AutoCloner

Multiple sequence alignment - TraesCS5B01G349500

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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	TraesCS5B01G349500	chr5B	100.000	2315	0	0	1	2315	530779575	530781889	0.000000e+00	4276.0
1	TraesCS5B01G349500	chr5B	93.782	579	32	4	1739	2315	613091089	613091665	0.000000e+00	867.0
2	TraesCS5B01G349500	chr5B	83.651	893	102	24	1	868	530723266	530724139	0.000000e+00	800.0
3	TraesCS5B01G349500	chr5B	88.038	627	37	19	866	1461	530724166	530724785	0.000000e+00	708.0
4	TraesCS5B01G349500	chr5B	86.354	491	48	9	870	1343	530798070	530798558	3.410000e-143	518.0
5	TraesCS5B01G349500	chr5B	85.924	476	54	6	875	1345	530762594	530763061	1.600000e-136	496.0
6	TraesCS5B01G349500	chr5B	90.598	234	22	0	1472	1705	530725192	530725425	6.210000e-81	311.0
7	TraesCS5B01G349500	chr5A	92.256	1640	86	26	1	1617	551244062	551245683	0.000000e+00	2287.0
8	TraesCS5B01G349500	chr5A	92.500	880	46	11	836	1705	551190761	551191630	0.000000e+00	1242.0
9	TraesCS5B01G349500	chr5A	91.955	808	36	10	1	795	551189894	551190685	0.000000e+00	1105.0
10	TraesCS5B01G349500	chr5A	92.523	749	33	12	716	1454	551435534	551436269	0.000000e+00	1051.0
11	TraesCS5B01G349500	chr5A	90.719	765	48	11	865	1615	551058911	551059666	0.000000e+00	998.0
12	TraesCS5B01G349500	chr5A	93.217	457	25	5	1	456	551429489	551429940	0.000000e+00	667.0
13	TraesCS5B01G349500	chr5A	83.681	576	58	23	865	1419	551194007	551194567	5.710000e-141	510.0
14	TraesCS5B01G349500	chr5A	92.481	266	14	6	454	717	551435035	551435296	2.170000e-100	375.0
15	TraesCS5B01G349500	chr5D	92.075	858	39	16	865	1701	436606176	436607025	0.000000e+00	1181.0
16	TraesCS5B01G349500	chr5D	83.929	560	59	19	865	1419	436621336	436621869	7.380000e-140	507.0
17	TraesCS5B01G349500	chr5D	95.082	61	3	0	818	878	436621230	436621290	1.890000e-16	97.1
18	TraesCS5B01G349500	chr3B	95.183	602	26	3	1716	2315	14980496	14981096	0.000000e+00	948.0
19	TraesCS5B01G349500	chr2B	95.008	601	27	3	1717	2315	759982036	759981437	0.000000e+00	941.0
20	TraesCS5B01G349500	chr7B	94.831	561	25	4	1757	2315	739000671	739000113	0.000000e+00	872.0
21	TraesCS5B01G349500	chr7A	93.961	563	31	3	1755	2315	730298942	730299503	0.000000e+00	848.0
22	TraesCS5B01G349500	chr6A	91.987	599	45	3	1719	2315	4100637	4100040	0.000000e+00	837.0
23	TraesCS5B01G349500	chr7D	91.960	597	44	4	1721	2315	553064714	553065308	0.000000e+00	833.0
24	TraesCS5B01G349500	chr6B	92.203	590	44	2	1727	2315	434182130	434182718	0.000000e+00	833.0
25	TraesCS5B01G349500	chr6D	91.500	600	45	6	1720	2315	456100953	456100356	0.000000e+00	821.0

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	TraesCS5B01G349500	chr5B	530779575	530781889	2314	False	4276.000000	4276	100.000000	1	2315	1	chr5B.!!$F2	2314
1	TraesCS5B01G349500	chr5B	613091089	613091665	576	False	867.000000	867	93.782000	1739	2315	1	chr5B.!!$F4	576
2	TraesCS5B01G349500	chr5B	530723266	530725425	2159	False	606.333333	800	87.429000	1	1705	3	chr5B.!!$F5	1704
3	TraesCS5B01G349500	chr5A	551244062	551245683	1621	False	2287.000000	2287	92.256000	1	1617	1	chr5A.!!$F2	1616
4	TraesCS5B01G349500	chr5A	551058911	551059666	755	False	998.000000	998	90.719000	865	1615	1	chr5A.!!$F1	750
5	TraesCS5B01G349500	chr5A	551189894	551194567	4673	False	952.333333	1242	89.378667	1	1705	3	chr5A.!!$F4	1704
6	TraesCS5B01G349500	chr5A	551435035	551436269	1234	False	713.000000	1051	92.502000	454	1454	2	chr5A.!!$F5	1000
7	TraesCS5B01G349500	chr5D	436606176	436607025	849	False	1181.000000	1181	92.075000	865	1701	1	chr5D.!!$F1	836
8	TraesCS5B01G349500	chr5D	436621230	436621869	639	False	302.050000	507	89.505500	818	1419	2	chr5D.!!$F2	601
9	TraesCS5B01G349500	chr3B	14980496	14981096	600	False	948.000000	948	95.183000	1716	2315	1	chr3B.!!$F1	599
10	TraesCS5B01G349500	chr2B	759981437	759982036	599	True	941.000000	941	95.008000	1717	2315	1	chr2B.!!$R1	598
11	TraesCS5B01G349500	chr7B	739000113	739000671	558	True	872.000000	872	94.831000	1757	2315	1	chr7B.!!$R1	558
12	TraesCS5B01G349500	chr7A	730298942	730299503	561	False	848.000000	848	93.961000	1755	2315	1	chr7A.!!$F1	560
13	TraesCS5B01G349500	chr6A	4100040	4100637	597	True	837.000000	837	91.987000	1719	2315	1	chr6A.!!$R1	596
14	TraesCS5B01G349500	chr7D	553064714	553065308	594	False	833.000000	833	91.960000	1721	2315	1	chr7D.!!$F1	594
15	TraesCS5B01G349500	chr6B	434182130	434182718	588	False	833.000000	833	92.203000	1727	2315	1	chr6B.!!$F1	588
16	TraesCS5B01G349500	chr6D	456100356	456100953	597	True	821.000000	821	91.500000	1720	2315	1	chr6D.!!$R1	595

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
747	1037	0.334676	CATTTTGGGCCCAGGAGGTA	59.665	55.0	26.87	5.91	38.26	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2085	3917	0.250234	CCGGAAGCCAGATCTGACAA	59.75	55.0	24.62	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
261	265	1.375551	ACGTGCCGATTTGGAATACC	58.624	50.000	1.50	0.00	42.00	2.73
264	268	2.223249	CGTGCCGATTTGGAATACCTTG	60.223	50.000	0.00	0.00	42.00	3.61
266	270	3.013921	TGCCGATTTGGAATACCTTGTC	58.986	45.455	0.00	0.00	42.00	3.18
283	288	6.653989	ACCTTGTCTTTTTGAGAAAGAGAGA	58.346	36.000	0.00	0.00	36.99	3.10
446	451	0.397675	ATCAGGATCGCAGACCAGGA	60.398	55.000	0.00	0.00	42.51	3.86
458	463	2.093764	CAGACCAGGAGGAAAGCTACAG	60.094	54.545	0.00	0.00	38.69	2.74
459	464	0.615850	ACCAGGAGGAAAGCTACAGC	59.384	55.000	0.00	0.00	38.91	4.40
460	465	0.908198	CCAGGAGGAAAGCTACAGCT	59.092	55.000	0.00	0.00	46.54	4.24
519	537	0.839946	CCCCTCGTGAGAAATCCCAT	59.160	55.000	0.00	0.00	41.32	4.00
567	585	8.128582	GGATATCATTTAGCATCGAACAAAACA	58.871	33.333	4.83	0.00	0.00	2.83
599	617	5.711506	AGTTTCACCAAGTGCATATTCATCA	59.288	36.000	0.00	0.00	32.98	3.07
663	681	3.820557	TGGCACCTATAAGATTTGCTCC	58.179	45.455	0.00	0.00	0.00	4.70
743	1033	1.055040	CAAACATTTTGGGCCCAGGA	58.945	50.000	26.87	18.19	0.00	3.86
744	1034	1.002315	CAAACATTTTGGGCCCAGGAG	59.998	52.381	26.87	18.34	0.00	3.69
745	1035	0.545071	AACATTTTGGGCCCAGGAGG	60.545	55.000	26.87	20.88	39.47	4.30
746	1036	1.079073	CATTTTGGGCCCAGGAGGT	59.921	57.895	26.87	8.02	38.26	3.85
747	1037	0.334676	CATTTTGGGCCCAGGAGGTA	59.665	55.000	26.87	5.91	38.26	3.08
748	1038	0.335019	ATTTTGGGCCCAGGAGGTAC	59.665	55.000	26.87	0.00	38.26	3.34
749	1039	2.132089	TTTTGGGCCCAGGAGGTACG	62.132	60.000	26.87	0.00	38.26	3.67
750	1040	3.857521	TTGGGCCCAGGAGGTACGT	62.858	63.158	26.87	0.00	38.26	3.57
751	1041	3.007323	GGGCCCAGGAGGTACGTT	61.007	66.667	19.95	0.00	38.26	3.99
752	1042	1.686800	GGGCCCAGGAGGTACGTTA	60.687	63.158	19.95	0.00	38.26	3.18
753	1043	1.052694	GGGCCCAGGAGGTACGTTAT	61.053	60.000	19.95	0.00	38.26	1.89
754	1044	0.835276	GGCCCAGGAGGTACGTTATT	59.165	55.000	0.00	0.00	38.26	1.40
755	1045	1.211212	GGCCCAGGAGGTACGTTATTT	59.789	52.381	0.00	0.00	38.26	1.40
756	1046	2.356432	GGCCCAGGAGGTACGTTATTTT	60.356	50.000	0.00	0.00	38.26	1.82
757	1047	3.349927	GCCCAGGAGGTACGTTATTTTT	58.650	45.455	0.00	0.00	38.26	1.94
773	1063	2.692709	TTTTTGAGAATCTGGGCCCA	57.307	45.000	26.67	26.67	34.92	5.36
774	1064	2.220653	TTTTGAGAATCTGGGCCCAG	57.779	50.000	41.73	41.73	44.86	4.45
805	1125	2.679930	GCTTGGTACCTGCCGTCTTTAT	60.680	50.000	14.36	0.00	0.00	1.40
932	1389	2.609459	CCGTAGGCAGCTTGATTTACTG	59.391	50.000	0.00	0.00	46.14	2.74
951	1418	7.859325	TTACTGCCGAAGCTTCTTTATTTAT	57.141	32.000	23.50	4.99	40.80	1.40
952	1419	8.951787	TTACTGCCGAAGCTTCTTTATTTATA	57.048	30.769	23.50	4.10	40.80	0.98
953	1420	7.247929	ACTGCCGAAGCTTCTTTATTTATAC	57.752	36.000	23.50	2.36	40.80	1.47
954	1421	6.018994	ACTGCCGAAGCTTCTTTATTTATACG	60.019	38.462	23.50	6.83	40.80	3.06
955	1422	6.044046	TGCCGAAGCTTCTTTATTTATACGA	58.956	36.000	23.50	0.00	40.80	3.43
956	1423	6.019318	TGCCGAAGCTTCTTTATTTATACGAC	60.019	38.462	23.50	0.27	40.80	4.34
957	1424	6.200475	GCCGAAGCTTCTTTATTTATACGACT	59.800	38.462	23.50	0.00	35.50	4.18
958	1425	7.380602	GCCGAAGCTTCTTTATTTATACGACTA	59.619	37.037	23.50	0.00	35.50	2.59
959	1426	8.689069	CCGAAGCTTCTTTATTTATACGACTAC	58.311	37.037	23.50	0.00	0.00	2.73
960	1427	9.229784	CGAAGCTTCTTTATTTATACGACTACA	57.770	33.333	23.50	0.00	0.00	2.74
1095	1572	3.693085	GGATCTTGGTCTATATCGCGGTA	59.307	47.826	6.13	2.77	0.00	4.02
1273	1750	1.870055	CTTCCGCAACAAGCATGCCT	61.870	55.000	15.66	0.00	46.13	4.75
1428	1916	6.770785	AGTTGTAACATCTTTTGTCCTTAGCA	59.229	34.615	0.00	0.00	37.68	3.49
1455	1943	6.870439	GTGGGAAACTTGTACGTACTAGATTT	59.130	38.462	33.71	27.71	34.05	2.17
1523	2407	3.679980	AGTGATTGATGCAGTTACACGTC	59.320	43.478	0.00	0.00	33.00	4.34
1547	2431	7.640240	GTCAATCTAGAATTTTAATCACGTGGC	59.360	37.037	17.00	0.00	0.00	5.01
1548	2432	5.712217	TCTAGAATTTTAATCACGTGGCG	57.288	39.130	17.00	0.00	0.00	5.69
1611	2495	7.118723	TGAGACATAATTAGAAAACATGCCCT	58.881	34.615	0.00	0.00	0.00	5.19
1617	2501	0.598065	AGAAAACATGCCCTTGCGTC	59.402	50.000	0.00	0.00	41.78	5.19
1661	2545	2.355010	AGGCCCTATCAAGATGCAAC	57.645	50.000	0.00	0.00	0.00	4.17
1705	2589	0.592637	TTGAAATGCTGCCACGACTG	59.407	50.000	0.00	0.00	0.00	3.51
1706	2590	0.250252	TGAAATGCTGCCACGACTGA	60.250	50.000	0.00	0.00	0.00	3.41
1708	2592	1.063174	GAAATGCTGCCACGACTGATC	59.937	52.381	0.00	0.00	0.00	2.92
1710	2594	2.512515	GCTGCCACGACTGATCCC	60.513	66.667	0.00	0.00	0.00	3.85
1712	2596	3.391665	CTGCCACGACTGATCCCCC	62.392	68.421	0.00	0.00	0.00	5.40
1900	3720	2.745884	TGTTTCGCGCAGGGGATG	60.746	61.111	8.75	0.00	42.39	3.51
2085	3917	2.115266	CCCAACCAGTTCGGCCTT	59.885	61.111	0.00	0.00	39.03	4.35
2151	4178	2.366569	GGTAGGGGTGGGGGAGAC	60.367	72.222	0.00	0.00	0.00	3.36
2182	4462	0.179000	AGAAATCCACGGCTGGCTAG	59.821	55.000	0.00	0.00	37.49	3.42
2276	5319	0.620121	CCTTCTGCCTCTCTCCCCTT	60.620	60.000	0.00	0.00	0.00	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
184	188	1.588082	CAGTTGCATCCACCCAAGC	59.412	57.895	0.00	0.00	0.00	4.01
261	265	7.443575	TGGATCTCTCTTTCTCAAAAAGACAAG	59.556	37.037	0.00	0.00	32.27	3.16
264	268	7.823799	AGATGGATCTCTCTTTCTCAAAAAGAC	59.176	37.037	0.00	0.00	33.20	3.01
458	463	4.676924	GTGTTAGATCTTGTGTTTTGCAGC	59.323	41.667	0.00	0.00	0.00	5.25
459	464	5.820131	TGTGTTAGATCTTGTGTTTTGCAG	58.180	37.500	0.00	0.00	0.00	4.41
460	465	5.826601	TGTGTTAGATCTTGTGTTTTGCA	57.173	34.783	0.00	0.00	0.00	4.08
567	585	3.616317	GCACTTGGTGAAACTTGGTTTGT	60.616	43.478	1.57	0.00	35.77	2.83
621	639	9.849166	GTGCCAACTATAAGCTTATTACAAAAA	57.151	29.630	23.47	3.65	0.00	1.94
622	640	8.463607	GGTGCCAACTATAAGCTTATTACAAAA	58.536	33.333	23.47	4.36	0.00	2.44
642	660	3.201930	TGGAGCAAATCTTATAGGTGCCA	59.798	43.478	0.00	0.00	35.80	4.92
754	1044	2.109834	TCTGGGCCCAGATTCTCAAAAA	59.890	45.455	44.71	23.01	46.80	1.94
755	1045	1.710244	TCTGGGCCCAGATTCTCAAAA	59.290	47.619	44.71	23.76	46.80	2.44
756	1046	1.371467	TCTGGGCCCAGATTCTCAAA	58.629	50.000	44.71	24.51	46.80	2.69
757	1047	3.103236	TCTGGGCCCAGATTCTCAA	57.897	52.632	44.71	25.27	46.80	3.02
758	1048	4.917476	TCTGGGCCCAGATTCTCA	57.083	55.556	44.71	26.02	46.80	3.27
765	1055	0.321671	CCATACGTATCTGGGCCCAG	59.678	60.000	41.73	41.73	44.86	4.45
766	1056	1.764571	GCCATACGTATCTGGGCCCA	61.765	60.000	26.67	26.67	38.70	5.36
767	1057	1.003718	GCCATACGTATCTGGGCCC	60.004	63.158	17.59	17.59	38.70	5.80
768	1058	0.396811	AAGCCATACGTATCTGGGCC	59.603	55.000	24.32	11.91	45.72	5.80
769	1059	1.512926	CAAGCCATACGTATCTGGGC	58.487	55.000	21.83	21.83	44.92	5.36
770	1060	1.416401	ACCAAGCCATACGTATCTGGG	59.584	52.381	15.33	14.47	32.90	4.45
771	1061	2.910688	ACCAAGCCATACGTATCTGG	57.089	50.000	4.74	8.01	35.53	3.86
772	1062	3.321111	AGGTACCAAGCCATACGTATCTG	59.679	47.826	15.94	1.07	0.00	2.90
773	1063	3.321111	CAGGTACCAAGCCATACGTATCT	59.679	47.826	15.94	0.00	0.00	1.98
774	1064	3.650139	CAGGTACCAAGCCATACGTATC	58.350	50.000	15.94	0.00	0.00	2.24
775	1065	2.224209	GCAGGTACCAAGCCATACGTAT	60.224	50.000	15.94	1.14	0.00	3.06
805	1125	5.200483	ACAAAGACATTTTGACTCTTGGGA	58.800	37.500	6.63	0.00	33.83	4.37
930	1387	6.200286	TCGTATAAATAAAGAAGCTTCGGCAG	59.800	38.462	20.43	4.51	44.74	4.85
932	1389	6.200475	AGTCGTATAAATAAAGAAGCTTCGGC	59.800	38.462	20.43	6.54	42.17	5.54
951	1418	2.032550	GCGCCTCTTGTATGTAGTCGTA	59.967	50.000	0.00	0.00	0.00	3.43
952	1419	1.202268	GCGCCTCTTGTATGTAGTCGT	60.202	52.381	0.00	0.00	0.00	4.34
953	1420	1.478137	GCGCCTCTTGTATGTAGTCG	58.522	55.000	0.00	0.00	0.00	4.18
954	1421	1.854227	GGCGCCTCTTGTATGTAGTC	58.146	55.000	22.15	0.00	0.00	2.59
955	1422	0.102481	CGGCGCCTCTTGTATGTAGT	59.898	55.000	26.68	0.00	0.00	2.73
956	1423	0.102481	ACGGCGCCTCTTGTATGTAG	59.898	55.000	26.68	6.43	0.00	2.74
957	1424	0.533491	AACGGCGCCTCTTGTATGTA	59.467	50.000	26.68	0.00	0.00	2.29
958	1425	0.739813	GAACGGCGCCTCTTGTATGT	60.740	55.000	26.68	9.42	0.00	2.29
959	1426	1.752501	CGAACGGCGCCTCTTGTATG	61.753	60.000	26.68	8.67	0.00	2.39
960	1427	1.518572	CGAACGGCGCCTCTTGTAT	60.519	57.895	26.68	5.79	0.00	2.29
1095	1572	1.096416	CGAAGAAGCCGAGGTAGAGT	58.904	55.000	0.00	0.00	0.00	3.24
1117	1594	0.818445	TAGGAGATCACGGCGGAGAC	60.818	60.000	13.24	4.77	0.00	3.36
1159	1636	0.250513	AAGATCTTGTCGGACCTGGC	59.749	55.000	7.30	0.00	0.00	4.85
1166	1643	3.334583	TCCCAAAGAAGATCTTGTCGG	57.665	47.619	14.00	12.73	36.71	4.79
1299	1776	2.125147	GGCTAGCACACATCGGCA	60.125	61.111	18.24	0.00	0.00	5.69
1428	1916	2.967887	AGTACGTACAAGTTTCCCACCT	59.032	45.455	26.55	0.00	0.00	4.00
1523	2407	6.628856	CGCCACGTGATTAAAATTCTAGATTG	59.371	38.462	19.30	0.00	0.00	2.67
1547	2431	9.546909	GCCTTCAAATATAATGTGATGATTACG	57.453	33.333	0.00	0.00	0.00	3.18
1617	2501	1.442520	CATGTTTGCTCCCGTTGCG	60.443	57.895	0.00	0.00	0.00	4.85
1625	2509	3.429410	GGGCCTTCATAACATGTTTGCTC	60.429	47.826	17.78	6.70	0.00	4.26
1694	2578	2.187946	GGGGATCAGTCGTGGCAG	59.812	66.667	0.00	0.00	0.00	4.85
1764	2651	4.603946	GCGGCGGCTAGGGTTAGG	62.604	72.222	9.78	0.00	35.83	2.69
2075	3907	1.625818	AGATCTGACAAAGGCCGAACT	59.374	47.619	0.00	0.00	0.00	3.01
2085	3917	0.250234	CCGGAAGCCAGATCTGACAA	59.750	55.000	24.62	0.00	0.00	3.18
2151	4178	1.527370	GATTTCTCCAGGTCCCCCG	59.473	63.158	0.00	0.00	35.12	5.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.