.10	0.00	0.00	3.32
2099	2812	3.412879	GAGGTAGACCAGCGACGCC	62.413	68.421	17.79	0.15	38.89	5.68
2129	2842	2.444895	ATCTGGCGGGAGAGGGAC	60.445	66.667	0.00	0.00	0.00	4.46
2246	2959	4.438346	CCGTAGAGGGGCATTTCG	57.562	61.111	0.00	0.00	35.97	3.46
2270	2983	0.389426	CGTAGGTGAACTCGTTGGGG	60.389	60.000	0.00	0.00	0.00	4.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.