AutoCloner

Multiple sequence alignment - TraesCS5A01G366500

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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	TraesCS5A01G366500	chr5A	100.000	2311	0	0	1	2311	566394598	566392288	0.000000e+00	4268
1	TraesCS5A01G366500	chr5A	94.559	533	28	1	1779	2311	564670822	564670291	0.000000e+00	822
2	TraesCS5A01G366500	chr2A	93.478	1426	92	1	886	2311	512513206	512511782	0.000000e+00	2117
3	TraesCS5A01G366500	chr2A	90.773	867	68	5	1	865	512514050	512513194	0.000000e+00	1147
4	TraesCS5A01G366500	chr2A	93.809	533	33	0	1779	2311	206525974	206525442	0.000000e+00	802
5	TraesCS5A01G366500	chr1A	94.302	860	34	2	1453	2311	563485353	563486198	0.000000e+00	1303
6	TraesCS5A01G366500	chr1A	94.934	533	27	0	1779	2311	31553643	31553111	0.000000e+00	835
7	TraesCS5A01G366500	chr1A	85.572	402	56	2	772	1173	421799491	421799890	9.870000e-114	420
8	TraesCS5A01G366500	chrUn	97.373	533	14	0	1779	2311	147959678	147959146	0.000000e+00	907
9	TraesCS5A01G366500	chrUn	85.407	651	89	6	1	647	104823583	104824231	0.000000e+00	671
10	TraesCS5A01G366500	chr1D	95.037	544	27	0	1492	2035	475432205	475431662	0.000000e+00	856
11	TraesCS5A01G366500	chr1D	93.939	396	24	0	1045	1440	475432600	475432205	1.180000e-167	599
12	TraesCS5A01G366500	chr3A	94.371	533	28	1	1779	2311	737159497	737158967	0.000000e+00	817
13	TraesCS5A01G366500	chr3A	93.797	532	33	0	1779	2310	718583134	718583665	0.000000e+00	800
14	TraesCS5A01G366500	chr3A	90.406	271	26	0	1208	1478	401131929	401132199	7.850000e-95	357
15	TraesCS5A01G366500	chr4A	93.797	532	32	1	1779	2310	635524194	635524724	0.000000e+00	798
16	TraesCS5A01G366500	chr4A	85.561	651	87	7	1	647	332921098	332921745	0.000000e+00	675
17	TraesCS5A01G366500	chr4A	90.561	392	27	1	1206	1597	661010479	661010098	5.700000e-141	510
18	TraesCS5A01G366500	chr4A	86.118	389	54	0	781	1169	661010862	661010474	9.870000e-114	420
19	TraesCS5A01G366500	chr4D	93.810	517	30	1	1493	2007	166138514	166139030	0.000000e+00	776
20	TraesCS5A01G366500	chr4D	93.230	517	33	1	1493	2007	150649509	150648993	0.000000e+00	760
21	TraesCS5A01G366500	chr4D	92.678	519	30	6	1492	2007	289494369	289494882	0.000000e+00	741
22	TraesCS5A01G366500	chr7B	93.230	517	33	1	1493	2007	597764645	597765161	0.000000e+00	760
23	TraesCS5A01G366500	chr7B	93.037	517	34	1	1493	2007	709578317	709577801	0.000000e+00	754
24	TraesCS5A01G366500	chr5B	87.673	649	74	5	1	647	25705107	25705751	0.000000e+00	750
25	TraesCS5A01G366500	chr4B	92.678	519	34	3	1492	2007	515363184	515363701	0.000000e+00	745
26	TraesCS5A01G366500	chr6B	87.017	647	77	6	1	644	455772827	455773469	0.000000e+00	723
27	TraesCS5A01G366500	chr6B	88.601	386	34	4	1061	1436	661851457	661851842	5.820000e-126	460
28	TraesCS5A01G366500	chr3B	86.595	649	81	5	1	647	693817728	693817084	0.000000e+00	712
29	TraesCS5A01G366500	chr5D	85.692	650	87	6	1	647	395203911	395204557	0.000000e+00	680
30	TraesCS5A01G366500	chr6A	85.362	649	91	4	1	647	47996512	47995866	0.000000e+00	669
31	TraesCS5A01G366500	chr6A	85.362	649	86	8	1	647	615786075	615786716	0.000000e+00	664
32	TraesCS5A01G366500	chr6A	90.306	392	31	5	1052	1436	585485792	585486183	7.370000e-140	507
33	TraesCS5A01G366500	chr2D	89.238	446	48	0	888	1333	512459078	512459523	2.010000e-155	558
34	TraesCS5A01G366500	chr2D	91.538	390	32	1	1208	1597	58561938	58561550	9.400000e-149	536
35	TraesCS5A01G366500	chr2D	82.353	136	15	8	666	798	291609532	291609403	2.430000e-20	110
36	TraesCS5A01G366500	chr6D	88.918	388	34	8	1048	1427	437281612	437281998	9.670000e-129	470
37	TraesCS5A01G366500	chr7D	82.639	144	15	8	659	798	142214819	142214682	4.030000e-23	119

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	TraesCS5A01G366500	chr5A	566392288	566394598	2310	True	4268.0	4268	100.0000	1	2311	1	chr5A.!!$R2	2310
1	TraesCS5A01G366500	chr5A	564670291	564670822	531	True	822.0	822	94.5590	1779	2311	1	chr5A.!!$R1	532
2	TraesCS5A01G366500	chr2A	512511782	512514050	2268	True	1632.0	2117	92.1255	1	2311	2	chr2A.!!$R2	2310
3	TraesCS5A01G366500	chr2A	206525442	206525974	532	True	802.0	802	93.8090	1779	2311	1	chr2A.!!$R1	532
4	TraesCS5A01G366500	chr1A	563485353	563486198	845	False	1303.0	1303	94.3020	1453	2311	1	chr1A.!!$F2	858
5	TraesCS5A01G366500	chr1A	31553111	31553643	532	True	835.0	835	94.9340	1779	2311	1	chr1A.!!$R1	532
6	TraesCS5A01G366500	chrUn	147959146	147959678	532	True	907.0	907	97.3730	1779	2311	1	chrUn.!!$R1	532
7	TraesCS5A01G366500	chrUn	104823583	104824231	648	False	671.0	671	85.4070	1	647	1	chrUn.!!$F1	646
8	TraesCS5A01G366500	chr1D	475431662	475432600	938	True	727.5	856	94.4880	1045	2035	2	chr1D.!!$R1	990
9	TraesCS5A01G366500	chr3A	737158967	737159497	530	True	817.0	817	94.3710	1779	2311	1	chr3A.!!$R1	532
10	TraesCS5A01G366500	chr3A	718583134	718583665	531	False	800.0	800	93.7970	1779	2310	1	chr3A.!!$F2	531
11	TraesCS5A01G366500	chr4A	635524194	635524724	530	False	798.0	798	93.7970	1779	2310	1	chr4A.!!$F2	531
12	TraesCS5A01G366500	chr4A	332921098	332921745	647	False	675.0	675	85.5610	1	647	1	chr4A.!!$F1	646
13	TraesCS5A01G366500	chr4A	661010098	661010862	764	True	465.0	510	88.3395	781	1597	2	chr4A.!!$R1	816
14	TraesCS5A01G366500	chr4D	166138514	166139030	516	False	776.0	776	93.8100	1493	2007	1	chr4D.!!$F1	514
15	TraesCS5A01G366500	chr4D	150648993	150649509	516	True	760.0	760	93.2300	1493	2007	1	chr4D.!!$R1	514
16	TraesCS5A01G366500	chr4D	289494369	289494882	513	False	741.0	741	92.6780	1492	2007	1	chr4D.!!$F2	515
17	TraesCS5A01G366500	chr7B	597764645	597765161	516	False	760.0	760	93.2300	1493	2007	1	chr7B.!!$F1	514
18	TraesCS5A01G366500	chr7B	709577801	709578317	516	True	754.0	754	93.0370	1493	2007	1	chr7B.!!$R1	514
19	TraesCS5A01G366500	chr5B	25705107	25705751	644	False	750.0	750	87.6730	1	647	1	chr5B.!!$F1	646
20	TraesCS5A01G366500	chr4B	515363184	515363701	517	False	745.0	745	92.6780	1492	2007	1	chr4B.!!$F1	515
21	TraesCS5A01G366500	chr6B	455772827	455773469	642	False	723.0	723	87.0170	1	644	1	chr6B.!!$F1	643
22	TraesCS5A01G366500	chr3B	693817084	693817728	644	True	712.0	712	86.5950	1	647	1	chr3B.!!$R1	646
23	TraesCS5A01G366500	chr5D	395203911	395204557	646	False	680.0	680	85.6920	1	647	1	chr5D.!!$F1	646
24	TraesCS5A01G366500	chr6A	47995866	47996512	646	True	669.0	669	85.3620	1	647	1	chr6A.!!$R1	646
25	TraesCS5A01G366500	chr6A	615786075	615786716	641	False	664.0	664	85.3620	1	647	1	chr6A.!!$F2	646

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
962	967	0.039617	GAGATCTACTGCAGCGCGAT	60.04	55.0	15.27	12.92	0.0	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2151	2159	0.601311	AGACGCAGGAAGCAAGACAC	60.601	55.0	0.0	0.0	46.13	3.67	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
37	38	6.845758	AGATTGATCATTTGGCTTGAAAGA	57.154	33.333	0.00	0.00	0.00	2.52
43	44	4.885413	TCATTTGGCTTGAAAGACATTGG	58.115	39.130	0.00	0.00	45.07	3.16
76	77	4.220821	AGGATAGCTCGTTTCTGAGAACAA	59.779	41.667	0.00	0.00	38.28	2.83
77	78	4.929808	GGATAGCTCGTTTCTGAGAACAAA	59.070	41.667	0.00	0.00	38.28	2.83
141	143	5.457487	CCTGGGAACTTGGCCACATATAATA	60.457	44.000	3.88	0.00	0.00	0.98
250	253	4.504858	CGTTCCTAGCTAGTGGTTGAATT	58.495	43.478	19.31	0.00	0.00	2.17
418	422	8.773033	AATGGCCAAAATAGATAGAAAGATGT	57.227	30.769	10.96	0.00	0.00	3.06
446	450	6.395426	TGCATTAAAGTTGATGATCATCCC	57.605	37.500	28.61	20.04	37.02	3.85
604	609	4.356561	TCCCCCGGATCACCCCAA	62.357	66.667	0.73	0.00	0.00	4.12
607	612	3.395702	CCCGGATCACCCCAACGA	61.396	66.667	0.73	0.00	0.00	3.85
616	621	0.173255	CACCCCAACGAATGCAATCC	59.827	55.000	0.00	0.00	0.00	3.01
698	703	0.829990	CTCTCCTCCCTTCCTTCTGC	59.170	60.000	0.00	0.00	0.00	4.26
702	707	3.689002	CTCCCTTCCTTCTGCCGCC	62.689	68.421	0.00	0.00	0.00	6.13
704	709	2.124942	CCTTCCTTCTGCCGCCTC	60.125	66.667	0.00	0.00	0.00	4.70
714	719	4.021925	GCCGCCTCCCACACTCTT	62.022	66.667	0.00	0.00	0.00	2.85
722	727	2.534990	CTCCCACACTCTTCCTCTCTT	58.465	52.381	0.00	0.00	0.00	2.85
725	730	1.552792	CCACACTCTTCCTCTCTTCCC	59.447	57.143	0.00	0.00	0.00	3.97
763	768	3.584848	CCTATCCCTCATCCAAACCCTAG	59.415	52.174	0.00	0.00	0.00	3.02
769	774	0.183731	CATCCAAACCCTAGCCTCCC	59.816	60.000	0.00	0.00	0.00	4.30
770	775	0.253630	ATCCAAACCCTAGCCTCCCA	60.254	55.000	0.00	0.00	0.00	4.37
798	803	2.666098	GCGGCACCCTCTTTCCCTA	61.666	63.158	0.00	0.00	0.00	3.53
856	861	3.506096	CGAGGACGTAGCAGCCGA	61.506	66.667	0.00	0.00	34.56	5.54
953	958	1.018148	AGTGACGCGGAGATCTACTG	58.982	55.000	12.47	0.00	0.00	2.74
955	960	1.029947	TGACGCGGAGATCTACTGCA	61.030	55.000	12.47	3.07	39.31	4.41
962	967	0.039617	GAGATCTACTGCAGCGCGAT	60.040	55.000	15.27	12.92	0.00	4.58
1087	1092	1.753078	CCTCACCTCCGTCGGATCA	60.753	63.158	15.81	0.00	0.00	2.92
1235	1240	0.892358	ACGCCGACTACAAGGACTCA	60.892	55.000	0.00	0.00	0.00	3.41
1239	1244	1.162698	CGACTACAAGGACTCACGGA	58.837	55.000	0.00	0.00	0.00	4.69
1432	1437	1.301795	TGTGGTTGCGCATCCGTTA	60.302	52.632	27.68	16.03	36.67	3.18
1450	1455	5.929992	TCCGTTATGCTACTAATAATGGTGC	59.070	40.000	12.06	0.00	43.10	5.01
1471	1476	3.681594	GCGAGGGGTTGTCAGATCAAATA	60.682	47.826	0.00	0.00	0.00	1.40
1480	1485	6.599244	GGTTGTCAGATCAAATATGTTCTCCA	59.401	38.462	0.00	0.00	34.17	3.86
1701	1708	1.328680	CAAGGCTATGTACGCTGCTTG	59.671	52.381	0.00	0.00	0.00	4.01
1747	1754	8.617491	TGATGGGATTAGGAATATGATCATGTT	58.383	33.333	18.72	17.63	0.00	2.71
1777	1785	5.082425	AGAATTGGATTTCTCTGGCTGTTT	58.918	37.500	0.00	0.00	29.99	2.83
2166	2188	1.534595	CTTCTGTGTCTTGCTTCCTGC	59.465	52.381	0.00	0.00	43.25	4.85
2237	2259	7.843490	TCTTTTGCTTCCTGTATGTATGTAC	57.157	36.000	0.00	0.00	0.00	2.90
2244	2266	6.238566	GCTTCCTGTATGTATGTACGTGTCTA	60.239	42.308	0.00	0.00	0.00	2.59
2246	2268	7.628769	TCCTGTATGTATGTACGTGTCTAAA	57.371	36.000	0.00	0.00	0.00	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	2.630889	TCCTCTCTGGAGACCAATGT	57.369	50.000	0.00	0.00	41.86	2.71
50	51	3.880490	TCTCAGAAACGAGCTATCCTCTC	59.120	47.826	0.00	0.00	38.49	3.20
54	55	4.111375	TGTTCTCAGAAACGAGCTATCC	57.889	45.455	0.00	0.00	32.75	2.59
103	105	8.371699	CCAAGTTCCCAGGAAAAATAATAAACA	58.628	33.333	0.00	0.00	35.75	2.83
141	143	4.116747	TGAAAAACCTTCGCATTGTGTT	57.883	36.364	0.00	0.00	0.00	3.32
199	202	1.003331	CGCAGTTTTGACCGCACTTTA	60.003	47.619	0.00	0.00	0.00	1.85
203	206	2.051345	CCGCAGTTTTGACCGCAC	60.051	61.111	0.00	0.00	0.00	5.34
250	253	6.313411	CAGAGATGCACCAAAAGTTTTTCAAA	59.687	34.615	0.00	0.00	0.00	2.69
417	421	8.692110	TGATCATCAACTTTAATGCATTTCAC	57.308	30.769	18.75	0.00	0.00	3.18
418	422	9.524106	GATGATCATCAACTTTAATGCATTTCA	57.476	29.630	27.30	10.60	37.74	2.69
446	450	9.619316	TTTCACTCAAATTATACCACATTTTCG	57.381	29.630	0.00	0.00	0.00	3.46
570	575	2.119495	GGGAGAGGTCCTGATTGCTTA	58.881	52.381	0.00	0.00	43.36	3.09
573	578	1.529309	GGGGAGAGGTCCTGATTGC	59.471	63.158	0.00	0.00	43.36	3.56
604	609	2.173669	CGGCTCGGATTGCATTCGT	61.174	57.895	2.69	0.00	0.00	3.85
607	612	1.819632	GGACGGCTCGGATTGCATT	60.820	57.895	0.00	0.00	0.00	3.56
639	644	1.000955	GGAAGCAAGGAGAGACGTTGA	59.999	52.381	0.00	0.00	44.13	3.18
698	703	2.266055	GAAGAGTGTGGGAGGCGG	59.734	66.667	0.00	0.00	0.00	6.13
702	707	2.230130	AGAGAGGAAGAGTGTGGGAG	57.770	55.000	0.00	0.00	0.00	4.30
704	709	1.552792	GGAAGAGAGGAAGAGTGTGGG	59.447	57.143	0.00	0.00	0.00	4.61
714	719	0.927029	TCTGGATCGGGAAGAGAGGA	59.073	55.000	0.00	0.00	0.00	3.71
779	784	4.035102	GGGAAAGAGGGTGCCGCT	62.035	66.667	0.00	0.00	34.48	5.52
785	790	1.306226	AGCGCTAGGGAAAGAGGGT	60.306	57.895	8.99	0.00	0.00	4.34
791	796	0.955428	CAAGTGCAGCGCTAGGGAAA	60.955	55.000	10.99	0.00	0.00	3.13
879	884	4.083862	GAGGGAGCCGACCACACC	62.084	72.222	0.00	0.00	0.00	4.16
880	885	4.436998	CGAGGGAGCCGACCACAC	62.437	72.222	0.00	0.00	0.00	3.82
936	941	1.029947	TGCAGTAGATCTCCGCGTCA	61.030	55.000	4.92	0.00	0.00	4.35
942	947	1.659954	CGCGCTGCAGTAGATCTCC	60.660	63.158	16.64	0.00	0.00	3.71
985	990	1.676635	GCATGTGGAAGCTGCAGGA	60.677	57.895	17.12	0.00	35.96	3.86
1131	1136	4.096003	CCCGTCCCGATGCACCTT	62.096	66.667	0.00	0.00	0.00	3.50
1194	1199	2.033757	CTGCAGCAACAGCTCCCT	59.966	61.111	0.00	0.00	36.19	4.20
1216	1221	0.892358	TGAGTCCTTGTAGTCGGCGT	60.892	55.000	6.85	0.00	0.00	5.68
1225	1230	2.571216	CCGGTCCGTGAGTCCTTGT	61.571	63.158	11.06	0.00	0.00	3.16
1239	1244	3.717294	GATGTCCCACTGGCCGGT	61.717	66.667	12.85	12.85	0.00	5.28
1274	1279	2.123812	GAGGAGTCCCCGACGGAT	60.124	66.667	17.49	0.00	44.66	4.18
1300	1305	3.268965	GAGCTCACTCACCGTGCGA	62.269	63.158	9.40	0.00	43.46	5.10
1432	1437	4.563580	CCCTCGCACCATTATTAGTAGCAT	60.564	45.833	0.00	0.00	0.00	3.79
1450	1455	2.472695	TTTGATCTGACAACCCCTCG	57.527	50.000	0.00	0.00	0.00	4.63
1471	1476	3.686241	CGATGTGTGACAATGGAGAACAT	59.314	43.478	0.00	0.00	43.07	2.71
1480	1485	0.881118	GCAACCCGATGTGTGACAAT	59.119	50.000	0.00	0.00	0.00	2.71
1519	1524	3.054287	AGGAGTAGAGACAACAGATCGGA	60.054	47.826	0.00	0.00	0.00	4.55
1598	1605	1.134491	ACTAATCAGCCCCGTTGCTAC	60.134	52.381	0.00	0.00	40.32	3.58
1684	1691	0.179084	TCCAAGCAGCGTACATAGCC	60.179	55.000	0.00	0.00	34.64	3.93
1701	1708	4.855340	TCAGGATTGTACAGGGAAATTCC	58.145	43.478	2.79	2.79	35.23	3.01
1747	1754	6.418101	CCAGAGAAATCCAATTCTACAGGAA	58.582	40.000	0.00	0.00	39.70	3.36
2151	2159	0.601311	AGACGCAGGAAGCAAGACAC	60.601	55.000	0.00	0.00	46.13	3.67
2237	2259	2.288030	ACCACCTTCGTCTTTAGACACG	60.288	50.000	10.27	0.00	44.99	4.49
2244	2266	3.877508	CTGAAGAAACCACCTTCGTCTTT	59.122	43.478	0.00	0.00	42.07	2.52
2246	2268	2.698797	TCTGAAGAAACCACCTTCGTCT	59.301	45.455	0.00	0.00	42.07	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.