AutoCloner

Multiple sequence alignment - TraesCS2B01G193400

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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	TraesCS2B01G193400	chr2B	100.000	3060	0	0	1	3060	169576963	169573904	0.000000e+00	5651
1	TraesCS2B01G193400	chr2B	93.191	1777	76	18	1318	3060	168823820	168825585	0.000000e+00	2569
2	TraesCS2B01G193400	chr2B	96.186	1416	45	2	1651	3060	169391319	169389907	0.000000e+00	2307
3	TraesCS2B01G193400	chr2B	95.975	1416	48	2	1651	3060	169405497	169404085	0.000000e+00	2290
4	TraesCS2B01G193400	chr2B	95.833	1416	50	2	1651	3060	169377390	169375978	0.000000e+00	2279
5	TraesCS2B01G193400	chr2B	94.024	820	39	5	665	1481	169378209	169377397	0.000000e+00	1234
6	TraesCS2B01G193400	chr2B	94.024	820	39	5	665	1481	169406316	169405504	0.000000e+00	1234
7	TraesCS2B01G193400	chr2B	93.537	820	42	6	665	1481	169392137	169391326	0.000000e+00	1210
8	TraesCS2B01G193400	chr2B	83.117	770	75	27	730	1461	169608685	169609437	0.000000e+00	651
9	TraesCS2B01G193400	chr2B	79.032	806	128	28	1602	2388	169609970	169610753	5.850000e-142	514
10	TraesCS2B01G193400	chr2B	95.956	272	11	0	1011	1282	168823552	168823823	2.800000e-120	442
11	TraesCS2B01G193400	chr2B	94.545	275	15	0	750	1024	168822392	168822666	2.820000e-115	425
12	TraesCS2B01G193400	chr4D	95.522	670	30	0	4	673	261162359	261163028	0.000000e+00	1072
13	TraesCS2B01G193400	chr4D	95.231	671	32	0	3	673	377879288	377879958	0.000000e+00	1062
14	TraesCS2B01G193400	chr6D	95.380	671	31	0	3	673	331807235	331806565	0.000000e+00	1068
15	TraesCS2B01G193400	chr3D	95.380	671	30	1	3	673	366444684	366444015	0.000000e+00	1066
16	TraesCS2B01G193400	chr3D	95.231	671	32	0	3	673	359506401	359507071	0.000000e+00	1062
17	TraesCS2B01G193400	chr3D	95.231	671	32	0	3	673	505195779	505195109	0.000000e+00	1062
18	TraesCS2B01G193400	chr1D	95.373	670	31	0	4	673	280345382	280344713	0.000000e+00	1066
19	TraesCS2B01G193400	chr1D	95.231	671	30	1	3	673	182609933	182609265	0.000000e+00	1061
20	TraesCS2B01G193400	chr7D	95.231	671	31	1	3	673	449843695	449844364	0.000000e+00	1061

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	TraesCS2B01G193400	chr2B	169573904	169576963	3059	True	5651.000000	5651	100.0000	1	3060	1	chr2B.!!$R1	3059
1	TraesCS2B01G193400	chr2B	169404085	169406316	2231	True	1762.000000	2290	94.9995	665	3060	2	chr2B.!!$R4	2395
2	TraesCS2B01G193400	chr2B	169389907	169392137	2230	True	1758.500000	2307	94.8615	665	3060	2	chr2B.!!$R3	2395
3	TraesCS2B01G193400	chr2B	169375978	169378209	2231	True	1756.500000	2279	94.9285	665	3060	2	chr2B.!!$R2	2395
4	TraesCS2B01G193400	chr2B	168822392	168825585	3193	False	1145.333333	2569	94.5640	750	3060	3	chr2B.!!$F1	2310
5	TraesCS2B01G193400	chr2B	169608685	169610753	2068	False	582.500000	651	81.0745	730	2388	2	chr2B.!!$F2	1658
6	TraesCS2B01G193400	chr4D	261162359	261163028	669	False	1072.000000	1072	95.5220	4	673	1	chr4D.!!$F1	669
7	TraesCS2B01G193400	chr4D	377879288	377879958	670	False	1062.000000	1062	95.2310	3	673	1	chr4D.!!$F2	670
8	TraesCS2B01G193400	chr6D	331806565	331807235	670	True	1068.000000	1068	95.3800	3	673	1	chr6D.!!$R1	670
9	TraesCS2B01G193400	chr3D	366444015	366444684	669	True	1066.000000	1066	95.3800	3	673	1	chr3D.!!$R1	670
10	TraesCS2B01G193400	chr3D	359506401	359507071	670	False	1062.000000	1062	95.2310	3	673	1	chr3D.!!$F1	670
11	TraesCS2B01G193400	chr3D	505195109	505195779	670	True	1062.000000	1062	95.2310	3	673	1	chr3D.!!$R2	670
12	TraesCS2B01G193400	chr1D	280344713	280345382	669	True	1066.000000	1066	95.3730	4	673	1	chr1D.!!$R2	669
13	TraesCS2B01G193400	chr1D	182609265	182609933	668	True	1061.000000	1061	95.2310	3	673	1	chr1D.!!$R1	670
14	TraesCS2B01G193400	chr7D	449843695	449844364	669	False	1061.000000	1061	95.2310	3	673	1	chr7D.!!$F1	670

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
974	993	0.261696	AGAGCACAAAACCAACCCCT	59.738	50.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2374	3742	0.106569	TACGATAGAGGGTTGGGCGA	60.107	55.0	0.0	0.0	41.38	5.54	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
100	101	5.437060	AGATTGTGCCCTATTTAACGTGAT	58.563	37.500	0.00	0.00	0.00	3.06
227	228	1.610624	CCATTACGCTGTGGTGTTCCT	60.611	52.381	0.00	0.00	37.38	3.36
401	402	9.681692	TCAAATGTTTCAGACTTATGTTTCATG	57.318	29.630	0.00	0.00	0.00	3.07
457	458	6.368791	TCTGTGAAGGTCAGAAAATAACGATG	59.631	38.462	0.00	0.00	38.71	3.84
485	486	1.860950	CGAGCATTAACACTCATCGGG	59.139	52.381	7.21	0.00	32.98	5.14
500	501	1.523711	CGGGCCGCATACATCAGTT	60.524	57.895	15.42	0.00	0.00	3.16
502	503	1.808512	CGGGCCGCATACATCAGTTTA	60.809	52.381	15.42	0.00	0.00	2.01
635	636	0.899720	CCAAAAGCCCATCAGCATGT	59.100	50.000	0.00	0.00	37.40	3.21
683	684	4.608170	ATGACCTAAACCATCCAACCAT	57.392	40.909	0.00	0.00	0.00	3.55
697	698	2.228582	CCAACCATTGCATTGTCGAGAA	59.771	45.455	7.75	0.00	0.00	2.87
698	699	3.236816	CAACCATTGCATTGTCGAGAAC	58.763	45.455	0.00	0.00	0.00	3.01
699	700	1.464608	ACCATTGCATTGTCGAGAACG	59.535	47.619	0.00	0.00	41.26	3.95
700	701	1.731709	CCATTGCATTGTCGAGAACGA	59.268	47.619	0.00	0.00	46.56	3.85
774	778	8.830580	CGAAAGATCAGACAATATAAATGTGGT	58.169	33.333	0.00	0.00	0.00	4.16
826	837	0.606604	GCACCGAGTAGGAAGGAACA	59.393	55.000	0.00	0.00	45.00	3.18
913	932	4.080072	TGGTTTGATATGCATCTACACCCA	60.080	41.667	0.19	8.06	31.93	4.51
934	953	4.849810	CCACCTATATATTTCCCTCACCCA	59.150	45.833	0.00	0.00	0.00	4.51
967	986	1.963515	ACCCATTCAGAGCACAAAACC	59.036	47.619	0.00	0.00	0.00	3.27
974	993	0.261696	AGAGCACAAAACCAACCCCT	59.738	50.000	0.00	0.00	0.00	4.79
1039	1957	6.483307	ACATATGTTTATCACCCTTGTCATCG	59.517	38.462	1.41	0.00	0.00	3.84
1088	2009	5.407049	AGCCCAAGGTATGTATAGACATCT	58.593	41.667	6.19	0.00	43.01	2.90
1090	2011	6.330250	AGCCCAAGGTATGTATAGACATCTTT	59.670	38.462	6.19	0.00	43.01	2.52
1140	2063	6.187727	AGAAGTGGACTTTTACCAGATTCA	57.812	37.500	0.00	0.00	37.06	2.57
1275	2201	7.748847	TCTCGAGTTTTAACATCTTTTATGGC	58.251	34.615	13.13	0.00	0.00	4.40
1282	2214	9.575783	GTTTTAACATCTTTTATGGCCGATTAA	57.424	29.630	0.00	0.00	0.00	1.40
1356	2295	4.879545	ACAAAGTTCGAACATTGTACACCT	59.120	37.500	36.81	19.79	45.57	4.00
1368	2307	9.120538	GAACATTGTACACCTATGGTTATTCAT	57.879	33.333	10.09	0.00	31.02	2.57
1586	2622	2.991540	GCCTTGTTGAGCCACCCC	60.992	66.667	0.00	0.00	0.00	4.95
1623	2973	8.708378	ACTTACTACCTAGGTTAAAAGTGTTGT	58.292	33.333	22.11	13.61	0.00	3.32
1826	3180	3.688235	TGATGTGCATGATGAACAGGAA	58.312	40.909	12.46	0.00	39.71	3.36
1847	3201	3.527533	ACAACAGAAAGTGTCGCAACTA	58.472	40.909	0.00	0.00	39.03	2.24
2012	3366	2.480845	GTCTCACTTGCGTTGGTACTT	58.519	47.619	0.00	0.00	0.00	2.24
2026	3380	4.634012	TGGTACTTTGCTCTATTGTGGT	57.366	40.909	0.00	0.00	0.00	4.16
2127	3485	9.862371	TTTGTGATACAAATGTGTTTTAGTTGT	57.138	25.926	0.00	0.00	42.55	3.32
2185	3544	6.160576	ACCTTGTTACGTTAAGTTCCACTA	57.839	37.500	0.00	0.00	0.00	2.74
2357	3725	9.275398	AGTGTTATGAAATTACGAGTTTGGTTA	57.725	29.630	0.00	0.00	0.00	2.85
2365	3733	6.753107	ATTACGAGTTTGGTTAATCCCAAG	57.247	37.500	0.00	0.00	44.93	3.61
2374	3742	6.590656	TTGGTTAATCCCAAGTATCTCCAT	57.409	37.500	0.00	0.00	39.56	3.41
2403	3771	5.263872	ACCCTCTATCGTATGGAAGAGAT	57.736	43.478	13.17	2.58	38.16	2.75
2491	3859	4.867608	GTCAAGTCATGCCTTAGAGACTTC	59.132	45.833	0.00	0.00	45.35	3.01
2498	3866	2.026169	TGCCTTAGAGACTTCCTCGAGA	60.026	50.000	15.71	0.00	46.49	4.04
2509	3877	6.966490	GAGACTTCCTCGAGATCCTTGATCTA	60.966	46.154	15.71	0.00	39.50	1.98
2532	3900	1.219664	CTTATTGCGTCGGGGGACA	59.780	57.895	0.00	0.00	0.00	4.02
2651	4019	2.764269	TCCTCGATGATCTTCCCCTTT	58.236	47.619	3.19	0.00	0.00	3.11
2675	4043	0.636647	TCTCCACCTCCTCTGGCATA	59.363	55.000	0.00	0.00	0.00	3.14
2844	4212	1.808945	GGTGAAGAGGTGTCATGCAAG	59.191	52.381	0.00	0.00	0.00	4.01
2927	4295	7.831691	TGGTTAGAGGATCAATCTTAGAGAG	57.168	40.000	5.14	0.00	37.82	3.20
2948	4316	9.278978	AGAGAGGAAGTTAGAAGAAAATTGAAC	57.721	33.333	0.00	0.00	0.00	3.18
3005	4373	3.887335	GACCTTTGGTACGGCCGCA	62.887	63.158	28.58	10.63	41.21	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.316868	TCGTTTCTTAAAGTTTGGGGCAG	59.683	43.478	0.00	0.00	0.00	4.85
100	101	2.812358	TGCTTTAGAGACGACTGCAA	57.188	45.000	0.00	0.00	0.00	4.08
227	228	3.741830	TTCGCAACTCACGCCACCA	62.742	57.895	0.00	0.00	0.00	4.17
331	332	6.702329	AGTGAAGAGGAAAATCATCGTAACT	58.298	36.000	0.00	0.00	31.60	2.24
472	473	1.966901	ATGCGGCCCGATGAGTGTTA	61.967	55.000	7.68	0.00	0.00	2.41
485	486	9.490663	GAAATAATATAAACTGATGTATGCGGC	57.509	33.333	0.00	0.00	0.00	6.53
522	523	1.098050	GGAACAATGGAGCGAGCAAT	58.902	50.000	0.00	0.00	0.00	3.56
555	556	3.123157	CCTCATGGGCAAGATGACTAG	57.877	52.381	0.00	0.00	0.00	2.57
635	636	7.987750	TGGTGTAAAGTGCATGAATAAACTA	57.012	32.000	0.00	0.00	0.00	2.24
697	698	8.691661	AATTTGGGAGCTATACATTTAATCGT	57.308	30.769	0.00	0.00	0.00	3.73
698	699	9.965824	AAAATTTGGGAGCTATACATTTAATCG	57.034	29.630	0.00	0.00	0.00	3.34
726	727	8.841444	TTCGATACTAAGATAAACGTAACCAC	57.159	34.615	0.00	0.00	0.00	4.16
747	751	9.045223	CCACATTTATATTGTCTGATCTTTCGA	57.955	33.333	0.00	0.00	0.00	3.71
748	752	8.830580	ACCACATTTATATTGTCTGATCTTTCG	58.169	33.333	0.00	0.00	0.00	3.46
774	778	6.101332	GCATTTTGGAGCAAGTATTCATTGA	58.899	36.000	0.00	0.00	0.00	2.57
826	837	8.854117	GCATTAAATCCCTTCTTGAGATATTGT	58.146	33.333	0.00	0.00	0.00	2.71
892	911	4.275936	GGTGGGTGTAGATGCATATCAAAC	59.724	45.833	0.00	0.00	35.70	2.93
893	912	4.165950	AGGTGGGTGTAGATGCATATCAAA	59.834	41.667	0.00	0.00	35.70	2.69
913	932	5.731678	GGATGGGTGAGGGAAATATATAGGT	59.268	44.000	0.00	0.00	0.00	3.08
934	953	6.078456	TCTGAATGGGTAGAAACATTGGAT	57.922	37.500	0.00	0.00	37.43	3.41
967	986	6.739331	ATAAGAGAGATCACTTAGGGGTTG	57.261	41.667	0.00	0.00	33.71	3.77
1039	1957	3.944087	AGTGGGCACTGAGAATAGAAAC	58.056	45.455	0.00	0.00	40.75	2.78
1090	2011	9.567776	TTTTGTAGATCTATCACTCCAACAAAA	57.432	29.630	17.30	17.30	40.18	2.44
1154	2077	2.093181	ACGCCTTGTGTCTATATTGGCA	60.093	45.455	0.00	0.00	38.87	4.92
1356	2295	9.353431	ACATTGAGCAACATATGAATAACCATA	57.647	29.630	10.38	0.00	33.98	2.74
1368	2307	9.409312	CAAACTTTATGAACATTGAGCAACATA	57.591	29.630	0.00	0.00	0.00	2.29
1562	2598	1.173913	GGCTCAACAAGGCGGTAATT	58.826	50.000	0.00	0.00	41.22	1.40
1586	2622	8.338072	ACCTAGGTAGTAAGTTATCATCGATG	57.662	38.462	19.61	19.61	0.00	3.84
1613	2963	2.333014	CCGCACAACAACAACACTTTT	58.667	42.857	0.00	0.00	0.00	2.27
1826	3180	2.356135	AGTTGCGACACTTTCTGTTGT	58.644	42.857	6.90	0.00	36.69	3.32
1847	3201	2.691526	TCCTGTCACGTACTGAGTTGTT	59.308	45.455	0.00	0.00	0.00	2.83
2012	3366	7.390823	TCAATAGTACAACCACAATAGAGCAA	58.609	34.615	0.00	0.00	0.00	3.91
2127	3485	9.273016	CTACTTCTTTTAGTCATCCTTGAAACA	57.727	33.333	0.00	0.00	32.48	2.83
2185	3544	7.380536	TCATCAAGCTTGCAAGTTTAATCATT	58.619	30.769	25.46	1.99	0.00	2.57
2357	3725	2.039084	GGCGATGGAGATACTTGGGATT	59.961	50.000	0.00	0.00	0.00	3.01
2365	3733	0.250338	GGGTTGGGCGATGGAGATAC	60.250	60.000	0.00	0.00	0.00	2.24
2374	3742	0.106569	TACGATAGAGGGTTGGGCGA	60.107	55.000	0.00	0.00	41.38	5.54
2403	3771	1.475280	CATGAAAGGTAGGGTCGACGA	59.525	52.381	9.92	0.00	0.00	4.20
2491	3859	3.699038	GGGATAGATCAAGGATCTCGAGG	59.301	52.174	13.56	0.00	45.03	4.63
2498	3866	5.338708	CGCAATAAGGGGATAGATCAAGGAT	60.339	44.000	0.00	0.00	0.00	3.24
2509	3877	1.450211	CCCGACGCAATAAGGGGAT	59.550	57.895	0.00	0.00	40.51	3.85
2532	3900	0.402121	GAGTGGGGAAAGGAACAGCT	59.598	55.000	0.00	0.00	0.00	4.24
2620	3988	4.959210	AGATCATCGAGGAAGAGAAGGAAA	59.041	41.667	2.91	0.00	0.00	3.13
2621	3989	4.541705	AGATCATCGAGGAAGAGAAGGAA	58.458	43.478	2.91	0.00	0.00	3.36
2622	3990	4.177537	AGATCATCGAGGAAGAGAAGGA	57.822	45.455	2.91	0.00	0.00	3.36
2651	4019	1.566703	CCAGAGGAGGTGGAGACTAGA	59.433	57.143	0.00	0.00	37.23	2.43
2741	4109	7.278135	CAACTTCCATCAAGATCATCTCCTTA	58.722	38.462	0.00	0.00	35.82	2.69
2844	4212	9.352784	CAATATCAATCTAATCTCGAGTCCTTC	57.647	37.037	13.13	0.00	0.00	3.46
2927	4295	9.594478	TTTTGGTTCAATTTTCTTCTAACTTCC	57.406	29.630	0.00	0.00	0.00	3.46
2945	4313	5.385509	TGATTCTTTCCGGATTTTGGTTC	57.614	39.130	4.15	0.00	0.00	3.62
2948	4316	5.643379	TCTTGATTCTTTCCGGATTTTGG	57.357	39.130	4.15	0.00	0.00	3.28
2984	4352	0.675522	CGGCCGTACCAAAGGTCATT	60.676	55.000	19.50	0.00	39.03	2.57
3005	4373	2.290514	ACAAGCAGTGATACACCTGCAT	60.291	45.455	13.44	0.00	39.27	3.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.