AutoCloner

Multiple sequence alignment - TraesCS2B01G024800

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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	TraesCS2B01G024800	chr2B	100.000	2957	0	0	1	2957	11444443	11447399	0.000000e+00	5461.0
1	TraesCS2B01G024800	chr2B	93.731	2568	133	13	407	2957	12996571	12994015	0.000000e+00	3825.0
2	TraesCS2B01G024800	chr2B	80.253	1580	273	28	998	2548	11454229	11452660	0.000000e+00	1153.0
3	TraesCS2B01G024800	chr2B	79.584	1587	274	33	998	2548	12966428	12968000	0.000000e+00	1090.0
4	TraesCS2B01G024800	chr2B	77.948	1569	288	30	1000	2546	12942429	12943961	0.000000e+00	928.0
5	TraesCS2B01G024800	chr2B	94.681	94	5	0	292	385	12996746	12996653	2.370000e-31	147.0
6	TraesCS2B01G024800	chr2B	88.158	76	9	0	2742	2817	361634723	361634648	1.130000e-14	91.6
7	TraesCS2B01G024800	chr2B	92.000	50	4	0	2677	2726	741952062	741952013	1.470000e-08	71.3
8	TraesCS2B01G024800	chr2D	95.286	2609	96	9	359	2957	9665887	9663296	0.000000e+00	4111.0
9	TraesCS2B01G024800	chr2D	87.057	1723	195	18	828	2526	8695486	8697204	0.000000e+00	1921.0
10	TraesCS2B01G024800	chr2D	83.813	1668	229	26	831	2474	19586841	19588491	0.000000e+00	1546.0
11	TraesCS2B01G024800	chr2D	82.777	1527	235	15	995	2511	8670684	8672192	0.000000e+00	1338.0
12	TraesCS2B01G024800	chr2D	88.889	261	6	3	1	240	9666455	9666197	1.720000e-77	300.0
13	TraesCS2B01G024800	chr2D	96.296	108	4	0	292	399	9666008	9665901	8.420000e-41	178.0
14	TraesCS2B01G024800	chr2D	100.000	56	0	0	241	296	9666170	9666115	1.450000e-18	104.0
15	TraesCS2B01G024800	chr2A	94.065	2443	103	12	359	2796	8737462	8735057	0.000000e+00	3670.0
16	TraesCS2B01G024800	chr2A	86.446	1210	137	16	828	2018	86432283	86431082	0.000000e+00	1301.0
17	TraesCS2B01G024800	chr2A	80.026	1562	273	25	998	2530	8727309	8728860	0.000000e+00	1120.0
18	TraesCS2B01G024800	chr2A	86.667	270	4	4	1	240	8738067	8737800	1.350000e-68	270.0
19	TraesCS2B01G024800	chr2A	96.296	108	4	0	292	399	8737583	8737476	8.420000e-41	178.0
20	TraesCS2B01G024800	chr2A	98.214	56	1	0	241	296	8737773	8737718	6.740000e-17	99.0
21	TraesCS2B01G024800	chrUn	87.997	1308	141	8	1254	2550	225597635	225596333	0.000000e+00	1531.0
22	TraesCS2B01G024800	chrUn	87.997	1308	141	8	1254	2550	261780590	261781892	0.000000e+00	1531.0
23	TraesCS2B01G024800	chrUn	87.997	1308	141	8	1254	2550	273226881	273225579	0.000000e+00	1531.0
24	TraesCS2B01G024800	chr3A	72.581	992	250	20	1390	2370	9951271	9952251	3.700000e-79	305.0
25	TraesCS2B01G024800	chr4D	90.141	71	5	2	2742	2811	61955088	61955019	1.130000e-14	91.6
26	TraesCS2B01G024800	chr4A	87.838	74	5	3	2742	2811	581503973	581504046	1.890000e-12	84.2
27	TraesCS2B01G024800	chr5B	85.366	82	8	2	2742	2819	131015877	131015796	6.790000e-12	82.4
28	TraesCS2B01G024800	chr3B	85.542	83	6	3	2742	2819	179349909	179349990	6.790000e-12	82.4
29	TraesCS2B01G024800	chr1A	82.609	92	13	2	2742	2831	505186483	505186393	8.790000e-11	78.7

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	TraesCS2B01G024800	chr2B	11444443	11447399	2956	False	5461.00	5461	100.00000	1	2957	1	chr2B.!!$F1	2956
1	TraesCS2B01G024800	chr2B	12994015	12996746	2731	True	1986.00	3825	94.20600	292	2957	2	chr2B.!!$R4	2665
2	TraesCS2B01G024800	chr2B	11452660	11454229	1569	True	1153.00	1153	80.25300	998	2548	1	chr2B.!!$R1	1550
3	TraesCS2B01G024800	chr2B	12966428	12968000	1572	False	1090.00	1090	79.58400	998	2548	1	chr2B.!!$F3	1550
4	TraesCS2B01G024800	chr2B	12942429	12943961	1532	False	928.00	928	77.94800	1000	2546	1	chr2B.!!$F2	1546
5	TraesCS2B01G024800	chr2D	8695486	8697204	1718	False	1921.00	1921	87.05700	828	2526	1	chr2D.!!$F2	1698
6	TraesCS2B01G024800	chr2D	19586841	19588491	1650	False	1546.00	1546	83.81300	831	2474	1	chr2D.!!$F3	1643
7	TraesCS2B01G024800	chr2D	8670684	8672192	1508	False	1338.00	1338	82.77700	995	2511	1	chr2D.!!$F1	1516
8	TraesCS2B01G024800	chr2D	9663296	9666455	3159	True	1173.25	4111	95.11775	1	2957	4	chr2D.!!$R1	2956
9	TraesCS2B01G024800	chr2A	86431082	86432283	1201	True	1301.00	1301	86.44600	828	2018	1	chr2A.!!$R1	1190
10	TraesCS2B01G024800	chr2A	8727309	8728860	1551	False	1120.00	1120	80.02600	998	2530	1	chr2A.!!$F1	1532
11	TraesCS2B01G024800	chr2A	8735057	8738067	3010	True	1054.25	3670	93.81050	1	2796	4	chr2A.!!$R2	2795
12	TraesCS2B01G024800	chrUn	225596333	225597635	1302	True	1531.00	1531	87.99700	1254	2550	1	chrUn.!!$R1	1296
13	TraesCS2B01G024800	chrUn	261780590	261781892	1302	False	1531.00	1531	87.99700	1254	2550	1	chrUn.!!$F1	1296
14	TraesCS2B01G024800	chrUn	273225579	273226881	1302	True	1531.00	1531	87.99700	1254	2550	1	chrUn.!!$R2	1296
15	TraesCS2B01G024800	chr3A	9951271	9952251	980	False	305.00	305	72.58100	1390	2370	1	chr3A.!!$F1	980

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
238	269	0.673022	GAGCAACCCAGCAGAGTGAG	60.673	60.0	0.0	0.0	36.85	3.51	F
817	1109	0.840722	ATCTCCCCTGGTGACCGTTT	60.841	55.0	0.0	0.0	0.00	3.60	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1146	1452	1.039068	CATCTGCCTCCTCGATGACT	58.961	55.0	0.0	0.0	37.35	3.41	R
2740	3092	0.533951	ACTGAGCGAGCACATCATCA	59.466	50.0	0.0	0.0	0.00	3.07	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
191	222	2.544844	TGGAGAACGGAGGGAGTATT	57.455	50.000	0.00	0.00	0.00	1.89
203	234	4.299978	GAGGGAGTATTGCGTAATCACTC	58.700	47.826	18.42	18.42	46.80	3.51
223	254	1.425412	GACTAGGAAAAACGCGAGCA	58.575	50.000	15.93	0.00	0.00	4.26
236	267	2.031516	CGAGCAACCCAGCAGAGTG	61.032	63.158	0.00	0.00	36.85	3.51
237	268	1.372683	GAGCAACCCAGCAGAGTGA	59.627	57.895	0.00	0.00	36.85	3.41
238	269	0.673022	GAGCAACCCAGCAGAGTGAG	60.673	60.000	0.00	0.00	36.85	3.51
399	648	4.443063	GCGTATATGAATGCGTCAAGTGTA	59.557	41.667	0.00	0.00	42.44	2.90
485	770	5.632034	ATTCTTCTACAGGTATTCCCACC	57.368	43.478	0.00	0.00	39.02	4.61
817	1109	0.840722	ATCTCCCCTGGTGACCGTTT	60.841	55.000	0.00	0.00	0.00	3.60
823	1115	1.336755	CCCTGGTGACCGTTTGAAAAG	59.663	52.381	0.00	0.00	0.00	2.27
843	1135	4.803098	AGAGCAAGGATACACGTTTACT	57.197	40.909	0.00	0.00	41.41	2.24
891	1183	2.917933	TCGCCATCAATAGTTTGGAGG	58.082	47.619	0.00	0.00	33.44	4.30
966	1265	4.140829	TCCAGAGTCCATAGAGATCACCAT	60.141	45.833	0.00	0.00	0.00	3.55
1146	1452	3.229293	CCTCCTGATGAGAGTCAGCATA	58.771	50.000	0.00	0.00	42.33	3.14
1341	1647	7.178274	AGCAACAACTTGTATTTATCCATTCCA	59.822	33.333	0.00	0.00	0.00	3.53
1355	1661	2.749076	CCATTCCATTCAAGCGTTCTCA	59.251	45.455	0.00	0.00	0.00	3.27
1386	1693	2.242965	TGAGATGGATGACAAGGCCATT	59.757	45.455	5.01	0.00	42.22	3.16
1577	1888	1.265365	GAGCTTCTTGTTGGAGCACAC	59.735	52.381	0.00	0.00	0.00	3.82
1693	2017	3.964688	TCGCCCACAATTCTCCTCTATTA	59.035	43.478	0.00	0.00	0.00	0.98
1732	2056	4.102524	ACAACCTCTTGATGGTACTTGACA	59.897	41.667	0.00	0.00	36.69	3.58
1738	2062	6.065976	TCTTGATGGTACTTGACAATGGAT	57.934	37.500	0.00	0.00	0.00	3.41
2131	2462	6.748658	CGTTGCATATTTGACAAGATGACAAT	59.251	34.615	13.57	0.00	34.03	2.71
2141	2472	6.614160	TGACAAGATGACAATGCATGTTAAG	58.386	36.000	0.00	0.00	44.12	1.85
2188	2519	1.341383	CCCCAGCAAGCTTATGGAACT	60.341	52.381	24.69	4.03	36.09	3.01
2281	2618	4.088634	CCAATCAAGGAGGAATCACCAAA	58.911	43.478	0.00	0.00	42.04	3.28
2456	2802	2.282958	TCAGGGAGGAAGCGACGT	60.283	61.111	0.00	0.00	0.00	4.34
2487	2835	6.710295	GCCAATCTAATTTTGTTTTGGGACTT	59.290	34.615	12.86	0.00	35.31	3.01
2600	2951	8.251383	TCTAATATGTTTTTGTTTTGGGTGGA	57.749	30.769	0.00	0.00	0.00	4.02
2645	2997	7.814264	ATTTCAGAATAAGGCATAGTTCCAG	57.186	36.000	0.00	0.00	0.00	3.86
2720	3072	4.538490	TGGTTAGGTGAACAATGGTATCCT	59.462	41.667	0.00	0.00	40.09	3.24
2729	3081	2.919602	ACAATGGTATCCTCAACCCACT	59.080	45.455	0.00	0.00	36.06	4.00
2751	3103	3.759581	AGGTTCAAGTTGATGATGTGCT	58.240	40.909	6.36	0.00	0.00	4.40
2752	3104	3.755378	AGGTTCAAGTTGATGATGTGCTC	59.245	43.478	6.36	0.00	0.00	4.26
2766	3118	0.658368	GTGCTCGCTCAGTATCTCGA	59.342	55.000	0.00	0.00	0.00	4.04
2814	3170	4.124238	GTGCGTTTATAGGGTTGAGCATA	58.876	43.478	0.00	0.00	35.76	3.14
2817	3173	4.755123	GCGTTTATAGGGTTGAGCATATGT	59.245	41.667	4.29	0.00	0.00	2.29
2823	3179	2.954318	AGGGTTGAGCATATGTGATTGC	59.046	45.455	4.29	0.00	39.17	3.56
2873	3229	6.920569	AGTCAACACGTTAATCCATAATCC	57.079	37.500	0.00	0.00	0.00	3.01
2874	3230	6.411376	AGTCAACACGTTAATCCATAATCCA	58.589	36.000	0.00	0.00	0.00	3.41
2875	3231	7.054124	AGTCAACACGTTAATCCATAATCCAT	58.946	34.615	0.00	0.00	0.00	3.41
2876	3232	8.208224	AGTCAACACGTTAATCCATAATCCATA	58.792	33.333	0.00	0.00	0.00	2.74
2919	3275	1.939974	TGATCTTGCGTATGACAGCC	58.060	50.000	0.00	0.00	0.00	4.85
2920	3276	1.221414	GATCTTGCGTATGACAGCCC	58.779	55.000	0.00	0.00	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
146	177	6.838382	AACTGAAGTTGTAGGTTTATCCTGT	58.162	36.000	0.00	0.00	40.98	4.00
168	199	2.108970	ACTCCCTCCGTTCTCCATAAC	58.891	52.381	0.00	0.00	0.00	1.89
191	222	2.635714	TCCTAGTCGAGTGATTACGCA	58.364	47.619	2.10	0.00	0.00	5.24
203	234	0.365859	GCTCGCGTTTTTCCTAGTCG	59.634	55.000	5.77	0.00	0.00	4.18
223	254	1.346068	GAAGTCTCACTCTGCTGGGTT	59.654	52.381	0.00	0.00	0.00	4.11
236	267	1.066502	GGCCTGACCTGAAGAAGTCTC	60.067	57.143	0.00	0.00	34.02	3.36
237	268	0.980423	GGCCTGACCTGAAGAAGTCT	59.020	55.000	0.00	0.00	34.02	3.24
238	269	0.390472	CGGCCTGACCTGAAGAAGTC	60.390	60.000	0.00	0.00	35.61	3.01
347	542	1.462541	GCGTCTCAACTGTTGATTCGC	60.463	52.381	33.26	33.26	45.81	4.70
388	637	5.840940	ATTAGACACTTTACACTTGACGC	57.159	39.130	0.00	0.00	0.00	5.19
399	648	6.094186	GCCTGCTTAGCTTAATTAGACACTTT	59.906	38.462	5.60	0.00	0.00	2.66
485	770	6.469410	TGAAGTTTACTATACAACACAGGGG	58.531	40.000	0.00	0.00	0.00	4.79
806	1098	1.673920	GCTCTTTTCAAACGGTCACCA	59.326	47.619	0.00	0.00	0.00	4.17
817	1109	4.002906	ACGTGTATCCTTGCTCTTTTCA	57.997	40.909	0.00	0.00	0.00	2.69
823	1115	3.062234	GCAGTAAACGTGTATCCTTGCTC	59.938	47.826	0.00	0.00	0.00	4.26
966	1265	1.548719	ACGGTCGATGATGGAAGTTGA	59.451	47.619	0.00	0.00	0.00	3.18
1146	1452	1.039068	CATCTGCCTCCTCGATGACT	58.961	55.000	0.00	0.00	37.35	3.41
1341	1647	5.066505	AGTTTTTGTCTGAGAACGCTTGAAT	59.933	36.000	0.00	0.00	0.00	2.57
1355	1661	5.624159	TGTCATCCATCTCAGTTTTTGTCT	58.376	37.500	0.00	0.00	0.00	3.41
1386	1693	1.378646	ACCATCTGACTCGAGGCGA	60.379	57.895	18.41	15.79	0.00	5.54
1577	1888	2.020131	GCAGGTGCATGAAGATCGG	58.980	57.895	0.00	0.00	41.59	4.18
1675	1999	6.294473	AGTGCATAATAGAGGAGAATTGTGG	58.706	40.000	0.00	0.00	0.00	4.17
1693	2017	2.821969	GGTTGTCTCCATTCAAGTGCAT	59.178	45.455	0.00	0.00	0.00	3.96
1721	2045	3.308117	GGTCCATCCATTGTCAAGTACCA	60.308	47.826	0.00	0.00	35.97	3.25
1738	2062	2.582172	AGATCATCCCAAACATGGTCCA	59.418	45.455	0.00	0.00	32.49	4.02
2057	2388	5.633601	TCTCAACACATGTGAGAACGTATTC	59.366	40.000	31.94	0.00	35.97	1.75
2141	2472	4.333926	GCACCATGTATGAAGAGGTTTCTC	59.666	45.833	0.00	0.00	40.25	2.87
2188	2519	2.429610	GTTATGTCGACTGGAAGGCCTA	59.570	50.000	17.92	0.00	40.92	3.93
2281	2618	3.418995	AGAAGCTCTGCAAATGTCACAT	58.581	40.909	0.00	0.00	0.00	3.21
2306	2643	2.376109	TCTGGTCTAACACTCGGATCC	58.624	52.381	0.00	0.00	0.00	3.36
2312	2649	4.083565	AGTCTCCTTCTGGTCTAACACTC	58.916	47.826	0.00	0.00	34.23	3.51
2576	2927	7.602265	CCTCCACCCAAAACAAAAACATATTAG	59.398	37.037	0.00	0.00	0.00	1.73
2579	2930	5.221823	CCCTCCACCCAAAACAAAAACATAT	60.222	40.000	0.00	0.00	0.00	1.78
2611	2963	7.491682	TGCCTTATTCTGAAATTTATTCAGGC	58.508	34.615	15.86	12.16	44.43	4.85
2662	3014	5.499047	GTTGGTTCACGTCTTCTGTTTTAG	58.501	41.667	0.00	0.00	0.00	1.85
2729	3081	4.910195	AGCACATCATCAACTTGAACCTA	58.090	39.130	0.00	0.00	0.00	3.08
2740	3092	0.533951	ACTGAGCGAGCACATCATCA	59.466	50.000	0.00	0.00	0.00	3.07
2751	3103	1.671328	CACCTTCGAGATACTGAGCGA	59.329	52.381	0.00	0.00	0.00	4.93
2752	3104	1.862008	GCACCTTCGAGATACTGAGCG	60.862	57.143	0.00	0.00	0.00	5.03
2766	3118	1.294068	TCCTACCCCTATGAGCACCTT	59.706	52.381	0.00	0.00	0.00	3.50
2814	3170	9.926158	TTTGTTTTTATCATAGTGCAATCACAT	57.074	25.926	0.00	0.00	45.49	3.21
2919	3275	9.109393	TCATATCTTTCAGACTTTTAAATCCGG	57.891	33.333	0.00	0.00	0.00	5.14
2920	3276	9.922305	GTCATATCTTTCAGACTTTTAAATCCG	57.078	33.333	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.