AutoCloner

Multiple sequence alignment - TraesCS2B01G238100

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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	TraesCS2B01G238100	chr2B	100.000	2410	0	0	1	2410	239464575	239466984	0.000000e+00	4451
1	TraesCS2B01G238100	chr2B	95.657	875	36	2	1536	2410	406698008	406697136	0.000000e+00	1404
2	TraesCS2B01G238100	chr2B	95.455	880	34	6	1535	2410	431154930	431155807	0.000000e+00	1399
3	TraesCS2B01G238100	chr2B	94.589	887	43	5	1528	2410	448363101	448362216	0.000000e+00	1367
4	TraesCS2B01G238100	chr5B	96.132	879	31	3	1534	2410	368788808	368789685	0.000000e+00	1432
5	TraesCS2B01G238100	chr1B	95.357	883	34	7	1532	2410	307140825	307141704	0.000000e+00	1397
6	TraesCS2B01G238100	chr1B	95.006	881	40	4	1533	2410	32488970	32489849	0.000000e+00	1380
7	TraesCS2B01G238100	chr1B	94.989	878	39	5	1536	2410	45812169	45811294	0.000000e+00	1373
8	TraesCS2B01G238100	chr3B	95.713	863	34	3	1550	2410	798140797	798139936	0.000000e+00	1386
9	TraesCS2B01G238100	chr3B	95.006	881	39	5	1534	2410	43236116	43236995	0.000000e+00	1378
10	TraesCS2B01G238100	chr2A	93.243	740	30	7	783	1502	197924233	197924972	0.000000e+00	1072
11	TraesCS2B01G238100	chr2A	87.744	767	75	13	3	762	197923347	197924101	0.000000e+00	878
12	TraesCS2B01G238100	chr2D	94.415	376	17	2	1131	1502	183629486	183629861	2.080000e-160	575
13	TraesCS2B01G238100	chr2D	90.343	321	18	6	783	1090	183619466	183619786	2.230000e-110	409
14	TraesCS2B01G238100	chr2D	90.811	185	13	1	595	775	183619179	183619363	6.660000e-61	244

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	TraesCS2B01G238100	chr2B	239464575	239466984	2409	False	4451.0	4451	100.0000	1	2410	1	chr2B.!!$F1	2409
1	TraesCS2B01G238100	chr2B	406697136	406698008	872	True	1404.0	1404	95.6570	1536	2410	1	chr2B.!!$R1	874
2	TraesCS2B01G238100	chr2B	431154930	431155807	877	False	1399.0	1399	95.4550	1535	2410	1	chr2B.!!$F2	875
3	TraesCS2B01G238100	chr2B	448362216	448363101	885	True	1367.0	1367	94.5890	1528	2410	1	chr2B.!!$R2	882
4	TraesCS2B01G238100	chr5B	368788808	368789685	877	False	1432.0	1432	96.1320	1534	2410	1	chr5B.!!$F1	876
5	TraesCS2B01G238100	chr1B	307140825	307141704	879	False	1397.0	1397	95.3570	1532	2410	1	chr1B.!!$F2	878
6	TraesCS2B01G238100	chr1B	32488970	32489849	879	False	1380.0	1380	95.0060	1533	2410	1	chr1B.!!$F1	877
7	TraesCS2B01G238100	chr1B	45811294	45812169	875	True	1373.0	1373	94.9890	1536	2410	1	chr1B.!!$R1	874
8	TraesCS2B01G238100	chr3B	798139936	798140797	861	True	1386.0	1386	95.7130	1550	2410	1	chr3B.!!$R1	860
9	TraesCS2B01G238100	chr3B	43236116	43236995	879	False	1378.0	1378	95.0060	1534	2410	1	chr3B.!!$F1	876
10	TraesCS2B01G238100	chr2A	197923347	197924972	1625	False	975.0	1072	90.4935	3	1502	2	chr2A.!!$F1	1499
11	TraesCS2B01G238100	chr2D	183619179	183619786	607	False	326.5	409	90.5770	595	1090	2	chr2D.!!$F2	495

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
957	1087	1.03813	ATTCCTCCGTCTGTCTCCCG	61.038	60.0	0.0	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2053	2196	6.53766	GCTTTTAACATTACTCCACCGACTAT	59.462	38.462	0.0	0.0	0.0	2.12	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
193	196	6.556874	TGTTCAGGTAATCAATTTTTCCCCTT	59.443	34.615	0.00	0.00	0.00	3.95
208	211	4.953940	TCCCCTTCCTTTCAAACAAATG	57.046	40.909	0.00	0.00	0.00	2.32
563	566	5.751586	AGTACTTTTTGGACCAGAAGACAA	58.248	37.500	20.47	0.00	0.00	3.18
572	575	4.597507	TGGACCAGAAGACAACTAGGAAAT	59.402	41.667	0.00	0.00	0.00	2.17
579	582	7.661847	CCAGAAGACAACTAGGAAATTAACAGT	59.338	37.037	0.00	0.00	0.00	3.55
581	584	7.661847	AGAAGACAACTAGGAAATTAACAGTGG	59.338	37.037	0.00	0.00	0.00	4.00
583	586	4.765339	ACAACTAGGAAATTAACAGTGGGC	59.235	41.667	0.00	0.00	0.00	5.36
588	591	1.476488	GAAATTAACAGTGGGCGGCAT	59.524	47.619	12.47	0.00	0.00	4.40
739	746	4.804665	GGCGAAAGAAATACTCCAGAGTAC	59.195	45.833	9.63	0.00	45.61	2.73
778	787	2.243602	TTGGTAAAAACTCGGTCGCT	57.756	45.000	0.00	0.00	0.00	4.93
780	789	1.868498	TGGTAAAAACTCGGTCGCTTG	59.132	47.619	0.00	0.00	0.00	4.01
781	790	1.196127	GGTAAAAACTCGGTCGCTTGG	59.804	52.381	0.00	0.00	0.00	3.61
815	933	6.954487	TGATCTCAGGAATGAATTCAATGG	57.046	37.500	13.09	1.23	38.53	3.16
842	960	5.438761	AAAAGGTCCAAAACTGATCGAAG	57.561	39.130	0.00	0.00	0.00	3.79
926	1056	1.518929	GCAACGTCATAGCAGATCGAC	59.481	52.381	0.00	0.00	0.00	4.20
957	1087	1.038130	ATTCCTCCGTCTGTCTCCCG	61.038	60.000	0.00	0.00	0.00	5.14
1027	1158	2.540383	ACAGCCTGAAGATGACCTGTA	58.460	47.619	0.00	0.00	32.32	2.74
1129	1260	3.444657	CGCGAGCAAATATTGAGCC	57.555	52.632	0.00	2.15	0.00	4.70
1139	1272	5.244626	AGCAAATATTGAGCCTTTCTGTTGT	59.755	36.000	8.96	0.00	0.00	3.32
1166	1300	3.300009	CTGATTGTTTTTCTGCCGTGAC	58.700	45.455	0.00	0.00	0.00	3.67
1169	1303	1.021202	TGTTTTTCTGCCGTGACTGG	58.979	50.000	0.00	0.00	0.00	4.00
1308	1442	2.435059	GCTGCTCCAGGTCGAACC	60.435	66.667	0.00	0.00	38.99	3.62
1485	1619	7.056006	AGGAGCCAAATGTTTTCTTTGAAAAT	58.944	30.769	8.43	0.00	35.99	1.82
1486	1620	7.012610	AGGAGCCAAATGTTTTCTTTGAAAATG	59.987	33.333	8.43	3.81	35.99	2.32
1502	1640	7.519032	TTGAAAATGTCTCCCGTCTATTTTT	57.481	32.000	0.00	0.00	32.79	1.94
1522	1660	2.443887	TTTTGAGTAACCGTCTCCCG	57.556	50.000	0.00	0.00	0.00	5.14
1523	1661	1.331214	TTTGAGTAACCGTCTCCCGT	58.669	50.000	0.00	0.00	33.66	5.28
1524	1662	0.883833	TTGAGTAACCGTCTCCCGTC	59.116	55.000	0.00	0.00	33.66	4.79
1525	1663	0.037303	TGAGTAACCGTCTCCCGTCT	59.963	55.000	0.00	0.00	33.66	4.18
1526	1664	1.278985	TGAGTAACCGTCTCCCGTCTA	59.721	52.381	0.00	0.00	33.66	2.59
1527	1665	2.092753	TGAGTAACCGTCTCCCGTCTAT	60.093	50.000	0.00	0.00	33.66	1.98
1528	1666	2.948315	GAGTAACCGTCTCCCGTCTATT	59.052	50.000	0.00	0.00	33.66	1.73
1529	1667	3.359950	AGTAACCGTCTCCCGTCTATTT	58.640	45.455	0.00	0.00	33.66	1.40
1530	1668	3.766051	AGTAACCGTCTCCCGTCTATTTT	59.234	43.478	0.00	0.00	33.66	1.82
1531	1669	2.667473	ACCGTCTCCCGTCTATTTTG	57.333	50.000	0.00	0.00	33.66	2.44
1683	1824	0.950555	CACACAGAGCGCTAAAGGCA	60.951	55.000	11.50	0.00	41.91	4.75
2028	2171	3.117738	AGGCAGACTCAATCCCATTAAGG	60.118	47.826	0.00	0.00	37.03	2.69
2053	2196	7.382898	GGAAGTCCCAAATAAAGCATTAACAA	58.617	34.615	0.00	0.00	34.14	2.83
2189	2332	4.960469	CCTAGTAGGTCCTGTCCAATTACA	59.040	45.833	8.17	0.00	0.00	2.41
2251	2394	6.102663	TGGACAAACCACATAAACACTTTTG	58.897	36.000	0.00	0.00	44.64	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	112	8.260818	TCAAGTGTATTTTTGAAAATGGGTGAA	58.739	29.630	11.02	0.00	38.90	3.18
111	113	7.708752	GTCAAGTGTATTTTTGAAAATGGGTGA	59.291	33.333	11.02	5.75	38.90	4.02
165	168	8.536175	GGGGAAAAATTGATTACCTGAACAATA	58.464	33.333	5.68	0.00	33.50	1.90
174	177	6.620877	AAGGAAGGGGAAAAATTGATTACC	57.379	37.500	0.00	0.00	0.00	2.85
183	186	5.763876	TTGTTTGAAAGGAAGGGGAAAAA	57.236	34.783	0.00	0.00	0.00	1.94
535	538	7.013369	GTCTTCTGGTCCAAAAAGTACTCAAAT	59.987	37.037	11.58	0.00	0.00	2.32
563	566	3.606687	CGCCCACTGTTAATTTCCTAGT	58.393	45.455	0.00	0.00	0.00	2.57
572	575	2.428544	AATATGCCGCCCACTGTTAA	57.571	45.000	0.00	0.00	0.00	2.01
579	582	0.840617	TGTCCTAAATATGCCGCCCA	59.159	50.000	0.00	0.00	0.00	5.36
581	584	2.256117	ACTGTCCTAAATATGCCGCC	57.744	50.000	0.00	0.00	0.00	6.13
583	586	5.635280	CAGTCATACTGTCCTAAATATGCCG	59.365	44.000	0.00	0.00	41.19	5.69
613	616	1.944676	GTCATCCGTCATCCGTCGC	60.945	63.158	0.00	0.00	33.66	5.19
615	618	1.299165	CCGTCATCCGTCATCCGTC	60.299	63.158	0.00	0.00	33.66	4.79
632	635	3.555966	CCCACCTGGTTAATCAGATTCC	58.444	50.000	17.60	0.00	36.93	3.01
634	637	2.311542	TGCCCACCTGGTTAATCAGATT	59.688	45.455	17.60	0.20	36.93	2.40
719	722	8.741841	ACTACTGTACTCTGGAGTATTTCTTTC	58.258	37.037	12.72	0.91	44.73	2.62
762	769	1.869132	ACCAAGCGACCGAGTTTTTAC	59.131	47.619	0.00	0.00	0.00	2.01
775	784	3.374058	AGATCAAACCGAATAACCAAGCG	59.626	43.478	0.00	0.00	0.00	4.68
778	787	4.941263	CCTGAGATCAAACCGAATAACCAA	59.059	41.667	0.00	0.00	0.00	3.67
780	789	4.766375	TCCTGAGATCAAACCGAATAACC	58.234	43.478	0.00	0.00	0.00	2.85
781	790	6.538742	TCATTCCTGAGATCAAACCGAATAAC	59.461	38.462	0.00	0.00	0.00	1.89
815	933	7.590279	TCGATCAGTTTTGGACCTTTTATTTC	58.410	34.615	0.00	0.00	0.00	2.17
842	960	2.159254	TCGAAGGCCAGCATTAATTTGC	60.159	45.455	5.01	0.00	43.09	3.68
904	1034	1.560923	GATCTGCTATGACGTTGCGT	58.439	50.000	0.00	0.00	45.10	5.24
926	1056	0.804989	GGAGGAATCGTTTGCTGTGG	59.195	55.000	4.86	0.00	33.10	4.17
957	1087	1.360911	GAGAGGATCGAGCGTTCCC	59.639	63.158	14.46	7.91	42.67	3.97
1109	1240	0.027979	GCTCAATATTTGCTCGCGCA	59.972	50.000	8.75	0.00	46.24	6.09
1125	1256	1.129437	GCGATCACAACAGAAAGGCTC	59.871	52.381	0.00	0.00	0.00	4.70
1126	1257	1.160137	GCGATCACAACAGAAAGGCT	58.840	50.000	0.00	0.00	0.00	4.58
1127	1258	1.135859	CAGCGATCACAACAGAAAGGC	60.136	52.381	0.00	0.00	0.00	4.35
1128	1259	2.416747	TCAGCGATCACAACAGAAAGG	58.583	47.619	0.00	0.00	0.00	3.11
1129	1260	4.083643	ACAATCAGCGATCACAACAGAAAG	60.084	41.667	0.00	0.00	0.00	2.62
1139	1272	3.366273	GGCAGAAAAACAATCAGCGATCA	60.366	43.478	0.00	0.00	30.82	2.92
1372	1506	1.083401	CACTTCTGTTGCACGACGC	60.083	57.895	0.00	0.00	42.89	5.19
1456	1590	2.893489	AGAAAACATTTGGCTCCTCCAC	59.107	45.455	0.00	0.00	46.55	4.02
1502	1640	2.758009	CGGGAGACGGTTACTCAAAAA	58.242	47.619	0.00	0.00	39.42	1.94
1503	1641	2.443887	CGGGAGACGGTTACTCAAAA	57.556	50.000	0.00	0.00	39.42	2.44
1558	1699	1.260538	ACTCTTGATGCAGAGGCCGA	61.261	55.000	0.00	0.00	44.23	5.54
1617	1758	8.306761	AGTTTGAGACTTTGAAACTTTGTTGAT	58.693	29.630	0.00	0.00	36.71	2.57
1618	1759	7.657336	AGTTTGAGACTTTGAAACTTTGTTGA	58.343	30.769	0.00	0.00	36.71	3.18
1648	1789	2.760092	TGTGTGAGCTGCCTTTTCTTTT	59.240	40.909	0.00	0.00	0.00	2.27
1683	1824	6.524101	TTTCTTGGCTAGTTTGTGTTTCTT	57.476	33.333	0.00	0.00	0.00	2.52
2028	2171	6.930731	TGTTAATGCTTTATTTGGGACTTCC	58.069	36.000	0.00	0.00	0.00	3.46
2053	2196	6.537660	GCTTTTAACATTACTCCACCGACTAT	59.462	38.462	0.00	0.00	0.00	2.12
2337	2480	7.183460	AGTTGACTAGGTCTGGAGTATTTACT	58.817	38.462	0.00	0.00	34.71	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.