AutoCloner

Multiple sequence alignment - TraesCS1B01G460800

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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	TraesCS1B01G460800	chr1B	100.000	2201	0	0	1	2201	674074840	674077040	0.000000e+00	4065.0
1	TraesCS1B01G460800	chr1B	83.560	663	80	17	708	1368	674053596	674054231	5.230000e-166	593.0
2	TraesCS1B01G460800	chr1B	80.928	776	102	28	1434	2201	674053458	674054195	2.450000e-159	571.0
3	TraesCS1B01G460800	chr1B	80.725	690	105	19	1517	2201	674065485	674066151	1.510000e-141	512.0
4	TraesCS1B01G460800	chr1B	100.000	41	0	0	1294	1334	674076095	674076135	2.340000e-10	76.8
5	TraesCS1B01G460800	chr1B	100.000	41	0	0	1256	1296	674076133	674076173	2.340000e-10	76.8
6	TraesCS1B01G460800	chr1B	88.679	53	3	2	437	486	40598882	40598830	6.560000e-06	62.1
7	TraesCS1B01G460800	chr1D	92.746	2192	95	27	19	2199	484112720	484114858	0.000000e+00	3109.0
8	TraesCS1B01G460800	chr1D	84.988	806	97	19	1408	2201	484113195	484113988	0.000000e+00	797.0
9	TraesCS1B01G460800	chr1D	84.423	719	87	15	526	1232	484114066	484114771	0.000000e+00	684.0
10	TraesCS1B01G460800	chr1D	84.043	658	78	18	715	1368	484004716	484005350	1.870000e-170	608.0
11	TraesCS1B01G460800	chr1D	81.682	666	94	21	707	1368	484030227	484030868	1.500000e-146	529.0
12	TraesCS1B01G460800	chr1D	82.143	616	97	12	1591	2201	484030225	484030832	1.170000e-142	516.0
13	TraesCS1B01G460800	chr1A	93.690	1775	82	16	438	2201	581254777	581256532	0.000000e+00	2630.0
14	TraesCS1B01G460800	chr1A	83.747	806	109	18	1408	2201	581254864	581255659	0.000000e+00	743.0
15	TraesCS1B01G460800	chr1A	81.904	851	113	23	524	1359	581255735	581256559	0.000000e+00	680.0
16	TraesCS1B01G460800	chr1A	81.312	808	118	21	1401	2201	581205727	581206508	1.860000e-175	625.0
17	TraesCS1B01G460800	chr1A	80.445	854	115	33	524	1368	581205734	581206544	2.420000e-169	604.0
18	TraesCS1B01G460800	chr1A	91.176	374	25	3	1	366	581254398	581254771	3.260000e-138	501.0
19	TraesCS1B01G460800	chr1A	81.138	615	97	10	611	1224	581433347	581433943	1.980000e-130	475.0
20	TraesCS1B01G460800	chr1A	100.000	28	0	0	454	481	351351072	351351045	4.000000e-03	52.8
21	TraesCS1B01G460800	chr5B	75.676	222	52	2	1894	2114	648287360	648287580	2.310000e-20	110.0

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	TraesCS1B01G460800	chr1B	674074840	674077040	2200	False	1406.2	4065	100.000000	1	2201	3	chr1B.!!$F3	2200
1	TraesCS1B01G460800	chr1B	674053458	674054231	773	False	582.0	593	82.244000	708	2201	2	chr1B.!!$F2	1493
2	TraesCS1B01G460800	chr1B	674065485	674066151	666	False	512.0	512	80.725000	1517	2201	1	chr1B.!!$F1	684
3	TraesCS1B01G460800	chr1D	484112720	484114858	2138	False	1530.0	3109	87.385667	19	2201	3	chr1D.!!$F3	2182
4	TraesCS1B01G460800	chr1D	484004716	484005350	634	False	608.0	608	84.043000	715	1368	1	chr1D.!!$F1	653
5	TraesCS1B01G460800	chr1D	484030225	484030868	643	False	522.5	529	81.912500	707	2201	2	chr1D.!!$F2	1494
6	TraesCS1B01G460800	chr1A	581254398	581256559	2161	False	1138.5	2630	87.629250	1	2201	4	chr1A.!!$F3	2200
7	TraesCS1B01G460800	chr1A	581205727	581206544	817	False	614.5	625	80.878500	524	2201	2	chr1A.!!$F2	1677
8	TraesCS1B01G460800	chr1A	581433347	581433943	596	False	475.0	475	81.138000	611	1224	1	chr1A.!!$F1	613

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
434	443	1.064685	TCTCGGAGGTGCTCATAGTGA	60.065	52.381	4.96	0.0	31.08	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1580	1642	1.927174	CATCTCGTGACCACCGAATTC	59.073	52.381	0.0	0.0	33.34	2.17	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
175	183	7.609097	AGACCTCAATGCAAATCTCTCTATA	57.391	36.000	0.00	0.00	0.00	1.31
197	205	2.430332	CTGCCAAGGTCCAAAAGTTGAA	59.570	45.455	0.00	0.00	0.00	2.69
235	243	6.157994	AGGCTTAGATGGTTAGGTTTCATGTA	59.842	38.462	0.00	0.00	0.00	2.29
324	333	1.926510	CATGCTTTCTCGCGATGTACA	59.073	47.619	10.36	5.28	0.00	2.90
366	375	8.038351	TGTTCCTGTTGATTATGATTTACGAGA	58.962	33.333	0.00	0.00	0.00	4.04
372	381	6.321848	TGATTATGATTTACGAGACGCCTA	57.678	37.500	0.00	0.00	0.00	3.93
383	392	3.630769	ACGAGACGCCTATAATGACTTCA	59.369	43.478	0.00	0.00	0.00	3.02
432	441	2.373335	ATCTCGGAGGTGCTCATAGT	57.627	50.000	4.96	0.00	31.08	2.12
433	442	1.393603	TCTCGGAGGTGCTCATAGTG	58.606	55.000	4.96	0.00	31.08	2.74
434	443	1.064685	TCTCGGAGGTGCTCATAGTGA	60.065	52.381	4.96	0.00	31.08	3.41
439	448	4.072839	CGGAGGTGCTCATAGTGATAGTA	58.927	47.826	0.00	0.00	31.08	1.82
479	488	7.187480	CGTTCATAGGGATGAGTGTATATACG	58.813	42.308	8.33	0.00	43.03	3.06
572	582	9.639636	CGTGTCATATATCTACAAGATACGATC	57.360	37.037	10.35	0.00	39.76	3.69
580	590	6.796705	TCTACAAGATACGATCGCTAATGA	57.203	37.500	16.60	0.00	0.00	2.57
950	982	6.115448	AGGATAAACCATAGACATACCAGC	57.885	41.667	0.00	0.00	42.04	4.85
963	995	5.597182	AGACATACCAGCGAAAGGAGTATTA	59.403	40.000	0.00	0.00	0.00	0.98
980	1012	8.280084	AGGAGTATTACATAGTGTTCTCTACCA	58.720	37.037	0.00	0.00	0.00	3.25
1203	1235	1.839994	TCCTCCACCAAGCCTTGATAG	59.160	52.381	5.89	0.00	0.00	2.08
1232	1264	4.730966	TCATTCTCCTCCGAGCTATAAGT	58.269	43.478	0.00	0.00	35.94	2.24
1234	1266	4.920640	TTCTCCTCCGAGCTATAAGTTG	57.079	45.455	0.00	0.00	35.94	3.16
1235	1267	3.899726	TCTCCTCCGAGCTATAAGTTGT	58.100	45.455	0.00	0.00	35.94	3.32
1237	1269	3.362706	TCCTCCGAGCTATAAGTTGTGT	58.637	45.455	0.00	0.00	0.00	3.72
1238	1270	3.767673	TCCTCCGAGCTATAAGTTGTGTT	59.232	43.478	0.00	0.00	0.00	3.32
1239	1271	3.865745	CCTCCGAGCTATAAGTTGTGTTG	59.134	47.826	0.00	0.00	0.00	3.33
1434	1493	5.380043	AGTTGGCATCCCTTAGATATTGTG	58.620	41.667	0.00	0.00	32.37	3.33
1480	1539	9.601217	AGTGACTAATGGTGAATTATCTTGTAC	57.399	33.333	0.00	0.00	30.26	2.90
1481	1540	9.378551	GTGACTAATGGTGAATTATCTTGTACA	57.621	33.333	0.00	0.00	30.26	2.90
1519	1578	9.712305	CTATCCAACATACCCTAAATACAAGAG	57.288	37.037	0.00	0.00	0.00	2.85
1539	1601	6.286240	AGAGGATTTTGCTTGGTTAATTCC	57.714	37.500	0.00	0.00	0.00	3.01
1608	1670	0.807667	GGTCACGAGATGCAGCGAAT	60.808	55.000	12.47	0.00	0.00	3.34
1764	1827	7.577303	TCAGTGGAATTTATTAGGAGAAGCAT	58.423	34.615	0.00	0.00	0.00	3.79
1854	1917	6.149973	TGAAAGGAGAATTGCATAGTGTTCTG	59.850	38.462	0.00	0.00	31.51	3.02
1857	1920	6.109359	AGGAGAATTGCATAGTGTTCTGTAC	58.891	40.000	0.00	0.00	31.51	2.90
1890	1953	6.030228	GTGAGCTTAGACAATGGCAAATAAC	58.970	40.000	0.00	0.00	0.00	1.89
1892	1955	6.208402	TGAGCTTAGACAATGGCAAATAACAA	59.792	34.615	0.00	0.00	0.00	2.83
1926	1989	5.239306	AGTCTTCATTGTTTTTCTCATCGCA	59.761	36.000	0.00	0.00	0.00	5.10
1931	1994	4.630894	TTGTTTTTCTCATCGCACAAGT	57.369	36.364	0.00	0.00	0.00	3.16
1955	2018	3.181437	TGCTTAGTCATGATGATGGCCAT	60.181	43.478	20.96	20.96	34.42	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	4.999311	ACTATTTCCCGGTTCAAAGTACAC	59.001	41.667	0.00	0.00	0.00	2.90
175	183	1.756538	CAACTTTTGGACCTTGGCAGT	59.243	47.619	0.00	0.00	0.00	4.40
197	205	3.501349	TCTAAGCCTCACTCAGTTCACT	58.499	45.455	0.00	0.00	0.00	3.41
253	261	5.598417	AGTGCCAAATTTAGGACTTGAACTT	59.402	36.000	5.00	0.00	0.00	2.66
324	333	2.507471	GGAACATCTCCTCCCACAGAAT	59.493	50.000	0.00	0.00	41.61	2.40
349	358	5.196341	AGGCGTCTCGTAAATCATAATCA	57.804	39.130	0.00	0.00	0.00	2.57
350	359	8.906636	TTATAGGCGTCTCGTAAATCATAATC	57.093	34.615	0.00	0.00	0.00	1.75
366	375	4.481368	TTGGTGAAGTCATTATAGGCGT	57.519	40.909	0.00	0.00	0.00	5.68
372	381	7.013083	GCATCTTGAGATTGGTGAAGTCATTAT	59.987	37.037	0.00	0.00	31.21	1.28
383	392	2.029623	GCATGGCATCTTGAGATTGGT	58.970	47.619	0.00	0.00	31.21	3.67
432	441	1.555477	CGCGTGCACACATACTATCA	58.445	50.000	18.64	0.00	0.00	2.15
433	442	0.229753	GCGCGTGCACACATACTATC	59.770	55.000	17.66	0.00	42.15	2.08
434	443	1.479420	CGCGCGTGCACACATACTAT	61.479	55.000	24.19	0.00	42.97	2.12
465	474	6.571731	GCCCACATACACGTATATACACTCAT	60.572	42.308	13.22	0.00	0.00	2.90
479	488	1.877637	TCGCATATGCCCACATACAC	58.122	50.000	21.77	0.00	41.50	2.90
621	634	8.416329	ACCATGCAAATCCTCTTGTATTAATTC	58.584	33.333	0.00	0.00	30.28	2.17
622	635	8.310122	ACCATGCAAATCCTCTTGTATTAATT	57.690	30.769	0.00	0.00	30.28	1.40
623	636	7.902920	ACCATGCAAATCCTCTTGTATTAAT	57.097	32.000	0.00	0.00	30.28	1.40
624	637	7.716799	AACCATGCAAATCCTCTTGTATTAA	57.283	32.000	0.00	0.00	30.28	1.40
625	638	8.815565	TTAACCATGCAAATCCTCTTGTATTA	57.184	30.769	0.00	0.00	30.28	0.98
932	964	4.481368	TTCGCTGGTATGTCTATGGTTT	57.519	40.909	0.00	0.00	0.00	3.27
950	982	8.407064	AGAGAACACTATGTAATACTCCTTTCG	58.593	37.037	0.00	0.00	0.00	3.46
980	1012	4.564406	CCATTGCCTAAGTTCACAGAGAGT	60.564	45.833	0.00	0.00	0.00	3.24
1203	1235	1.278127	TCGGAGGAGAATGAAACCACC	59.722	52.381	0.00	0.00	0.00	4.61
1384	1443	5.105432	TGGATCTTGTCAAGACAGAGAGATG	60.105	44.000	17.49	0.47	42.94	2.90
1455	1514	9.378551	TGTACAAGATAATTCACCATTAGTCAC	57.621	33.333	0.00	0.00	30.48	3.67
1493	1552	9.712305	CTCTTGTATTTAGGGTATGTTGGATAG	57.288	37.037	0.00	0.00	0.00	2.08
1494	1553	8.656806	CCTCTTGTATTTAGGGTATGTTGGATA	58.343	37.037	0.00	0.00	0.00	2.59
1495	1554	7.349859	TCCTCTTGTATTTAGGGTATGTTGGAT	59.650	37.037	0.00	0.00	0.00	3.41
1496	1555	6.674861	TCCTCTTGTATTTAGGGTATGTTGGA	59.325	38.462	0.00	0.00	0.00	3.53
1497	1556	6.895782	TCCTCTTGTATTTAGGGTATGTTGG	58.104	40.000	0.00	0.00	0.00	3.77
1499	1558	9.990868	AAAATCCTCTTGTATTTAGGGTATGTT	57.009	29.630	0.00	0.00	0.00	2.71
1501	1560	8.352942	GCAAAATCCTCTTGTATTTAGGGTATG	58.647	37.037	0.00	0.00	0.00	2.39
1502	1561	8.282256	AGCAAAATCCTCTTGTATTTAGGGTAT	58.718	33.333	0.00	0.00	0.00	2.73
1503	1562	7.639378	AGCAAAATCCTCTTGTATTTAGGGTA	58.361	34.615	0.00	0.00	0.00	3.69
1504	1563	6.494059	AGCAAAATCCTCTTGTATTTAGGGT	58.506	36.000	0.00	0.00	0.00	4.34
1505	1564	7.260603	CAAGCAAAATCCTCTTGTATTTAGGG	58.739	38.462	0.00	0.00	34.20	3.53
1506	1565	7.093771	ACCAAGCAAAATCCTCTTGTATTTAGG	60.094	37.037	0.00	0.00	36.41	2.69
1507	1566	7.830739	ACCAAGCAAAATCCTCTTGTATTTAG	58.169	34.615	0.00	0.00	36.41	1.85
1508	1567	7.775053	ACCAAGCAAAATCCTCTTGTATTTA	57.225	32.000	0.00	0.00	36.41	1.40
1509	1568	6.670695	ACCAAGCAAAATCCTCTTGTATTT	57.329	33.333	0.00	0.00	36.41	1.40
1510	1569	6.670695	AACCAAGCAAAATCCTCTTGTATT	57.329	33.333	0.00	0.00	36.41	1.89
1511	1570	7.775053	TTAACCAAGCAAAATCCTCTTGTAT	57.225	32.000	0.00	0.00	36.41	2.29
1512	1571	7.775053	ATTAACCAAGCAAAATCCTCTTGTA	57.225	32.000	0.00	0.00	36.41	2.41
1514	1573	6.591448	GGAATTAACCAAGCAAAATCCTCTTG	59.409	38.462	0.00	0.00	37.52	3.02
1515	1574	6.295859	GGGAATTAACCAAGCAAAATCCTCTT	60.296	38.462	0.00	0.00	0.00	2.85
1517	1576	5.419542	GGGAATTAACCAAGCAAAATCCTC	58.580	41.667	0.00	0.00	0.00	3.71
1519	1578	4.513442	GGGGAATTAACCAAGCAAAATCC	58.487	43.478	1.52	0.00	0.00	3.01
1539	1601	8.115384	TCCACAAGATATGATAATTAATGGGGG	58.885	37.037	0.00	0.00	29.82	5.40
1568	1630	6.594547	TGACCACCGAATTCGATATAAAAACA	59.405	34.615	28.76	12.91	43.02	2.83
1580	1642	1.927174	CATCTCGTGACCACCGAATTC	59.073	52.381	0.00	0.00	33.34	2.17
1890	1953	4.763793	ACAATGAAGACTTGGAGGATGTTG	59.236	41.667	0.00	0.00	0.00	3.33
1892	1955	4.647564	ACAATGAAGACTTGGAGGATGT	57.352	40.909	0.00	0.00	0.00	3.06
1926	1989	5.411831	TCATCATGACTAAGCAGACTTGT	57.588	39.130	0.00	0.00	36.57	3.16
1931	1994	3.495629	GGCCATCATCATGACTAAGCAGA	60.496	47.826	0.00	0.00	30.57	4.26
1959	2022	2.590007	CCGGCTGCCTGCACTATC	60.590	66.667	17.92	0.00	45.15	2.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.