AutoCloner

Multiple sequence alignment - TraesCS7A01G086500

Loading Multiple Alignment...

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	TraesCS7A01G086500	chr7A	100.000	2396	0	0	1	2396	50576528	50574133	0.000000e+00	4425
1	TraesCS7A01G086500	chrUn	94.441	1745	92	5	1	1744	27117563	27119303	0.000000e+00	2680
2	TraesCS7A01G086500	chrUn	92.268	1746	127	6	1	1744	43653168	43651429	0.000000e+00	2470
3	TraesCS7A01G086500	chrUn	90.415	626	51	6	1748	2366	49634710	49634087	0.000000e+00	815
4	TraesCS7A01G086500	chrUn	90.000	400	35	4	1748	2143	48669161	48668763	1.640000e-141	512
5	TraesCS7A01G086500	chrUn	90.751	173	9	2	2146	2318	48654200	48654035	8.620000e-55	224
6	TraesCS7A01G086500	chr6D	94.097	1745	97	6	1	1744	344719623	344721362	0.000000e+00	2647
7	TraesCS7A01G086500	chr5D	93.832	1751	104	4	1	1750	502658629	502656882	0.000000e+00	2632
8	TraesCS7A01G086500	chr5D	93.811	1745	102	6	1	1744	417724004	417725743	0.000000e+00	2619
9	TraesCS7A01G086500	chr1D	92.489	1744	120	6	1	1744	484198616	484200348	0.000000e+00	2484
10	TraesCS7A01G086500	chr1D	90.863	1762	142	12	1	1751	192735239	192736992	0.000000e+00	2344
11	TraesCS7A01G086500	chr4D	92.198	1615	101	7	131	1744	445486624	445488214	0.000000e+00	2261
12	TraesCS7A01G086500	chr4A	89.943	1760	157	13	1	1744	498206947	498208702	0.000000e+00	2252
13	TraesCS7A01G086500	chr7D	93.531	371	12	6	1748	2106	47816163	47815793	2.100000e-150	542
14	TraesCS7A01G086500	chr7D	94.719	303	11	3	2092	2391	47815628	47815328	1.300000e-127	466

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	TraesCS7A01G086500	chr7A	50574133	50576528	2395	True	4425	4425	100.000	1	2396	1	chr7A.!!$R1	2395
1	TraesCS7A01G086500	chrUn	27117563	27119303	1740	False	2680	2680	94.441	1	1744	1	chrUn.!!$F1	1743
2	TraesCS7A01G086500	chrUn	43651429	43653168	1739	True	2470	2470	92.268	1	1744	1	chrUn.!!$R1	1743
3	TraesCS7A01G086500	chrUn	49634087	49634710	623	True	815	815	90.415	1748	2366	1	chrUn.!!$R4	618
4	TraesCS7A01G086500	chr6D	344719623	344721362	1739	False	2647	2647	94.097	1	1744	1	chr6D.!!$F1	1743
5	TraesCS7A01G086500	chr5D	502656882	502658629	1747	True	2632	2632	93.832	1	1750	1	chr5D.!!$R1	1749
6	TraesCS7A01G086500	chr5D	417724004	417725743	1739	False	2619	2619	93.811	1	1744	1	chr5D.!!$F1	1743
7	TraesCS7A01G086500	chr1D	484198616	484200348	1732	False	2484	2484	92.489	1	1744	1	chr1D.!!$F2	1743
8	TraesCS7A01G086500	chr1D	192735239	192736992	1753	False	2344	2344	90.863	1	1751	1	chr1D.!!$F1	1750
9	TraesCS7A01G086500	chr4D	445486624	445488214	1590	False	2261	2261	92.198	131	1744	1	chr4D.!!$F1	1613
10	TraesCS7A01G086500	chr4A	498206947	498208702	1755	False	2252	2252	89.943	1	1744	1	chr4A.!!$F1	1743
11	TraesCS7A01G086500	chr7D	47815328	47816163	835	True	504	542	94.125	1748	2391	2	chr7D.!!$R1	643

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
207	209	0.319211	TGGACAAGCACCGTCGTAAG	60.319	55.0	0.0	0.0	34.04	2.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1415	1435	0.482446	ATCACAACCAGGGGCAGAAA	59.518	50.0	0.0	0.0	0.0	2.52	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
133	135	3.181478	GCTTACCTTGGTACTATCGCAGT	60.181	47.826	0.00	0.00	41.62	4.40
139	141	5.009811	ACCTTGGTACTATCGCAGTTATCTC	59.990	44.000	0.00	0.00	38.80	2.75
207	209	0.319211	TGGACAAGCACCGTCGTAAG	60.319	55.000	0.00	0.00	34.04	2.34
222	225	1.662026	CGTAAGTTTTTCTGGCACGGC	60.662	52.381	0.00	0.00	32.53	5.68
331	335	2.036346	AGGAAACAAAACATCAGCCTGC	59.964	45.455	0.00	0.00	0.00	4.85
395	399	1.408702	GCAAAACTTGGTGAGAGCCAA	59.591	47.619	0.00	0.00	45.37	4.52
411	415	9.255304	GTGAGAGCCAAATATTTACAAAACAAA	57.745	29.630	0.00	0.00	0.00	2.83
412	416	9.823647	TGAGAGCCAAATATTTACAAAACAAAA	57.176	25.926	0.00	0.00	0.00	2.44
426	430	5.106237	ACAAAACAAAACGGTAGCAACTGTA	60.106	36.000	0.00	0.00	44.70	2.74
444	448	6.859112	ACTGTACAACCTAGACAATCTGAT	57.141	37.500	0.00	0.00	0.00	2.90
455	459	2.883386	GACAATCTGATTCCCCATGCTC	59.117	50.000	0.00	0.00	0.00	4.26
745	752	7.039644	GGCTTAATACTACAGCTGAGGAAGATA	60.040	40.741	23.35	0.00	33.76	1.98
825	832	2.893489	GCTGGAAAAACCTCTTCATGGT	59.107	45.455	0.00	0.00	39.91	3.55
890	897	6.520272	AGATACATATCTTCTTGTGGCAGAC	58.480	40.000	0.00	0.00	39.96	3.51
940	947	4.344104	GGTGATGAGGAGGAAAAATTGGA	58.656	43.478	0.00	0.00	0.00	3.53
942	949	4.766891	GTGATGAGGAGGAAAAATTGGACA	59.233	41.667	0.00	0.00	0.00	4.02
1001	1008	1.349688	TGCGTCCCACCTGTTCTTTAT	59.650	47.619	0.00	0.00	0.00	1.40
1007	1014	3.650942	TCCCACCTGTTCTTTATGTGTCT	59.349	43.478	0.00	0.00	0.00	3.41
1041	1048	1.002868	CTGGAGGGCAGTTGGAGTG	60.003	63.158	0.00	0.00	0.00	3.51
1110	1117	5.248705	TGTGTGGTGTAATATGTTCCTACCA	59.751	40.000	0.00	0.00	34.61	3.25
1149	1156	2.015227	CTGTTGGTTTGGCGGCAGTT	62.015	55.000	12.87	0.00	0.00	3.16
1202	1209	8.785329	AAGGCTACTTTTGAAAAACAATTGAA	57.215	26.923	13.59	0.00	38.36	2.69
1231	1238	6.697395	TCTCCTTTTGAGATTGTGTATTCGA	58.303	36.000	0.00	0.00	45.29	3.71
1277	1284	1.376037	GTCTTCAGCCGGTGGAAGG	60.376	63.158	26.48	14.49	40.65	3.46
1382	1389	1.298014	CAGGAGACAAGGGTGAGGC	59.702	63.158	0.00	0.00	0.00	4.70
1383	1390	1.152030	AGGAGACAAGGGTGAGGCA	60.152	57.895	0.00	0.00	0.00	4.75
1415	1435	1.079266	GCTGCTGCTGTGCTCTACT	60.079	57.895	8.53	0.00	36.03	2.57
1446	1466	1.377987	TTGTGATAGGGGGCGTTGC	60.378	57.895	0.00	0.00	0.00	4.17
1475	1495	3.767711	TCTAAGTCTCAGGCTTCACTGA	58.232	45.455	0.00	0.00	44.74	3.41
1483	1503	2.089980	CAGGCTTCACTGATGGGAAAG	58.910	52.381	0.00	0.00	40.97	2.62
1484	1504	0.813821	GGCTTCACTGATGGGAAAGC	59.186	55.000	0.00	0.00	0.00	3.51
1485	1505	1.615384	GGCTTCACTGATGGGAAAGCT	60.615	52.381	5.50	0.00	0.00	3.74
1497	1518	4.654091	TGGGAAAGCTTTTTGAAGTCTG	57.346	40.909	14.05	0.00	0.00	3.51
1538	1568	1.021968	ACCTCGTGTTTGTGCCTTTC	58.978	50.000	0.00	0.00	0.00	2.62
1563	1593	6.365520	CCCCTGGTTTGTAATAGCTAGATTT	58.634	40.000	0.00	0.00	0.00	2.17
1564	1594	6.263168	CCCCTGGTTTGTAATAGCTAGATTTG	59.737	42.308	0.00	0.00	0.00	2.32
1619	1649	2.332654	GCTCGTTTTGATGGCGGGT	61.333	57.895	0.00	0.00	0.00	5.28
1624	1654	1.074775	TTTTGATGGCGGGTGAGCT	59.925	52.632	0.00	0.00	37.29	4.09
1645	1675	0.258774	AGTGGGTTTTCTGGCAGTGT	59.741	50.000	15.27	0.00	0.00	3.55
1662	1692	0.463654	TGTGTTGAACTCGCTGCCTT	60.464	50.000	0.00	0.00	0.00	4.35
1672	1702	1.882623	CTCGCTGCCTTTCTTTCCTTT	59.117	47.619	0.00	0.00	0.00	3.11
1744	1775	1.947146	GCACGCCCGGTTCAAAAAC	60.947	57.895	0.00	0.00	34.46	2.43
1754	1785	4.340950	CCCGGTTCAAAAACATATATGGCT	59.659	41.667	16.96	0.92	37.10	4.75
1799	1836	5.686753	TCATGGACATTGATGATGATGACA	58.313	37.500	0.00	0.00	39.15	3.58
2102	2327	3.286329	TGCACCTGAATGCTGATATGT	57.714	42.857	0.00	0.00	46.28	2.29
2245	2473	3.159472	TCTGCAATGTTCATCAGCCTTT	58.841	40.909	0.00	0.00	0.00	3.11
2252	2480	6.623486	CAATGTTCATCAGCCTTTTACATCA	58.377	36.000	0.00	0.00	0.00	3.07
2259	2487	4.460263	TCAGCCTTTTACATCAGTGTTGT	58.540	39.130	11.44	11.44	39.77	3.32
2265	2493	6.072728	GCCTTTTACATCAGTGTTGTATGTCA	60.073	38.462	13.49	0.00	39.77	3.58
2268	2496	4.952262	ACATCAGTGTTGTATGTCATGC	57.048	40.909	5.00	0.00	34.01	4.06
2306	2534	3.371102	TGTTCAGTCAGTGTAGCTGTC	57.629	47.619	0.00	0.00	45.23	3.51
2391	2619	9.165035	CCTTTTTGTGCATGGTATTTCAATTAT	57.835	29.630	0.00	0.00	0.00	1.28
2395	2623	9.761504	TTTGTGCATGGTATTTCAATTATATGG	57.238	29.630	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	7.844009	TCTACGATAAACTCCCACACTAAATT	58.156	34.615	0.00	0.00	0.00	1.82
23	24	8.523915	TTTATCTACGATAAACTCCCACACTA	57.476	34.615	5.24	0.00	0.00	2.74
39	40	8.749499	CCGAAACACTTAAGGTATTTATCTACG	58.251	37.037	7.53	4.12	0.00	3.51
119	121	9.327628	GATATAGAGATAACTGCGATAGTACCA	57.672	37.037	0.00	0.00	39.18	3.25
139	141	9.269453	CATAAGCCACATGGACATATGATATAG	57.731	37.037	10.38	0.00	37.39	1.31
207	209	1.661509	GCAGCCGTGCCAGAAAAAC	60.662	57.895	0.00	0.00	44.72	2.43
331	335	1.993956	TTCCACCACCATTTCACCAG	58.006	50.000	0.00	0.00	0.00	4.00
395	399	9.530633	TTGCTACCGTTTTGTTTTGTAAATATT	57.469	25.926	0.00	0.00	0.00	1.28
411	415	2.103601	AGGTTGTACAGTTGCTACCGTT	59.896	45.455	6.52	0.00	38.09	4.44
412	416	1.690352	AGGTTGTACAGTTGCTACCGT	59.310	47.619	6.52	0.00	38.09	4.83
426	430	4.080299	GGGGAATCAGATTGTCTAGGTTGT	60.080	45.833	0.00	0.00	0.00	3.32
444	448	1.839994	AGAGATTTCGAGCATGGGGAA	59.160	47.619	0.00	0.00	0.00	3.97
745	752	6.607019	TCTTACTCAAACCCCAAAACACTAT	58.393	36.000	0.00	0.00	0.00	2.12
825	832	5.903923	TCCCAGATCCATCTATAGTTGCTA	58.096	41.667	5.42	0.00	34.85	3.49
1001	1008	3.268603	CACGCGCCACAAGACACA	61.269	61.111	5.73	0.00	0.00	3.72
1041	1048	2.711542	CATAAGTCAGTCCCCAACACC	58.288	52.381	0.00	0.00	0.00	4.16
1149	1156	2.099405	GCAAGCCAAATAGCCCAAGTA	58.901	47.619	0.00	0.00	0.00	2.24
1231	1238	5.238650	CCCAATACAAGAGAAACGAACAAGT	59.761	40.000	0.00	0.00	0.00	3.16
1296	1303	3.954258	TCGCTCTAATCATCTCAACTCCA	59.046	43.478	0.00	0.00	0.00	3.86
1365	1372	0.548682	ATGCCTCACCCTTGTCTCCT	60.549	55.000	0.00	0.00	0.00	3.69
1382	1389	2.550180	CAGCAGCATCATCCAGAGAATG	59.450	50.000	0.00	0.00	0.00	2.67
1383	1390	2.852449	CAGCAGCATCATCCAGAGAAT	58.148	47.619	0.00	0.00	0.00	2.40
1415	1435	0.482446	ATCACAACCAGGGGCAGAAA	59.518	50.000	0.00	0.00	0.00	2.52
1446	1466	2.611518	CCTGAGACTTAGAACCTTGCG	58.388	52.381	0.00	0.00	0.00	4.85
1449	1469	3.904339	TGAAGCCTGAGACTTAGAACCTT	59.096	43.478	0.00	0.00	0.00	3.50
1475	1495	4.502087	GCAGACTTCAAAAAGCTTTCCCAT	60.502	41.667	13.10	0.00	35.81	4.00
1483	1503	7.809806	ACATAAAGTATGCAGACTTCAAAAAGC	59.190	33.333	25.76	0.00	38.75	3.51
1484	1504	9.683069	AACATAAAGTATGCAGACTTCAAAAAG	57.317	29.630	25.76	14.85	38.75	2.27
1485	1505	9.677567	GAACATAAAGTATGCAGACTTCAAAAA	57.322	29.630	25.76	10.57	38.75	1.94
1497	1518	4.035675	GTGCCAGAGGAACATAAAGTATGC	59.964	45.833	0.00	0.00	39.79	3.14
1538	1568	3.714798	TCTAGCTATTACAAACCAGGGGG	59.285	47.826	0.00	0.00	41.29	5.40
1563	1593	3.258372	CCTGACAGCACCTACTTAGTTCA	59.742	47.826	0.00	0.00	0.00	3.18
1564	1594	3.258622	ACCTGACAGCACCTACTTAGTTC	59.741	47.826	0.00	0.00	0.00	3.01
1600	1630	2.485122	CCGCCATCAAAACGAGCC	59.515	61.111	0.00	0.00	0.00	4.70
1619	1649	1.202806	CCAGAAAACCCACTGAGCTCA	60.203	52.381	17.19	17.19	36.38	4.26
1624	1654	0.550914	ACTGCCAGAAAACCCACTGA	59.449	50.000	0.00	0.00	36.38	3.41
1645	1675	0.944386	GAAAGGCAGCGAGTTCAACA	59.056	50.000	0.00	0.00	0.00	3.33
1662	1692	6.426937	CGTACAATCAGGAAGAAAGGAAAGAA	59.573	38.462	0.00	0.00	0.00	2.52
1672	1702	3.444034	CAGTCTCCGTACAATCAGGAAGA	59.556	47.826	0.00	0.00	33.10	2.87
1744	1775	6.096987	AGTTCGTACCATCCTAGCCATATATG	59.903	42.308	5.68	5.68	0.00	1.78
1775	1806	6.303839	TGTCATCATCATCAATGTCCATGAT	58.696	36.000	0.00	1.72	39.83	2.45
1799	1836	7.159372	TCTTCATCATCATCATGATCATCGTT	58.841	34.615	4.86	0.00	45.26	3.85
1822	1859	9.599056	TCATCATATTCTTCTTCTACCTCATCT	57.401	33.333	0.00	0.00	0.00	2.90
1899	1942	1.688772	CAAATCCATCTCAGCAGGGG	58.311	55.000	0.00	0.00	0.00	4.79
1909	1952	1.322538	AAGCGCACCCCAAATCCATC	61.323	55.000	11.47	0.00	0.00	3.51
2058	2102	7.492344	GCAAATCTGAAGGAAAAGAAAACAAGA	59.508	33.333	0.00	0.00	0.00	3.02
2245	2473	5.063312	CGCATGACATACAACACTGATGTAA	59.937	40.000	0.00	0.00	38.45	2.41
2252	2480	1.737838	CCCGCATGACATACAACACT	58.262	50.000	0.00	0.00	0.00	3.55
2259	2487	1.078778	AACACGCCCGCATGACATA	60.079	52.632	0.00	0.00	0.00	2.29
2265	2493	1.714899	GCTAATGAACACGCCCGCAT	61.715	55.000	0.00	0.00	0.00	4.73
2268	2496	0.027979	CATGCTAATGAACACGCCCG	59.972	55.000	0.00	0.00	35.67	6.13
2306	2534	2.496794	CCGCGCACTCGAAAAACG	60.497	61.111	8.75	0.00	44.09	3.60
2318	2546	2.099062	CAGATGCAAGAACCGCGC	59.901	61.111	0.00	0.00	0.00	6.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.