AutoCloner

Multiple sequence alignment - TraesCS6B01G378700

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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	TraesCS6B01G378700	chr6B	100.000	2447	0	0	1	2447	653699327	653696881	0.000000e+00	4519.0
1	TraesCS6B01G378700	chr6B	95.223	963	35	6	753	1709	653872129	653871172	0.000000e+00	1513.0
2	TraesCS6B01G378700	chr6B	88.974	1170	112	6	750	1913	653856025	653854867	0.000000e+00	1430.0
3	TraesCS6B01G378700	chr6B	89.041	1168	87	12	750	1904	653715131	653713992	0.000000e+00	1410.0
4	TraesCS6B01G378700	chr6B	90.313	702	57	4	66	757	653872853	653872153	0.000000e+00	909.0
5	TraesCS6B01G378700	chr6B	85.008	647	82	11	1704	2343	653871014	653870376	0.000000e+00	643.0
6	TraesCS6B01G378700	chr6B	83.429	700	95	13	71	757	653195014	653194323	4.440000e-177	630.0
7	TraesCS6B01G378700	chr6B	80.000	175	22	6	1492	1662	654836498	654836663	1.540000e-22	117.0
8	TraesCS6B01G378700	chr6B	92.647	68	5	0	1	68	653872940	653872873	5.570000e-17	99.0
9	TraesCS6B01G378700	chr6D	91.156	1696	127	18	750	2431	433154825	433153139	0.000000e+00	2279.0
10	TraesCS6B01G378700	chr6D	92.412	1331	85	7	750	2069	432931015	432929690	0.000000e+00	1884.0
11	TraesCS6B01G378700	chr6D	91.416	1165	81	8	750	1907	432913935	432912783	0.000000e+00	1580.0
12	TraesCS6B01G378700	chr6D	90.204	1174	95	9	750	1913	433258609	433257446	0.000000e+00	1513.0
13	TraesCS6B01G378700	chr6D	94.427	969	42	7	750	1712	433280158	433279196	0.000000e+00	1480.0
14	TraesCS6B01G378700	chr6D	91.298	701	51	3	67	757	433280879	433280179	0.000000e+00	948.0
15	TraesCS6B01G378700	chr6D	90.975	687	51	4	81	757	433155531	433154846	0.000000e+00	915.0
16	TraesCS6B01G378700	chr6D	89.744	702	58	4	66	757	432931733	432931036	0.000000e+00	885.0
17	TraesCS6B01G378700	chr6D	83.977	699	93	11	71	757	433259321	433258630	0.000000e+00	652.0
18	TraesCS6B01G378700	chr6D	82.996	741	89	17	1708	2418	433279038	433278305	9.540000e-179	636.0
19	TraesCS6B01G378700	chr6D	84.354	588	78	7	183	757	432914542	432913956	4.570000e-157	564.0
20	TraesCS6B01G378700	chr6D	93.103	58	4	0	1	58	433280968	433280911	4.340000e-13	86.1
21	TraesCS6B01G378700	chr6A	94.306	966	43	7	750	1709	579142619	579141660	0.000000e+00	1469.0
22	TraesCS6B01G378700	chr6A	90.161	1057	88	6	750	1800	579124408	579123362	0.000000e+00	1362.0
23	TraesCS6B01G378700	chr6A	91.168	702	52	3	66	757	579143341	579142640	0.000000e+00	944.0
24	TraesCS6B01G378700	chr6A	84.675	646	86	9	1704	2343	579141502	579140864	1.230000e-177	632.0
25	TraesCS6B01G378700	chr6A	83.503	588	82	8	183	757	579125014	579124429	3.580000e-148	534.0
26	TraesCS6B01G378700	chr7A	82.020	495	77	9	1928	2419	30870382	30870867	6.300000e-111	411.0
27	TraesCS6B01G378700	chr7A	80.645	496	81	12	1928	2419	30868695	30869179	1.070000e-98	370.0
28	TraesCS6B01G378700	chr1A	83.333	450	65	10	1987	2431	561586283	561586727	8.150000e-110	407.0
29	TraesCS6B01G378700	chr5A	80.321	498	88	8	1925	2418	589001987	589002478	3.840000e-98	368.0
30	TraesCS6B01G378700	chr7B	80.793	479	80	11	1959	2431	690023446	690023918	4.970000e-97	364.0

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	TraesCS6B01G378700	chr6B	653696881	653699327	2446	True	4519.000	4519	100.000000	1	2447	1	chr6B.!!$R2	2446
1	TraesCS6B01G378700	chr6B	653854867	653856025	1158	True	1430.000	1430	88.974000	750	1913	1	chr6B.!!$R4	1163
2	TraesCS6B01G378700	chr6B	653713992	653715131	1139	True	1410.000	1410	89.041000	750	1904	1	chr6B.!!$R3	1154
3	TraesCS6B01G378700	chr6B	653870376	653872940	2564	True	791.000	1513	90.797750	1	2343	4	chr6B.!!$R5	2342
4	TraesCS6B01G378700	chr6B	653194323	653195014	691	True	630.000	630	83.429000	71	757	1	chr6B.!!$R1	686
5	TraesCS6B01G378700	chr6D	433153139	433155531	2392	True	1597.000	2279	91.065500	81	2431	2	chr6D.!!$R3	2350
6	TraesCS6B01G378700	chr6D	432929690	432931733	2043	True	1384.500	1884	91.078000	66	2069	2	chr6D.!!$R2	2003
7	TraesCS6B01G378700	chr6D	433257446	433259321	1875	True	1082.500	1513	87.090500	71	1913	2	chr6D.!!$R4	1842
8	TraesCS6B01G378700	chr6D	432912783	432914542	1759	True	1072.000	1580	87.885000	183	1907	2	chr6D.!!$R1	1724
9	TraesCS6B01G378700	chr6D	433278305	433280968	2663	True	787.525	1480	90.456000	1	2418	4	chr6D.!!$R5	2417
10	TraesCS6B01G378700	chr6A	579140864	579143341	2477	True	1015.000	1469	90.049667	66	2343	3	chr6A.!!$R2	2277
11	TraesCS6B01G378700	chr6A	579123362	579125014	1652	True	948.000	1362	86.832000	183	1800	2	chr6A.!!$R1	1617
12	TraesCS6B01G378700	chr7A	30868695	30870867	2172	False	390.500	411	81.332500	1928	2419	2	chr7A.!!$F1	491

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
739	777	0.31716	TCGATGCACTTCCGACAACT	59.683	50.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2230	2754	0.903236	GAAACTCTAACCTCCCCGCT	59.097	55.0	0.0	0.0	0.0	5.52	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
61	62	1.317431	ATGCATTGCACAGACGGCAT	61.317	50.000	14.66	0.00	43.04	4.40
177	202	5.205056	TGTTTGATTTATACCACCATCCCC	58.795	41.667	0.00	0.00	0.00	4.81
181	206	4.230733	TGATTTATACCACCATCCCCACAA	59.769	41.667	0.00	0.00	0.00	3.33
195	220	2.235402	CCCCACAACAGACGGTAAGTAT	59.765	50.000	0.00	0.00	0.00	2.12
317	345	4.700213	ACACCCAATTCCATTCGTAGAAAG	59.300	41.667	0.00	0.00	45.90	2.62
318	346	3.694566	ACCCAATTCCATTCGTAGAAAGC	59.305	43.478	0.00	0.00	45.90	3.51
430	458	4.261801	GGATGCCTTTGCTTCTACAGTTA	58.738	43.478	0.00	0.00	40.52	2.24
433	461	2.420372	GCCTTTGCTTCTACAGTTAGGC	59.580	50.000	0.00	0.00	36.17	3.93
435	463	2.380084	TTGCTTCTACAGTTAGGCCG	57.620	50.000	0.00	0.00	0.00	6.13
455	483	4.024698	GCAGCTCGCGAGATCAAT	57.975	55.556	38.74	15.51	40.84	2.57
476	504	0.740868	ATGACTTGTCGATGGTGGCG	60.741	55.000	0.00	0.00	0.00	5.69
478	506	0.460284	GACTTGTCGATGGTGGCGAT	60.460	55.000	0.00	0.00	40.19	4.58
495	523	1.270147	CGATGCATGAGAGCTGGATGA	60.270	52.381	2.46	0.00	34.99	2.92
506	534	3.136077	AGAGCTGGATGATGCAGTACAAT	59.864	43.478	15.39	0.00	38.17	2.71
544	572	3.570550	ACTACTGAGAAGGCATACCGATC	59.429	47.826	0.00	0.00	42.76	3.69
549	577	2.887783	GAGAAGGCATACCGATCTGAGA	59.112	50.000	0.00	0.00	42.76	3.27
587	625	2.731968	CGGGTTCATCGAGCCAAAAATG	60.732	50.000	0.00	0.00	34.53	2.32
603	641	7.120789	CCAAAAATGACAAGTTCTATTTGGC	57.879	36.000	0.00	0.00	36.25	4.52
617	655	3.788333	ATTTGGCCATCAATCAGTTCG	57.212	42.857	6.09	0.00	34.98	3.95
651	689	2.348472	TGAGGAGTTCAAGGGGACAAT	58.652	47.619	0.00	0.00	31.34	2.71
653	691	1.177401	GGAGTTCAAGGGGACAATGC	58.823	55.000	0.00	0.00	0.00	3.56
707	745	3.196254	GGTTCCTACCGAATTCAGGTACA	59.804	47.826	18.96	10.20	42.81	2.90
715	753	5.805728	ACCGAATTCAGGTACAAGAATCTT	58.194	37.500	16.92	0.00	40.80	2.40
734	772	1.746470	TAGTCTCGATGCACTTCCGA	58.254	50.000	0.00	0.00	0.00	4.55
739	777	0.317160	TCGATGCACTTCCGACAACT	59.683	50.000	0.00	0.00	0.00	3.16
1380	1447	6.202188	GCGAGAACGGATATTTAAGAATGGAA	59.798	38.462	0.00	0.00	40.15	3.53
1523	1596	9.537848	CACACGTCCACTTTAATTAAGTATTTC	57.462	33.333	0.00	0.00	45.29	2.17
1656	1732	9.547753	AGAATTTGTGTTAGCTATATCATTCGT	57.452	29.630	0.00	0.00	0.00	3.85
1682	1762	6.434028	AGATTGTTAAATTGTGCTGCCTCTTA	59.566	34.615	0.00	0.00	0.00	2.10
1889	2137	2.580322	TCTCCCCCAATTGCTATTGTCA	59.420	45.455	17.66	0.62	39.62	3.58
1913	2161	1.810532	GTTCAACCCACAACGCCAA	59.189	52.632	0.00	0.00	0.00	4.52
1919	2167	1.067250	CCCACAACGCCAACCAAAG	59.933	57.895	0.00	0.00	0.00	2.77
1920	2168	1.388065	CCCACAACGCCAACCAAAGA	61.388	55.000	0.00	0.00	0.00	2.52
1921	2169	0.673437	CCACAACGCCAACCAAAGAT	59.327	50.000	0.00	0.00	0.00	2.40
1922	2170	1.068434	CCACAACGCCAACCAAAGATT	59.932	47.619	0.00	0.00	0.00	2.40
1923	2171	2.126467	CACAACGCCAACCAAAGATTG	58.874	47.619	0.00	0.00	0.00	2.67
1924	2172	1.139163	CAACGCCAACCAAAGATTGC	58.861	50.000	0.00	0.00	0.00	3.56
1925	2173	1.039856	AACGCCAACCAAAGATTGCT	58.960	45.000	0.00	0.00	0.00	3.91
1935	2456	5.876651	ACCAAAGATTGCTTTTCTTTCCT	57.123	34.783	6.25	0.00	42.27	3.36
1936	2457	5.604565	ACCAAAGATTGCTTTTCTTTCCTG	58.395	37.500	6.25	2.88	42.27	3.86
1979	2500	1.290134	AAGCCTTTCTCCCCTCGATT	58.710	50.000	0.00	0.00	0.00	3.34
1984	2505	1.480954	CTTTCTCCCCTCGATTTCCGA	59.519	52.381	0.00	0.00	46.35	4.55
2010	2531	2.049627	GCCCATGGATTCGCCTCTCT	62.050	60.000	15.22	0.00	37.63	3.10
2048	2572	4.974438	TCAGTGGCGGGGAGGGTT	62.974	66.667	0.00	0.00	0.00	4.11
2049	2573	3.966543	CAGTGGCGGGGAGGGTTT	61.967	66.667	0.00	0.00	0.00	3.27
2082	2606	1.338864	CGGCTCCGGCTAGTAGATAGA	60.339	57.143	0.00	0.00	38.73	1.98
2127	2651	3.044809	CGTTTGGACGGACGATGAT	57.955	52.632	0.00	0.00	45.32	2.45
2139	2663	2.869192	GGACGATGATGCTTCTTCTTCC	59.131	50.000	18.59	18.59	37.32	3.46
2151	2675	4.819088	GCTTCTTCTTCCAGTCAGTCTTTT	59.181	41.667	0.00	0.00	0.00	2.27
2160	2684	0.250338	GTCAGTCTTTTGGGCTCCGT	60.250	55.000	0.00	0.00	0.00	4.69
2166	2690	1.298859	CTTTTGGGCTCCGTTCCTCG	61.299	60.000	0.00	0.00	39.52	4.63
2195	2719	5.567037	TCGTTCATTGGGATGGATTAGAT	57.433	39.130	0.00	0.00	33.93	1.98
2199	2723	6.251471	GTTCATTGGGATGGATTAGATGGAT	58.749	40.000	0.00	0.00	33.93	3.41
2205	2729	5.028802	GGGATGGATTAGATGGATCTCTGA	58.971	45.833	0.00	0.00	38.32	3.27
2214	2738	7.825331	TTAGATGGATCTCTGACGTAGATTT	57.175	36.000	1.02	0.00	38.32	2.17
2230	2754	0.615331	ATTTCTGCCAGCTCTTCGGA	59.385	50.000	0.00	0.00	0.00	4.55
2252	2776	2.176889	CGGGGAGGTTAGAGTTTCTCA	58.823	52.381	0.00	0.00	32.06	3.27
2352	2900	2.105128	CGCTGGTCCTTAGAGGCG	59.895	66.667	0.00	0.00	34.61	5.52
2422	2971	4.148825	GGGAGCGGCGACAGTGAT	62.149	66.667	12.98	0.00	0.00	3.06
2440	2989	3.419759	GCGTCGGCAATGGTCGTT	61.420	61.111	0.00	0.00	44.04	3.85
2441	2990	2.961669	GCGTCGGCAATGGTCGTTT	61.962	57.895	0.00	0.00	44.04	3.60
2442	2991	1.154488	CGTCGGCAATGGTCGTTTG	60.154	57.895	0.00	0.00	44.04	2.93
2443	2992	1.209127	GTCGGCAATGGTCGTTTGG	59.791	57.895	0.00	0.00	44.04	3.28
2444	2993	1.228003	TCGGCAATGGTCGTTTGGT	60.228	52.632	0.00	0.00	44.04	3.67
2445	2994	1.081509	CGGCAATGGTCGTTTGGTG	60.082	57.895	0.00	0.00	37.35	4.17
2446	2995	1.288752	GGCAATGGTCGTTTGGTGG	59.711	57.895	0.00	0.00	0.00	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	9.866798	TCTGTGCAATGCATGTATAAAAATTTA	57.133	25.926	12.38	0.00	41.91	1.40
61	62	1.680735	AGCATTTTGGCGTGAGTTTGA	59.319	42.857	0.00	0.00	39.27	2.69
101	125	7.447374	TGTTGACGGATTTTTCTATCAATGT	57.553	32.000	0.00	0.00	0.00	2.71
177	202	5.924254	TCAAAGATACTTACCGTCTGTTGTG	59.076	40.000	0.00	0.00	0.00	3.33
195	220	7.872138	AGTGGGAGGATGTTATAAATCAAAGA	58.128	34.615	8.77	0.00	0.00	2.52
317	345	1.134075	CGATGTGTGCTCTGCTTGC	59.866	57.895	0.00	0.00	0.00	4.01
318	346	1.134075	GCGATGTGTGCTCTGCTTG	59.866	57.895	0.00	0.00	0.00	4.01
433	461	3.187699	ATCTCGCGAGCTGCTACGG	62.188	63.158	30.97	5.49	43.27	4.02
435	463	0.248661	TTGATCTCGCGAGCTGCTAC	60.249	55.000	30.97	16.65	43.27	3.58
455	483	1.675714	GCCACCATCGACAAGTCATCA	60.676	52.381	0.72	0.00	0.00	3.07
476	504	2.545537	TCATCCAGCTCTCATGCATC	57.454	50.000	0.00	0.00	34.99	3.91
478	506	1.814248	GCATCATCCAGCTCTCATGCA	60.814	52.381	0.00	0.00	37.24	3.96
544	572	3.618351	ACATTGGCCTTGAAGATCTCAG	58.382	45.455	3.32	0.00	34.81	3.35
549	577	1.683011	CCCGACATTGGCCTTGAAGAT	60.683	52.381	3.32	0.00	0.00	2.40
587	625	5.643379	TTGATGGCCAAATAGAACTTGTC	57.357	39.130	10.96	0.00	0.00	3.18
603	641	0.652592	GTCGGCGAACTGATTGATGG	59.347	55.000	12.92	0.00	32.57	3.51
617	655	4.208632	CTCATTGGTGAGGTCGGC	57.791	61.111	0.00	0.00	46.56	5.54
651	689	2.489437	GGTTTGTACCCCTTGTTAGGCA	60.489	50.000	0.00	0.00	40.50	4.75
653	691	3.512219	TGGTTTGTACCCCTTGTTAGG	57.488	47.619	0.00	0.00	44.35	2.69
707	745	5.590530	AGTGCATCGAGACTAAGATTCTT	57.409	39.130	4.03	4.03	0.00	2.52
715	753	1.400846	GTCGGAAGTGCATCGAGACTA	59.599	52.381	0.00	0.00	33.41	2.59
734	772	2.249139	GGTCCTCCAGTCTACAGTTGT	58.751	52.381	0.00	0.00	0.00	3.32
739	777	1.938585	CCTTGGTCCTCCAGTCTACA	58.061	55.000	0.00	0.00	45.22	2.74
1380	1447	3.307480	CCCTCTTGTCGGTAATGTCCTTT	60.307	47.826	0.00	0.00	0.00	3.11
1607	1680	7.535997	TCTTCATCGATCTTTATATACGTGGG	58.464	38.462	0.00	0.00	0.00	4.61
1656	1732	5.945784	AGAGGCAGCACAATTTAACAATCTA	59.054	36.000	0.00	0.00	0.00	1.98
1667	1743	1.064166	AGGCATAAGAGGCAGCACAAT	60.064	47.619	0.00	0.00	36.37	2.71
1780	2026	6.127730	CCTTCGGGCTTCAACATTTATTTACT	60.128	38.462	0.00	0.00	0.00	2.24
1800	2048	4.764679	TCATCATTTTGTTCCACCTTCG	57.235	40.909	0.00	0.00	0.00	3.79
1889	2137	1.314730	GTTGTGGGTTGAACGACCAT	58.685	50.000	12.54	0.00	41.65	3.55
1913	2161	5.129320	ACAGGAAAGAAAAGCAATCTTTGGT	59.871	36.000	13.86	8.12	44.81	3.67
1919	2167	4.214332	ACGAGACAGGAAAGAAAAGCAATC	59.786	41.667	0.00	0.00	0.00	2.67
1920	2168	4.137543	ACGAGACAGGAAAGAAAAGCAAT	58.862	39.130	0.00	0.00	0.00	3.56
1921	2169	3.541632	ACGAGACAGGAAAGAAAAGCAA	58.458	40.909	0.00	0.00	0.00	3.91
1922	2170	3.194005	ACGAGACAGGAAAGAAAAGCA	57.806	42.857	0.00	0.00	0.00	3.91
1923	2171	4.989168	TCTTACGAGACAGGAAAGAAAAGC	59.011	41.667	0.00	0.00	0.00	3.51
1946	2467	4.749976	GAAAGGCTTTCTGATCTAGTCGT	58.250	43.478	28.27	0.00	36.73	4.34
1979	2500	3.479203	ATGGGCTCGCCATCGGAA	61.479	61.111	10.51	0.00	37.98	4.30
1984	2505	1.228367	GAATCCATGGGCTCGCCAT	60.228	57.895	13.02	0.00	37.98	4.40
1985	2506	2.192979	GAATCCATGGGCTCGCCA	59.807	61.111	13.02	0.00	37.98	5.69
2033	2554	2.774633	AAAAACCCTCCCCGCCACT	61.775	57.895	0.00	0.00	0.00	4.00
2082	2606	2.434702	CCTGCGAGGACTAAAACCCTAT	59.565	50.000	0.00	0.00	37.67	2.57
2121	2645	3.529533	ACTGGAAGAAGAAGCATCATCG	58.470	45.455	0.00	0.00	37.43	3.84
2124	2648	3.326006	ACTGACTGGAAGAAGAAGCATCA	59.674	43.478	0.00	0.00	37.43	3.07
2127	2651	2.968574	AGACTGACTGGAAGAAGAAGCA	59.031	45.455	0.00	0.00	37.43	3.91
2139	2663	1.528129	GGAGCCCAAAAGACTGACTG	58.472	55.000	0.00	0.00	0.00	3.51
2160	2684	4.083537	CCAATGAACGAATTTGACGAGGAA	60.084	41.667	0.00	0.00	34.70	3.36
2166	2690	4.157656	TCCATCCCAATGAACGAATTTGAC	59.842	41.667	0.00	0.00	34.61	3.18
2195	2719	4.202060	GCAGAAATCTACGTCAGAGATCCA	60.202	45.833	0.00	0.00	36.48	3.41
2199	2723	3.089284	TGGCAGAAATCTACGTCAGAGA	58.911	45.455	0.00	0.00	36.48	3.10
2205	2729	1.827969	AGAGCTGGCAGAAATCTACGT	59.172	47.619	20.86	0.00	0.00	3.57
2214	2738	3.292656	CTCCGAAGAGCTGGCAGA	58.707	61.111	20.86	0.00	32.13	4.26
2230	2754	0.903236	GAAACTCTAACCTCCCCGCT	59.097	55.000	0.00	0.00	0.00	5.52
2235	2759	2.561858	ACGGTGAGAAACTCTAACCTCC	59.438	50.000	8.31	0.00	44.48	4.30
2252	2776	4.532490	CCGTTGGATATGCACGGT	57.468	55.556	21.44	0.00	46.90	4.83
2352	2900	1.557443	CCGGAAGTCTTCGTGCACAC	61.557	60.000	18.64	7.33	0.00	3.82
2421	2970	3.195002	CGACCATTGCCGACGCAT	61.195	61.111	0.00	0.00	46.67	4.73
2422	2971	4.673298	ACGACCATTGCCGACGCA	62.673	61.111	0.00	0.00	45.49	5.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.