AutoCloner

Multiple sequence alignment - TraesCS3A01G142300

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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	TraesCS3A01G142300	chr3A	100.000	2471	0	0	1	2471	122209537	122207067	0.000000e+00	4564.0
1	TraesCS3A01G142300	chr3A	98.476	1509	21	2	1	1507	247672881	247674389	0.000000e+00	2658.0
2	TraesCS3A01G142300	chr3A	92.982	912	61	2	1562	2471	121859069	121858159	0.000000e+00	1327.0
3	TraesCS3A01G142300	chr3A	92.426	911	67	2	1562	2471	121954625	121953716	0.000000e+00	1299.0
4	TraesCS3A01G142300	chr1A	98.873	1509	15	1	1	1507	238107641	238106133	0.000000e+00	2691.0
5	TraesCS3A01G142300	chr1A	98.873	1509	15	1	1	1507	238153026	238151518	0.000000e+00	2691.0
6	TraesCS3A01G142300	chr1A	100.000	38	0	0	1526	1563	238106181	238106144	1.230000e-08	71.3
7	TraesCS3A01G142300	chr1A	100.000	38	0	0	1526	1563	238151566	238151529	1.230000e-08	71.3
8	TraesCS3A01G142300	chr5A	98.806	1508	17	1	1	1507	16575816	16574309	0.000000e+00	2684.0
9	TraesCS3A01G142300	chr7A	98.674	1508	18	2	1	1507	60326906	60325400	0.000000e+00	2673.0
10	TraesCS3A01G142300	chr6B	98.479	1512	18	4	1	1507	596655206	596653695	0.000000e+00	2660.0
11	TraesCS3A01G142300	chrUn	97.819	1513	27	1	1	1507	371043360	371041848	0.000000e+00	2606.0
12	TraesCS3A01G142300	chrUn	97.753	1513	28	1	1	1507	237255732	237254220	0.000000e+00	2601.0
13	TraesCS3A01G142300	chrUn	100.000	38	0	0	1526	1563	189418364	189418327	1.230000e-08	71.3
14	TraesCS3A01G142300	chrUn	100.000	38	0	0	1526	1563	237254268	237254231	1.230000e-08	71.3
15	TraesCS3A01G142300	chrUn	100.000	38	0	0	1526	1563	371041896	371041859	1.230000e-08	71.3
16	TraesCS3A01G142300	chrUn	100.000	38	0	0	1526	1563	410183438	410183475	1.230000e-08	71.3
17	TraesCS3A01G142300	chr7D	97.751	1512	28	2	1	1507	579017679	579019189	0.000000e+00	2599.0
18	TraesCS3A01G142300	chr6D	92.905	902	60	4	1573	2471	272069857	272068957	0.000000e+00	1308.0
19	TraesCS3A01G142300	chr6D	92.114	913	62	6	1562	2471	252141937	252142842	0.000000e+00	1279.0
20	TraesCS3A01G142300	chr1D	92.461	902	65	3	1573	2471	366506162	366505261	0.000000e+00	1286.0
21	TraesCS3A01G142300	chr1D	92.004	913	69	4	1562	2471	438445360	438446271	0.000000e+00	1279.0
22	TraesCS3A01G142300	chr2D	92.376	905	61	7	1573	2471	541604989	541604087	0.000000e+00	1282.0
23	TraesCS3A01G142300	chr2D	91.904	914	63	7	1562	2470	295602289	295603196	0.000000e+00	1267.0
24	TraesCS3A01G142300	chr2A	91.895	913	67	6	1562	2471	381449399	381450307	0.000000e+00	1269.0
25	TraesCS3A01G142300	chr5D	100.000	38	0	0	1526	1563	562921013	562920976	1.230000e-08	71.3
26	TraesCS3A01G142300	chr4D	100.000	38	0	0	1526	1563	123746737	123746700	1.230000e-08	71.3
27	TraesCS3A01G142300	chr4D	100.000	38	0	0	1526	1563	172092161	172092198	1.230000e-08	71.3

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	TraesCS3A01G142300	chr3A	122207067	122209537	2470	True	4564.00	4564	100.0000	1	2471	1	chr3A.!!$R3	2470
1	TraesCS3A01G142300	chr3A	247672881	247674389	1508	False	2658.00	2658	98.4760	1	1507	1	chr3A.!!$F1	1506
2	TraesCS3A01G142300	chr3A	121858159	121859069	910	True	1327.00	1327	92.9820	1562	2471	1	chr3A.!!$R1	909
3	TraesCS3A01G142300	chr3A	121953716	121954625	909	True	1299.00	1299	92.4260	1562	2471	1	chr3A.!!$R2	909
4	TraesCS3A01G142300	chr1A	238106133	238107641	1508	True	1381.15	2691	99.4365	1	1563	2	chr1A.!!$R1	1562
5	TraesCS3A01G142300	chr1A	238151518	238153026	1508	True	1381.15	2691	99.4365	1	1563	2	chr1A.!!$R2	1562
6	TraesCS3A01G142300	chr5A	16574309	16575816	1507	True	2684.00	2684	98.8060	1	1507	1	chr5A.!!$R1	1506
7	TraesCS3A01G142300	chr7A	60325400	60326906	1506	True	2673.00	2673	98.6740	1	1507	1	chr7A.!!$R1	1506
8	TraesCS3A01G142300	chr6B	596653695	596655206	1511	True	2660.00	2660	98.4790	1	1507	1	chr6B.!!$R1	1506
9	TraesCS3A01G142300	chrUn	371041848	371043360	1512	True	1338.65	2606	98.9095	1	1563	2	chrUn.!!$R3	1562
10	TraesCS3A01G142300	chrUn	237254220	237255732	1512	True	1336.15	2601	98.8765	1	1563	2	chrUn.!!$R2	1562
11	TraesCS3A01G142300	chr7D	579017679	579019189	1510	False	2599.00	2599	97.7510	1	1507	1	chr7D.!!$F1	1506
12	TraesCS3A01G142300	chr6D	272068957	272069857	900	True	1308.00	1308	92.9050	1573	2471	1	chr6D.!!$R1	898
13	TraesCS3A01G142300	chr6D	252141937	252142842	905	False	1279.00	1279	92.1140	1562	2471	1	chr6D.!!$F1	909
14	TraesCS3A01G142300	chr1D	366505261	366506162	901	True	1286.00	1286	92.4610	1573	2471	1	chr1D.!!$R1	898
15	TraesCS3A01G142300	chr1D	438445360	438446271	911	False	1279.00	1279	92.0040	1562	2471	1	chr1D.!!$F1	909
16	TraesCS3A01G142300	chr2D	541604087	541604989	902	True	1282.00	1282	92.3760	1573	2471	1	chr2D.!!$R1	898
17	TraesCS3A01G142300	chr2D	295602289	295603196	907	False	1267.00	1267	91.9040	1562	2470	1	chr2D.!!$F1	908
18	TraesCS3A01G142300	chr2A	381449399	381450307	908	False	1269.00	1269	91.8950	1562	2471	1	chr2A.!!$F1	909

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
653	654	1.205893	GCTCGGTGAACCAGATTCTCT	59.794	52.381	0.0	0.0	38.25	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2320	0.326595	TGGCTCTCCCGCAAACATTA	59.673	50.0	0.0	0.0	35.87	1.9	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
81	82	2.098934	TCGCGCTTTATGGCATTTCAAT	59.901	40.909	4.78	0.00	0.00	2.57
653	654	1.205893	GCTCGGTGAACCAGATTCTCT	59.794	52.381	0.00	0.00	38.25	3.10
787	788	3.931907	AAAGGTGGGATGATGATTCGA	57.068	42.857	0.00	0.00	0.00	3.71
1146	1158	2.158871	ACTACGGAACCAACTGCTTTCA	60.159	45.455	0.00	0.00	0.00	2.69
1148	1160	0.041312	CGGAACCAACTGCTTTCACG	60.041	55.000	0.00	0.00	0.00	4.35
1321	1337	7.769970	GGAAAATCACTCTGATCTCTGATTTCT	59.230	37.037	14.99	9.35	40.72	2.52
1322	1338	8.721019	AAAATCACTCTGATCTCTGATTTCTC	57.279	34.615	14.99	0.00	40.72	2.87
1323	1339	5.850557	TCACTCTGATCTCTGATTTCTCC	57.149	43.478	0.00	0.00	0.00	3.71
1503	1519	8.016652	TCTGATAATCTTTCTATAGGTTCCCCA	58.983	37.037	0.00	0.00	0.00	4.96
1507	1523	5.710409	TCTTTCTATAGGTTCCCCAAAGG	57.290	43.478	0.00	0.00	0.00	3.11
1508	1524	5.105853	TCTTTCTATAGGTTCCCCAAAGGT	58.894	41.667	0.00	0.00	36.75	3.50
1509	1525	5.191124	TCTTTCTATAGGTTCCCCAAAGGTC	59.809	44.000	0.00	0.00	36.75	3.85
1510	1526	4.083080	TCTATAGGTTCCCCAAAGGTCA	57.917	45.455	0.00	0.00	36.75	4.02
1511	1527	4.641868	TCTATAGGTTCCCCAAAGGTCAT	58.358	43.478	0.00	0.00	36.75	3.06
1512	1528	5.795079	TCTATAGGTTCCCCAAAGGTCATA	58.205	41.667	0.00	0.00	36.75	2.15
1513	1529	6.214278	TCTATAGGTTCCCCAAAGGTCATAA	58.786	40.000	0.00	0.00	36.75	1.90
1514	1530	6.855061	TCTATAGGTTCCCCAAAGGTCATAAT	59.145	38.462	0.00	0.00	36.75	1.28
1515	1531	8.020253	TCTATAGGTTCCCCAAAGGTCATAATA	58.980	37.037	0.00	0.00	36.75	0.98
1516	1532	7.663501	ATAGGTTCCCCAAAGGTCATAATAT	57.336	36.000	0.00	0.00	36.75	1.28
1517	1533	5.953571	AGGTTCCCCAAAGGTCATAATATC	58.046	41.667	0.00	0.00	36.75	1.63
1518	1534	5.435041	AGGTTCCCCAAAGGTCATAATATCA	59.565	40.000	0.00	0.00	36.75	2.15
1519	1535	6.104691	AGGTTCCCCAAAGGTCATAATATCAT	59.895	38.462	0.00	0.00	36.75	2.45
1520	1536	7.297108	AGGTTCCCCAAAGGTCATAATATCATA	59.703	37.037	0.00	0.00	36.75	2.15
1521	1537	7.947890	GGTTCCCCAAAGGTCATAATATCATAA	59.052	37.037	0.00	0.00	36.75	1.90
1522	1538	9.533831	GTTCCCCAAAGGTCATAATATCATAAT	57.466	33.333	0.00	0.00	36.75	1.28
1546	1562	9.896645	AATATCATAATATCATGAAAGCCGTCT	57.103	29.630	0.00	0.00	38.39	4.18
1547	1563	7.606858	ATCATAATATCATGAAAGCCGTCTG	57.393	36.000	0.00	0.00	38.39	3.51
1548	1564	6.758254	TCATAATATCATGAAAGCCGTCTGA	58.242	36.000	0.00	0.00	32.01	3.27
1549	1565	7.389232	TCATAATATCATGAAAGCCGTCTGAT	58.611	34.615	0.00	0.00	32.01	2.90
1550	1566	8.531146	TCATAATATCATGAAAGCCGTCTGATA	58.469	33.333	0.00	0.00	34.37	2.15
1551	1567	9.154847	CATAATATCATGAAAGCCGTCTGATAA	57.845	33.333	0.00	0.00	33.78	1.75
1552	1568	9.896645	ATAATATCATGAAAGCCGTCTGATAAT	57.103	29.630	0.00	0.00	33.78	1.28
1553	1569	7.840342	ATATCATGAAAGCCGTCTGATAATC	57.160	36.000	0.00	0.00	33.78	1.75
1554	1570	5.282055	TCATGAAAGCCGTCTGATAATCT	57.718	39.130	0.00	0.00	0.00	2.40
1555	1571	5.674525	TCATGAAAGCCGTCTGATAATCTT	58.325	37.500	0.00	0.00	0.00	2.40
1556	1572	6.115446	TCATGAAAGCCGTCTGATAATCTTT	58.885	36.000	0.00	0.00	0.00	2.52
1557	1573	6.258727	TCATGAAAGCCGTCTGATAATCTTTC	59.741	38.462	0.00	13.05	39.59	2.62
1558	1574	5.734720	TGAAAGCCGTCTGATAATCTTTCT	58.265	37.500	17.20	0.00	39.76	2.52
1559	1575	6.873997	TGAAAGCCGTCTGATAATCTTTCTA	58.126	36.000	17.20	8.14	39.76	2.10
1560	1576	7.500992	TGAAAGCCGTCTGATAATCTTTCTAT	58.499	34.615	17.20	0.00	39.76	1.98
1565	1581	6.750039	GCCGTCTGATAATCTTTCTATAGAGC	59.250	42.308	2.02	0.00	0.00	4.09
1619	1635	3.202151	ACATTCCCTACCGAAACCATCAT	59.798	43.478	0.00	0.00	0.00	2.45
1806	1833	2.970324	GTTTGCGGCCGAGTGACA	60.970	61.111	33.48	14.73	0.00	3.58
1812	1839	4.008933	GGCCGAGTGACAGTGGCT	62.009	66.667	17.70	0.00	46.72	4.75
1855	1882	3.686016	GTTTCTTGCATGGGACCTAAGA	58.314	45.455	0.00	0.00	0.00	2.10
1925	1954	3.426695	GGAGCATGTGCATGTAGTTCAAC	60.427	47.826	12.96	0.00	45.16	3.18
1997	2029	3.235200	TGTCCAAATGAACCCCGAAAAT	58.765	40.909	0.00	0.00	0.00	1.82
2012	2044	7.332557	ACCCCGAAAATTTCCATAATTTAACC	58.667	34.615	0.00	0.00	30.38	2.85
2045	2077	7.039011	TCCTGTTGTTCTATGTTGACACTAGAT	60.039	37.037	0.00	0.00	0.00	1.98
2286	2320	7.459234	ACTAGAATTACAAAAGCAGGTACCTT	58.541	34.615	13.15	0.00	0.00	3.50
2296	2330	2.747446	AGCAGGTACCTTAATGTTTGCG	59.253	45.455	13.15	0.00	35.59	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
81	82	4.016444	GTGGGATTGGATTAGTTTGCTCA	58.984	43.478	0.00	0.00	0.00	4.26
787	788	3.377346	CGAATCATCATCTTCGGACCT	57.623	47.619	0.00	0.00	40.31	3.85
1038	1050	6.688073	AAGAGGAGAAGACATAACCAGAAA	57.312	37.500	0.00	0.00	0.00	2.52
1321	1337	1.546923	TCGTGAGCCACTTATTTCGGA	59.453	47.619	4.21	0.00	31.34	4.55
1322	1338	1.927174	CTCGTGAGCCACTTATTTCGG	59.073	52.381	4.21	0.00	31.34	4.30
1323	1339	1.927174	CCTCGTGAGCCACTTATTTCG	59.073	52.381	4.21	0.00	31.34	3.46
1520	1536	9.896645	AGACGGCTTTCATGATATTATGATATT	57.103	29.630	10.68	0.00	36.97	1.28
1521	1537	9.322773	CAGACGGCTTTCATGATATTATGATAT	57.677	33.333	10.68	0.00	36.97	1.63
1522	1538	8.531146	TCAGACGGCTTTCATGATATTATGATA	58.469	33.333	10.68	5.85	36.97	2.15
1523	1539	7.389232	TCAGACGGCTTTCATGATATTATGAT	58.611	34.615	10.68	0.00	36.97	2.45
1524	1540	6.758254	TCAGACGGCTTTCATGATATTATGA	58.242	36.000	6.09	6.09	35.38	2.15
1525	1541	7.606858	ATCAGACGGCTTTCATGATATTATG	57.393	36.000	0.00	1.04	0.00	1.90
1526	1542	9.896645	ATTATCAGACGGCTTTCATGATATTAT	57.103	29.630	0.00	0.00	33.98	1.28
1527	1543	9.371136	GATTATCAGACGGCTTTCATGATATTA	57.629	33.333	0.00	0.00	33.98	0.98
1528	1544	8.099537	AGATTATCAGACGGCTTTCATGATATT	58.900	33.333	0.00	0.00	33.98	1.28
1529	1545	7.619050	AGATTATCAGACGGCTTTCATGATAT	58.381	34.615	0.00	0.00	33.98	1.63
1530	1546	6.997655	AGATTATCAGACGGCTTTCATGATA	58.002	36.000	0.00	0.00	32.99	2.15
1531	1547	5.862845	AGATTATCAGACGGCTTTCATGAT	58.137	37.500	0.00	0.00	35.01	2.45
1532	1548	5.282055	AGATTATCAGACGGCTTTCATGA	57.718	39.130	0.00	0.00	0.00	3.07
1533	1549	5.998454	AAGATTATCAGACGGCTTTCATG	57.002	39.130	0.00	0.00	0.00	3.07
1534	1550	6.352516	AGAAAGATTATCAGACGGCTTTCAT	58.647	36.000	1.03	0.00	42.03	2.57
1535	1551	5.734720	AGAAAGATTATCAGACGGCTTTCA	58.265	37.500	1.03	0.00	42.03	2.69
1536	1552	7.954788	ATAGAAAGATTATCAGACGGCTTTC	57.045	36.000	0.00	0.00	40.69	2.62
1537	1553	8.861086	TCTATAGAAAGATTATCAGACGGCTTT	58.139	33.333	0.00	0.00	0.00	3.51
1538	1554	8.410673	TCTATAGAAAGATTATCAGACGGCTT	57.589	34.615	0.00	0.00	0.00	4.35
1539	1555	7.362574	GCTCTATAGAAAGATTATCAGACGGCT	60.363	40.741	3.57	0.00	0.00	5.52
1540	1556	6.750039	GCTCTATAGAAAGATTATCAGACGGC	59.250	42.308	3.57	0.00	0.00	5.68
1541	1557	7.094162	TGGCTCTATAGAAAGATTATCAGACGG	60.094	40.741	3.57	0.00	0.00	4.79
1542	1558	7.821652	TGGCTCTATAGAAAGATTATCAGACG	58.178	38.462	3.57	0.00	0.00	4.18
1543	1559	9.418045	GTTGGCTCTATAGAAAGATTATCAGAC	57.582	37.037	3.57	0.00	0.00	3.51
1544	1560	9.147732	TGTTGGCTCTATAGAAAGATTATCAGA	57.852	33.333	3.57	0.00	0.00	3.27
1545	1561	9.941325	ATGTTGGCTCTATAGAAAGATTATCAG	57.059	33.333	3.57	0.00	0.00	2.90
1552	1568	9.244292	ACGATATATGTTGGCTCTATAGAAAGA	57.756	33.333	3.57	0.00	0.00	2.52
1553	1569	9.862371	AACGATATATGTTGGCTCTATAGAAAG	57.138	33.333	3.57	0.00	0.00	2.62
1555	1571	9.856488	GAAACGATATATGTTGGCTCTATAGAA	57.144	33.333	3.57	0.00	0.00	2.10
1556	1572	9.020731	TGAAACGATATATGTTGGCTCTATAGA	57.979	33.333	1.69	1.69	0.00	1.98
1557	1573	9.809096	ATGAAACGATATATGTTGGCTCTATAG	57.191	33.333	0.00	0.00	0.00	1.31
1558	1574	9.803315	GATGAAACGATATATGTTGGCTCTATA	57.197	33.333	0.00	0.00	0.00	1.31
1559	1575	7.766278	GGATGAAACGATATATGTTGGCTCTAT	59.234	37.037	0.00	0.00	0.00	1.98
1560	1576	7.097192	GGATGAAACGATATATGTTGGCTCTA	58.903	38.462	0.00	0.00	0.00	2.43
1565	1581	5.312895	TGGGGATGAAACGATATATGTTGG	58.687	41.667	0.00	0.00	0.00	3.77
1619	1635	2.627515	AGAGCTTCTCACAACAAGCA	57.372	45.000	6.44	0.00	46.37	3.91
1696	1722	0.394762	ATGGAGCGGCATCAACATGT	60.395	50.000	1.45	0.00	31.86	3.21
1776	1802	3.003378	GGCCGCAAACATTAAGATACCTC	59.997	47.826	0.00	0.00	0.00	3.85
1806	1833	2.086610	ATTTCAAACACCCAGCCACT	57.913	45.000	0.00	0.00	0.00	4.00
1812	1839	3.006323	CGGGAATGAATTTCAAACACCCA	59.994	43.478	21.65	0.00	35.94	4.51
1855	1882	1.786937	TTTGTGTCCTTGGGTGCATT	58.213	45.000	0.00	0.00	0.00	3.56
1925	1954	8.761575	AGGTATTTTATGTGCACAATTCAAAG	57.238	30.769	25.72	0.00	0.00	2.77
1934	1963	7.094118	TGGGTTTTCTAGGTATTTTATGTGCAC	60.094	37.037	10.75	10.75	0.00	4.57
1967	1996	7.343316	TCGGGGTTCATTTGGACATTTTTATAT	59.657	33.333	0.00	0.00	0.00	0.86
1997	2029	7.013834	AGGAGTGTTGGGTTAAATTATGGAAA	58.986	34.615	0.00	0.00	0.00	3.13
2058	2090	7.770897	AGAAACGATATCTGTTGCCTCTTATTT	59.229	33.333	11.80	0.00	0.00	1.40
2195	2228	1.140652	TGGAGCGGCATCAATATGTCA	59.859	47.619	1.45	0.00	37.59	3.58
2286	2320	0.326595	TGGCTCTCCCGCAAACATTA	59.673	50.000	0.00	0.00	35.87	1.90
2296	2330	4.436998	CGACACCGTGGCTCTCCC	62.437	72.222	2.13	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.