AutoCloner

Multiple sequence alignment - TraesCS1B01G169000

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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	TraesCS1B01G169000	chr1B	100.000	2432	0	0	1	2432	300316739	300319170	0.000000e+00	4492
1	TraesCS1B01G169000	chr1B	86.330	1485	159	34	975	2429	234980206	234978736	0.000000e+00	1578
2	TraesCS1B01G169000	chr3B	85.781	1498	157	27	973	2431	355307976	355309456	0.000000e+00	1535
3	TraesCS1B01G169000	chr3B	87.513	929	94	13	1490	2414	364347869	364346959	0.000000e+00	1053
4	TraesCS1B01G169000	chr3B	91.935	248	20	0	731	978	386411439	386411686	4.980000e-92	348
5	TraesCS1B01G169000	chr2D	84.953	1482	175	31	972	2426	175863176	175861716	0.000000e+00	1458
6	TraesCS1B01G169000	chr4B	84.719	1479	189	24	973	2426	350506574	350508040	0.000000e+00	1445
7	TraesCS1B01G169000	chr4B	88.889	495	55	0	973	1467	147693791	147693297	5.750000e-171	610
8	TraesCS1B01G169000	chr4B	86.847	517	64	2	973	1487	129615030	129615544	2.100000e-160	575
9	TraesCS1B01G169000	chr5B	84.273	1507	169	29	963	2432	177714030	177712555	0.000000e+00	1408
10	TraesCS1B01G169000	chr5B	85.635	1086	124	20	1360	2426	210127242	210126170	0.000000e+00	1112
11	TraesCS1B01G169000	chr5B	87.182	983	105	17	1	977	670465404	670464437	0.000000e+00	1098
12	TraesCS1B01G169000	chr5B	87.117	978	107	10	3	977	670436442	670435481	0.000000e+00	1090
13	TraesCS1B01G169000	chr5B	84.526	685	81	13	973	1635	525590038	525590719	0.000000e+00	654
14	TraesCS1B01G169000	chr5B	88.462	520	58	2	973	1490	178936684	178937203	5.710000e-176	627
15	TraesCS1B01G169000	chr5B	88.417	518	60	0	973	1490	178916985	178917502	2.050000e-175	625
16	TraesCS1B01G169000	chr5B	87.500	520	60	3	973	1490	177677910	177677394	1.610000e-166	595
17	TraesCS1B01G169000	chr6B	90.381	946	80	8	1487	2431	382063946	382064881	0.000000e+00	1232
18	TraesCS1B01G169000	chr6B	86.660	982	115	11	1	977	465665158	465666128	0.000000e+00	1074
19	TraesCS1B01G169000	chr5D	88.355	979	95	12	2	977	305239555	305238593	0.000000e+00	1158
20	TraesCS1B01G169000	chr7D	88.098	983	99	8	2	978	412014399	412013429	0.000000e+00	1151
21	TraesCS1B01G169000	chrUn	86.952	981	109	10	1	977	175703080	175702115	0.000000e+00	1085
22	TraesCS1B01G169000	chrUn	86.877	983	108	17	1	977	175732324	175731357	0.000000e+00	1081
23	TraesCS1B01G169000	chrUn	89.382	518	55	0	973	1490	85410113	85410630	0.000000e+00	652
24	TraesCS1B01G169000	chr2B	89.130	874	80	11	1559	2426	397817820	397816956	0.000000e+00	1074
25	TraesCS1B01G169000	chr5A	89.975	798	72	6	11	806	139933065	139933856	0.000000e+00	1024
26	TraesCS1B01G169000	chr3D	86.268	954	115	6	27	978	26160502	26159563	0.000000e+00	1022
27	TraesCS1B01G169000	chr7B	86.349	945	112	15	1490	2426	301631486	301632421	0.000000e+00	1014
28	TraesCS1B01G169000	chr6D	85.823	924	116	11	1490	2408	108227165	108228078	0.000000e+00	966

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	TraesCS1B01G169000	chr1B	300316739	300319170	2431	False	4492	4492	100.000	1	2432	1	chr1B.!!$F1	2431
1	TraesCS1B01G169000	chr1B	234978736	234980206	1470	True	1578	1578	86.330	975	2429	1	chr1B.!!$R1	1454
2	TraesCS1B01G169000	chr3B	355307976	355309456	1480	False	1535	1535	85.781	973	2431	1	chr3B.!!$F1	1458
3	TraesCS1B01G169000	chr3B	364346959	364347869	910	True	1053	1053	87.513	1490	2414	1	chr3B.!!$R1	924
4	TraesCS1B01G169000	chr2D	175861716	175863176	1460	True	1458	1458	84.953	972	2426	1	chr2D.!!$R1	1454
5	TraesCS1B01G169000	chr4B	350506574	350508040	1466	False	1445	1445	84.719	973	2426	1	chr4B.!!$F2	1453
6	TraesCS1B01G169000	chr4B	129615030	129615544	514	False	575	575	86.847	973	1487	1	chr4B.!!$F1	514
7	TraesCS1B01G169000	chr5B	177712555	177714030	1475	True	1408	1408	84.273	963	2432	1	chr5B.!!$R2	1469
8	TraesCS1B01G169000	chr5B	210126170	210127242	1072	True	1112	1112	85.635	1360	2426	1	chr5B.!!$R3	1066
9	TraesCS1B01G169000	chr5B	670464437	670465404	967	True	1098	1098	87.182	1	977	1	chr5B.!!$R5	976
10	TraesCS1B01G169000	chr5B	670435481	670436442	961	True	1090	1090	87.117	3	977	1	chr5B.!!$R4	974
11	TraesCS1B01G169000	chr5B	525590038	525590719	681	False	654	654	84.526	973	1635	1	chr5B.!!$F3	662
12	TraesCS1B01G169000	chr5B	178936684	178937203	519	False	627	627	88.462	973	1490	1	chr5B.!!$F2	517
13	TraesCS1B01G169000	chr5B	178916985	178917502	517	False	625	625	88.417	973	1490	1	chr5B.!!$F1	517
14	TraesCS1B01G169000	chr5B	177677394	177677910	516	True	595	595	87.500	973	1490	1	chr5B.!!$R1	517
15	TraesCS1B01G169000	chr6B	382063946	382064881	935	False	1232	1232	90.381	1487	2431	1	chr6B.!!$F1	944
16	TraesCS1B01G169000	chr6B	465665158	465666128	970	False	1074	1074	86.660	1	977	1	chr6B.!!$F2	976
17	TraesCS1B01G169000	chr5D	305238593	305239555	962	True	1158	1158	88.355	2	977	1	chr5D.!!$R1	975
18	TraesCS1B01G169000	chr7D	412013429	412014399	970	True	1151	1151	88.098	2	978	1	chr7D.!!$R1	976
19	TraesCS1B01G169000	chrUn	175702115	175703080	965	True	1085	1085	86.952	1	977	1	chrUn.!!$R1	976
20	TraesCS1B01G169000	chrUn	175731357	175732324	967	True	1081	1081	86.877	1	977	1	chrUn.!!$R2	976
21	TraesCS1B01G169000	chrUn	85410113	85410630	517	False	652	652	89.382	973	1490	1	chrUn.!!$F1	517
22	TraesCS1B01G169000	chr2B	397816956	397817820	864	True	1074	1074	89.130	1559	2426	1	chr2B.!!$R1	867
23	TraesCS1B01G169000	chr5A	139933065	139933856	791	False	1024	1024	89.975	11	806	1	chr5A.!!$F1	795
24	TraesCS1B01G169000	chr3D	26159563	26160502	939	True	1022	1022	86.268	27	978	1	chr3D.!!$R1	951
25	TraesCS1B01G169000	chr7B	301631486	301632421	935	False	1014	1014	86.349	1490	2426	1	chr7B.!!$F1	936
26	TraesCS1B01G169000	chr6D	108227165	108228078	913	False	966	966	85.823	1490	2408	1	chr6D.!!$F1	918

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
355	373	0.316204	CCGACAAGTACTCAACCGGT	59.684	55.0	0.0	0.0	0.0	5.28	F
733	753	0.912486	AGAAGGGAAGCAACGCCTAT	59.088	50.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1198	1219	0.313043	TCGGTGTCCTTGTCGTCTTC	59.687	55.0	0.00	0.0	0.0	2.87	R
1814	1925	0.322546	GGTCTTGAATTCGCCTGGGT	60.323	55.0	0.04	0.0	0.0	4.51	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
44	50	4.360405	CTTTCCCCCACCCACCGG	62.360	72.222	0.00	0.00	0.00	5.28
70	76	2.202824	CGCCGCCTACGATTCCAA	60.203	61.111	0.00	0.00	43.93	3.53
80	86	4.038883	GCCTACGATTCCAACCATACTAGT	59.961	45.833	0.00	0.00	0.00	2.57
119	137	2.434884	CCGCCACACGCTTGAGAT	60.435	61.111	0.00	0.00	41.76	2.75
120	138	2.034879	CCGCCACACGCTTGAGATT	61.035	57.895	0.00	0.00	41.76	2.40
121	139	1.421485	CGCCACACGCTTGAGATTC	59.579	57.895	0.00	0.00	34.21	2.52
122	140	1.291184	CGCCACACGCTTGAGATTCA	61.291	55.000	0.00	0.00	34.21	2.57
210	228	4.520846	CGCGGCCGTCAGATTTGC	62.521	66.667	28.70	5.06	0.00	3.68
218	236	0.871722	CGTCAGATTTGCCGTTTCCA	59.128	50.000	0.00	0.00	0.00	3.53
339	357	3.369400	CCGCCATTGGTTTGCCGA	61.369	61.111	4.26	0.00	37.67	5.54
350	368	2.215196	GGTTTGCCGACAAGTACTCAA	58.785	47.619	0.00	0.00	37.04	3.02
355	373	0.316204	CCGACAAGTACTCAACCGGT	59.684	55.000	0.00	0.00	0.00	5.28
464	482	2.781595	CTAGCACGCCGAAACACCCT	62.782	60.000	0.00	0.00	0.00	4.34
491	510	6.166984	TGGGTATTCTTCAAATGCAAAACA	57.833	33.333	0.00	0.00	0.00	2.83
520	539	5.408299	GGTATGTTCTTGTTTTCATTTGGCC	59.592	40.000	0.00	0.00	0.00	5.36
525	544	5.096443	TCTTGTTTTCATTTGGCCTTGTT	57.904	34.783	3.32	0.00	0.00	2.83
600	619	5.334724	AGATGGATGCTCATTTTGGTTTC	57.665	39.130	0.00	0.00	0.00	2.78
601	620	5.021458	AGATGGATGCTCATTTTGGTTTCT	58.979	37.500	0.00	0.00	0.00	2.52
602	621	6.189859	AGATGGATGCTCATTTTGGTTTCTA	58.810	36.000	0.00	0.00	0.00	2.10
604	623	4.706476	TGGATGCTCATTTTGGTTTCTAGG	59.294	41.667	0.00	0.00	0.00	3.02
662	682	6.477033	ACTTAATAGATGTTCATGCACTCGTC	59.523	38.462	0.00	0.00	0.00	4.20
683	703	4.446051	GTCGCTAGAATTGAGGCTAATGAC	59.554	45.833	0.00	0.00	0.00	3.06
687	707	2.159099	AGAATTGAGGCTAATGACGCGA	60.159	45.455	15.93	0.00	0.00	5.87
729	749	1.809684	AACTAGAAGGGAAGCAACGC	58.190	50.000	0.00	0.00	0.00	4.84
733	753	0.912486	AGAAGGGAAGCAACGCCTAT	59.088	50.000	0.00	0.00	0.00	2.57
747	767	6.037610	AGCAACGCCTATTTCTTTAGAATCAG	59.962	38.462	0.00	0.00	33.54	2.90
811	831	4.978083	ACAATGAATGCATGGAGAAGAC	57.022	40.909	0.00	0.00	34.26	3.01
1136	1157	3.702045	GAGACATGGCTACTACCTCAAGT	59.298	47.826	0.00	0.00	0.00	3.16
1144	1165	4.504340	GGCTACTACCTCAAGTGGAAACAA	60.504	45.833	0.00	0.00	46.06	2.83
1198	1219	3.209410	GGAACAGCTACATCCAATGGAG	58.791	50.000	8.40	2.69	44.35	3.86
1207	1230	2.567169	ACATCCAATGGAGAAGACGACA	59.433	45.455	8.40	0.00	34.05	4.35
1437	1467	1.591703	CAACACCTCCTAGCGAGCA	59.408	57.895	0.00	0.00	37.27	4.26
1470	1500	2.260434	CCGAACGACCGACACCAT	59.740	61.111	0.00	0.00	0.00	3.55
1473	1503	0.457853	CGAACGACCGACACCATCAT	60.458	55.000	0.00	0.00	0.00	2.45
1474	1504	0.999406	GAACGACCGACACCATCATG	59.001	55.000	0.00	0.00	0.00	3.07
1488	1571	0.106569	ATCATGCCCGAGCCAAATCA	60.107	50.000	0.00	0.00	38.69	2.57
1549	1639	8.169977	TCAACAGAATGAAAATAGCAGAAGTT	57.830	30.769	0.00	0.00	39.69	2.66
1567	1657	0.033781	TTTGAACCCTACCGGACGTG	59.966	55.000	9.46	0.00	34.64	4.49
1629	1721	3.359523	CGCTGCCTGTGTGTGCAT	61.360	61.111	0.00	0.00	36.79	3.96
1637	1729	2.412870	CCTGTGTGTGCATAGTTTCGA	58.587	47.619	0.00	0.00	32.76	3.71
1639	1731	3.317150	CTGTGTGTGCATAGTTTCGAGA	58.683	45.455	0.00	0.00	0.00	4.04
1661	1753	0.463833	GAGGCCCATGTACCCTTTCG	60.464	60.000	0.00	0.00	0.00	3.46
1712	1814	0.553862	AGACCTCCTCCTCCTCCTCA	60.554	60.000	0.00	0.00	0.00	3.86
1755	1863	9.815306	TGGTTTAGCTCATATTAGAGATAGAGT	57.185	33.333	0.00	0.00	37.74	3.24
1776	1886	3.719268	TGTGCTCATCCACTTGGTTAT	57.281	42.857	0.00	0.00	36.68	1.89
1823	1934	0.537188	GAAGAAGATCACCCAGGCGA	59.463	55.000	0.00	0.00	0.00	5.54
1860	1972	2.773458	GGAAGACCCCTCAAGACCA	58.227	57.895	0.00	0.00	0.00	4.02
1962	2083	3.747193	CACATGTGTAACCGAATCTTGC	58.253	45.455	18.03	0.00	34.36	4.01
1963	2084	2.747446	ACATGTGTAACCGAATCTTGCC	59.253	45.455	0.00	0.00	34.36	4.52
2029	2160	3.711704	GTGTTCTTCATAGGATCCCCTCA	59.288	47.826	8.55	0.00	43.14	3.86
2060	2192	2.890311	AGATCGAGCATCTAGGGTTCTG	59.110	50.000	2.38	0.00	40.41	3.02
2120	2254	2.062773	TTTGGAGCCCCTACCCTTTA	57.937	50.000	0.00	0.00	0.00	1.85
2170	2304	2.569404	CCCCAATTTCGAAAATCCCCAA	59.431	45.455	15.66	0.00	0.00	4.12
2384	2522	3.674050	ATCGCCCAGGTACCGGACT	62.674	63.158	20.26	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	76	2.158711	TGATCCCGACGACTAGTATGGT	60.159	50.000	0.00	0.00	0.00	3.55
112	130	3.866651	ACAATCTCGGGTGAATCTCAAG	58.133	45.455	0.00	0.00	0.00	3.02
113	131	3.369471	GGACAATCTCGGGTGAATCTCAA	60.369	47.826	0.00	0.00	0.00	3.02
114	132	2.168521	GGACAATCTCGGGTGAATCTCA	59.831	50.000	0.00	0.00	0.00	3.27
115	133	2.432510	AGGACAATCTCGGGTGAATCTC	59.567	50.000	0.00	0.00	0.00	2.75
116	134	2.432510	GAGGACAATCTCGGGTGAATCT	59.567	50.000	0.00	0.00	0.00	2.40
117	135	2.483889	GGAGGACAATCTCGGGTGAATC	60.484	54.545	0.00	0.00	34.74	2.52
118	136	1.486726	GGAGGACAATCTCGGGTGAAT	59.513	52.381	0.00	0.00	34.74	2.57
119	137	0.902531	GGAGGACAATCTCGGGTGAA	59.097	55.000	0.00	0.00	34.74	3.18
120	138	0.252057	TGGAGGACAATCTCGGGTGA	60.252	55.000	0.00	0.00	34.74	4.02
121	139	0.108138	GTGGAGGACAATCTCGGGTG	60.108	60.000	0.00	0.00	34.74	4.61
122	140	1.265454	GGTGGAGGACAATCTCGGGT	61.265	60.000	0.00	0.00	34.74	5.28
188	206	3.989698	ATCTGACGGCCGCGACAAG	62.990	63.158	28.58	15.59	0.00	3.16
210	228	2.046314	ATCGGTGGCTGGAAACGG	60.046	61.111	0.00	0.00	40.79	4.44
327	345	2.812011	GAGTACTTGTCGGCAAACCAAT	59.188	45.455	3.10	0.00	33.73	3.16
339	357	1.000938	GACGACCGGTTGAGTACTTGT	60.001	52.381	29.00	2.56	0.00	3.16
432	450	2.616960	CGTGCTAGATGTTAGCCACAA	58.383	47.619	0.00	0.00	39.50	3.33
435	453	0.179084	GGCGTGCTAGATGTTAGCCA	60.179	55.000	0.00	0.00	42.37	4.75
464	482	4.608269	TGCATTTGAAGAATACCCATCCA	58.392	39.130	0.00	0.00	0.00	3.41
491	510	4.208746	TGAAAACAAGAACATACCCCGTT	58.791	39.130	0.00	0.00	0.00	4.44
652	672	2.159240	TCAATTCTAGCGACGAGTGCAT	60.159	45.455	0.00	0.00	33.85	3.96
662	682	3.426859	CGTCATTAGCCTCAATTCTAGCG	59.573	47.826	0.00	0.00	0.00	4.26
747	767	7.317842	TCTTGCATTCATCATTCTTCTTCTC	57.682	36.000	0.00	0.00	0.00	2.87
761	781	5.011586	TGTGGATTCTTGATCTTGCATTCA	58.988	37.500	0.00	0.00	35.02	2.57
873	893	6.225981	AGCAAGACCAAAGAAAACAAGAAT	57.774	33.333	0.00	0.00	0.00	2.40
918	939	5.995282	TCAAGGGCATTGGATACGTAATAAG	59.005	40.000	12.41	0.00	39.54	1.73
925	946	2.917933	TCTTCAAGGGCATTGGATACG	58.082	47.619	12.41	0.00	39.54	3.06
1136	1157	5.569355	ACCTGATCACACATATTGTTTCCA	58.431	37.500	0.00	0.00	35.67	3.53
1144	1165	5.070981	CCTCCAAGTACCTGATCACACATAT	59.929	44.000	0.00	0.00	0.00	1.78
1198	1219	0.313043	TCGGTGTCCTTGTCGTCTTC	59.687	55.000	0.00	0.00	0.00	2.87
1207	1230	1.006758	TCCCTCATACTCGGTGTCCTT	59.993	52.381	0.00	0.00	0.00	3.36
1331	1361	2.184322	GCTTCAGGCGTCGGATGA	59.816	61.111	7.22	0.00	0.00	2.92
1408	1438	2.110213	GGTGTTGCCAGTCGTCCA	59.890	61.111	0.00	0.00	37.17	4.02
1456	1486	1.019278	GCATGATGGTGTCGGTCGTT	61.019	55.000	0.00	0.00	0.00	3.85
1470	1500	0.749091	CTGATTTGGCTCGGGCATGA	60.749	55.000	10.74	0.00	38.08	3.07
1473	1503	2.045045	CCTGATTTGGCTCGGGCA	60.045	61.111	10.74	2.21	40.87	5.36
1474	1504	2.115291	GTCCTGATTTGGCTCGGGC	61.115	63.158	0.00	0.00	40.88	6.13
1488	1571	1.753463	GGAGATGGTCGGTCGTCCT	60.753	63.158	7.98	0.00	0.00	3.85
1549	1639	1.667151	CACGTCCGGTAGGGTTCAA	59.333	57.895	0.00	0.00	38.33	2.69
1629	1721	1.318158	GGGCCTCGGTCTCGAAACTA	61.318	60.000	0.84	0.00	45.47	2.24
1637	1729	2.064581	GGTACATGGGCCTCGGTCT	61.065	63.158	4.53	0.00	0.00	3.85
1639	1731	3.087906	GGGTACATGGGCCTCGGT	61.088	66.667	4.53	2.56	0.00	4.69
1661	1753	1.141665	GTGCAAATGGGGGCGAATC	59.858	57.895	0.00	0.00	0.00	2.52
1712	1814	6.771267	GCTAAACCATTGCTAACCCTAACTAT	59.229	38.462	0.00	0.00	0.00	2.12
1755	1863	2.363306	AACCAAGTGGATGAGCACAA	57.637	45.000	3.83	0.00	38.94	3.33
1757	1865	4.702131	AGAAATAACCAAGTGGATGAGCAC	59.298	41.667	3.83	0.00	38.94	4.40
1776	1886	3.306088	GGTCGTGAACTCTGATGGAGAAA	60.306	47.826	0.00	0.00	44.45	2.52
1805	1915	0.984230	TTCGCCTGGGTGATCTTCTT	59.016	50.000	3.60	0.00	34.40	2.52
1814	1925	0.322546	GGTCTTGAATTCGCCTGGGT	60.323	55.000	0.04	0.00	0.00	4.51
1860	1972	3.652055	AGCTAGTTCATCTCCATGAGGT	58.348	45.455	0.00	0.00	40.28	3.85
2029	2160	4.437239	AGATGCTCGATCTTTCACGATTT	58.563	39.130	0.00	0.00	38.35	2.17
2060	2192	4.284490	TCTGATACCAAGATGATGTAGGGC	59.716	45.833	0.00	0.00	0.00	5.19
2120	2254	8.947055	AACACAACAAAATCAAGCTAGAAAAT	57.053	26.923	0.00	0.00	0.00	1.82
2236	2374	2.228582	CCACTCGTGGCAAATCAAATCA	59.771	45.455	2.72	0.00	44.73	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.