AutoCloner

Multiple sequence alignment - TraesCS2D01G117000

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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	TraesCS2D01G117000	chr2D	100.000	2915	0	0	1	2915	66462816	66459902	0.000000e+00	5384.0
1	TraesCS2D01G117000	chr2D	84.211	2014	267	26	1	1985	65719033	65717042	0.000000e+00	1910.0
2	TraesCS2D01G117000	chr2A	94.436	1977	105	4	1	1975	68503850	68505823	0.000000e+00	3037.0
3	TraesCS2D01G117000	chr2A	82.935	2010	289	32	2	1982	68811412	68813396	0.000000e+00	1762.0
4	TraesCS2D01G117000	chr2A	93.003	686	40	5	2235	2915	68506603	68507285	0.000000e+00	994.0
5	TraesCS2D01G117000	chr2A	81.292	449	59	14	2472	2902	68821990	68822431	1.000000e-89	340.0
6	TraesCS2D01G117000	chr2A	89.130	230	17	2	2028	2249	68506103	68506332	2.210000e-71	279.0
7	TraesCS2D01G117000	chr2A	85.714	98	11	2	2805	2902	682633040	682633134	1.850000e-17	100.0
8	TraesCS2D01G117000	chr2A	94.118	51	1	2	1986	2034	68505979	68506029	3.120000e-10	76.8
9	TraesCS2D01G117000	chr2B	92.211	1990	128	11	1	1988	104894273	104896237	0.000000e+00	2791.0
10	TraesCS2D01G117000	chr2B	83.532	2010	278	33	2	1982	105372512	105374497	0.000000e+00	1829.0
11	TraesCS2D01G117000	chr2B	94.331	829	36	4	2087	2915	104896723	104897540	0.000000e+00	1260.0
12	TraesCS2D01G117000	chr2B	84.598	435	57	5	2472	2902	105381505	105381933	9.660000e-115	424.0
13	TraesCS2D01G117000	chr3B	96.512	86	3	0	2615	2700	131538933	131538848	3.030000e-30	143.0
14	TraesCS2D01G117000	chr7A	83.333	90	14	1	2775	2863	696118361	696118272	6.700000e-12	82.4
15	TraesCS2D01G117000	chr1D	90.000	50	5	0	2853	2902	483467170	483467219	6.740000e-07	65.8

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	TraesCS2D01G117000	chr2D	66459902	66462816	2914	True	5384.0	5384	100.00000	1	2915	1	chr2D.!!$R2	2914
1	TraesCS2D01G117000	chr2D	65717042	65719033	1991	True	1910.0	1910	84.21100	1	1985	1	chr2D.!!$R1	1984
2	TraesCS2D01G117000	chr2A	68811412	68813396	1984	False	1762.0	1762	82.93500	2	1982	1	chr2A.!!$F1	1980
3	TraesCS2D01G117000	chr2A	68503850	68507285	3435	False	1096.7	3037	92.67175	1	2915	4	chr2A.!!$F4	2914
4	TraesCS2D01G117000	chr2B	104894273	104897540	3267	False	2025.5	2791	93.27100	1	2915	2	chr2B.!!$F3	2914
5	TraesCS2D01G117000	chr2B	105372512	105374497	1985	False	1829.0	1829	83.53200	2	1982	1	chr2B.!!$F1	1980

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
650	674	0.767375	ATGCTAATCACCGCATCCCT	59.233	50.0	0.0	0.0	42.83	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2125	2611	0.040204	AAAGGAACCCAGGAGGCATG	59.96	55.0	0.0	0.0	40.58	4.06	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
148	152	2.416836	CGAACAAATAGCGAGGACAGGA	60.417	50.000	0.00	0.00	0.00	3.86
343	349	4.927425	GTCTTAGACAAATGGCTCGTGTAA	59.073	41.667	7.59	0.00	33.72	2.41
352	358	1.574702	GGCTCGTGTAAGCACCCAAC	61.575	60.000	0.00	0.00	44.35	3.77
356	362	0.816018	CGTGTAAGCACCCAACCACA	60.816	55.000	0.00	0.00	42.39	4.17
408	414	3.137544	GGGATACATGAACACCCACCATA	59.862	47.826	0.00	0.00	40.20	2.74
650	674	0.767375	ATGCTAATCACCGCATCCCT	59.233	50.000	0.00	0.00	42.83	4.20
740	764	6.503589	TGGTTTGTAGAACCAAATATTCCG	57.496	37.500	8.10	0.00	46.44	4.30
741	765	5.416326	TGGTTTGTAGAACCAAATATTCCGG	59.584	40.000	8.10	0.00	46.44	5.14
762	786	4.601019	GGCATCCTCAACATTCATTAACG	58.399	43.478	0.00	0.00	0.00	3.18
787	811	6.939163	GGCCATATCCTAGCTTCATATATTGG	59.061	42.308	0.00	0.00	0.00	3.16
821	863	5.559148	AGTCTAAATCATCCCATCCTCAC	57.441	43.478	0.00	0.00	0.00	3.51
824	866	3.303351	AAATCATCCCATCCTCACCAC	57.697	47.619	0.00	0.00	0.00	4.16
863	905	5.882557	GCCCTAACTCCATATATTGTCCATG	59.117	44.000	0.00	0.00	0.00	3.66
885	927	7.561356	CCATGGTTTTTAGTCTAAATCATCCCT	59.439	37.037	2.57	0.00	34.87	4.20
949	992	6.703607	CACATAATGTCCATGAGTTCCTAGTC	59.296	42.308	0.00	0.00	0.00	2.59
1221	1275	2.047655	CCCTACGCGCACAAGGAA	60.048	61.111	18.49	0.00	31.64	3.36
1443	1497	1.798234	GCAAGTGTGATGCAGGCACA	61.798	55.000	18.10	18.10	43.41	4.57
1449	1503	3.052082	GATGCAGGCACACGCTGT	61.052	61.111	0.00	0.00	38.60	4.40
1584	1638	3.402681	CCCCACATCCTCCAGCGT	61.403	66.667	0.00	0.00	0.00	5.07
1668	1722	1.304713	CCTGCAGGCCACTCCAAAT	60.305	57.895	22.33	0.00	37.29	2.32
1808	1862	4.840168	GCCCTTAATGGCGTACGA	57.160	55.556	21.65	0.00	42.54	3.43
1809	1863	2.601562	GCCCTTAATGGCGTACGAG	58.398	57.895	21.65	5.90	42.54	4.18
1810	1864	0.878961	GCCCTTAATGGCGTACGAGG	60.879	60.000	21.65	15.18	42.54	4.63
1950	2019	9.330063	GTATGACAATGAATAAATCTCTGGACA	57.670	33.333	0.00	0.00	0.00	4.02
2017	2391	1.750399	GTGGCGGTAGTCGGTCCTA	60.750	63.158	0.00	0.00	39.69	2.94
2018	2392	1.452651	TGGCGGTAGTCGGTCCTAG	60.453	63.158	0.00	0.00	39.69	3.02
2020	2394	1.153086	GCGGTAGTCGGTCCTAGGA	60.153	63.158	7.62	7.62	39.69	2.94
2021	2395	1.165284	GCGGTAGTCGGTCCTAGGAG	61.165	65.000	13.15	0.91	39.69	3.69
2022	2396	1.165284	CGGTAGTCGGTCCTAGGAGC	61.165	65.000	27.87	27.87	39.05	4.70
2085	2541	2.281517	CCGTCGGGCAAATGTGTAATA	58.718	47.619	2.34	0.00	0.00	0.98
2099	2555	7.582667	AATGTGTAATATTTCCCTAAGCACC	57.417	36.000	0.00	0.00	0.00	5.01
2135	2621	1.271543	TGTCAAACTCCATGCCTCCTG	60.272	52.381	0.00	0.00	0.00	3.86
2152	2638	3.826729	CTCCTGGGTTCCTTTTAGTTTGG	59.173	47.826	0.00	0.00	0.00	3.28
2161	2647	6.387465	GTTCCTTTTAGTTTGGCTGATAACC	58.613	40.000	0.00	0.00	0.00	2.85
2340	3111	8.897872	ATAAGTAAAGACGAAAGAAGTTGGAA	57.102	30.769	0.00	0.00	0.00	3.53
2403	3177	5.971436	TGAAATAAATTCTCCGATCCGGTCC	60.971	44.000	0.00	0.00	40.86	4.46
2419	3193	2.046864	TCCGAGGAAGCACCGAGAG	61.047	63.158	0.00	0.00	44.74	3.20
2420	3194	2.046864	CCGAGGAAGCACCGAGAGA	61.047	63.158	0.00	0.00	44.74	3.10
2495	3270	7.883391	AGTATAGTACTCCCCATTATGATCG	57.117	40.000	0.00	0.00	32.47	3.69
2511	3286	7.633361	TTATGATCGATACGCCTTTACTTTC	57.367	36.000	0.00	0.00	0.00	2.62
2624	3399	1.762708	ACGGGGTTATGGAAGCATTG	58.237	50.000	0.00	0.00	34.60	2.82
2642	3417	6.449698	AGCATTGTTCTTTTCTTGGTACATG	58.550	36.000	0.00	0.00	39.30	3.21
2667	3442	6.327386	TCCTTTTGCTAATTCCAGGAGTAT	57.673	37.500	0.00	0.00	0.00	2.12
2737	3512	6.560003	TGAGGGCATTTCTGATTAAGACTA	57.440	37.500	0.00	0.00	33.46	2.59
2738	3513	6.586344	TGAGGGCATTTCTGATTAAGACTAG	58.414	40.000	0.00	0.00	33.46	2.57
2752	3527	9.862371	TGATTAAGACTAGAAATTCTGTCTGTC	57.138	33.333	20.45	18.39	36.09	3.51
2824	3599	4.745620	GCTATTCTTCACTCGTGGGATTAC	59.254	45.833	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	34	6.995686	TGGTCATAACTCCACGCATAAAATAT	59.004	34.615	0.00	0.00	0.00	1.28
94	97	0.037697	TGTGGCCACGATGACTACAC	60.038	55.000	30.07	2.81	0.00	2.90
148	152	7.063074	CGGTCAATTAAGACTTATTTGTCGTCT	59.937	37.037	20.97	0.00	41.47	4.18
188	193	3.408634	CGAGTGTAGAAACCCACCATTT	58.591	45.455	0.00	0.00	31.88	2.32
253	258	0.826715	CCCCGAGAGATGAGCTCAAA	59.173	55.000	22.50	0.00	46.45	2.69
343	349	2.700185	AAGGGTGTGGTTGGGTGCT	61.700	57.895	0.00	0.00	0.00	4.40
352	358	0.742281	CATCTCGAGCAAGGGTGTGG	60.742	60.000	7.81	0.00	0.00	4.17
356	362	2.586792	GCCATCTCGAGCAAGGGT	59.413	61.111	7.81	0.00	0.00	4.34
408	414	3.966979	TGTGATAAGATGGGTTGTGCAT	58.033	40.909	0.00	0.00	0.00	3.96
650	674	4.891756	GGCCGTGGGTATATATAGCTCTAA	59.108	45.833	18.77	3.42	0.00	2.10
740	764	4.498009	CCGTTAATGAATGTTGAGGATGCC	60.498	45.833	0.00	0.00	0.00	4.40
741	765	4.601019	CCGTTAATGAATGTTGAGGATGC	58.399	43.478	0.00	0.00	0.00	3.91
762	786	6.939163	CCAATATATGAAGCTAGGATATGGCC	59.061	42.308	0.00	0.00	35.62	5.36
787	811	6.017523	GGATGATTTAGACTAAAAGCTCTGGC	60.018	42.308	11.57	0.76	39.06	4.85
821	863	0.524862	GCATGGCTGTGAAAGAGTGG	59.475	55.000	0.00	0.00	0.00	4.00
824	866	0.323178	AGGGCATGGCTGTGAAAGAG	60.323	55.000	19.78	0.00	0.00	2.85
863	905	8.753497	ATGAGGGATGATTTAGACTAAAAACC	57.247	34.615	11.57	11.41	0.00	3.27
885	927	8.522830	GGTTTTGAAAGAATGTTGAGGATATGA	58.477	33.333	0.00	0.00	0.00	2.15
922	965	5.188434	AGGAACTCATGGACATTATGTGTG	58.812	41.667	1.24	0.00	42.36	3.82
949	992	7.966753	CCAACAGATGAACAATACTGATCAAAG	59.033	37.037	0.00	0.00	37.82	2.77
1098	1152	2.994995	AGTCGGTGCCCATCGTGA	60.995	61.111	0.49	0.00	36.14	4.35
1377	1431	1.516386	CAGCTCGAATACGCCGTGT	60.516	57.895	0.00	0.00	39.58	4.49
1443	1497	1.738099	GATCTGGCGTTGACAGCGT	60.738	57.895	13.36	0.00	38.81	5.07
1449	1503	0.610174	AGAAGCAGATCTGGCGTTGA	59.390	50.000	23.89	0.00	36.08	3.18
1525	1579	3.197790	CGAAGATGGCACCGCTGG	61.198	66.667	0.00	0.00	0.00	4.85
1536	1590	1.098050	GCATGGCAAAGGTCGAAGAT	58.902	50.000	0.00	0.00	40.67	2.40
1584	1638	1.191489	TCACCGAAGTGGATGGAGCA	61.191	55.000	0.00	0.00	44.64	4.26
1610	1664	0.770499	TGGAGTTGGAACATCCTGCA	59.230	50.000	0.00	0.00	39.30	4.41
1808	1862	1.087725	TCCTCCTCCTCCTCCTCCT	59.912	63.158	0.00	0.00	0.00	3.69
1809	1863	1.231928	GTCCTCCTCCTCCTCCTCC	59.768	68.421	0.00	0.00	0.00	4.30
1810	1864	1.152839	CGTCCTCCTCCTCCTCCTC	60.153	68.421	0.00	0.00	0.00	3.71
1950	2019	3.532155	GGATCGACTCGGCCTGCT	61.532	66.667	0.00	0.00	0.00	4.24
2017	2391	1.568504	TCAACAATAGGGACGCTCCT	58.431	50.000	0.00	2.63	40.79	3.69
2018	2392	2.622064	ATCAACAATAGGGACGCTCC	57.378	50.000	0.00	0.00	35.23	4.70
2020	2394	5.437060	ACAATAATCAACAATAGGGACGCT	58.563	37.500	0.00	0.00	0.00	5.07
2021	2395	5.751243	ACAATAATCAACAATAGGGACGC	57.249	39.130	0.00	0.00	0.00	5.19
2022	2396	8.836413	ACAATACAATAATCAACAATAGGGACG	58.164	33.333	0.00	0.00	0.00	4.79
2106	2592	5.988561	GGCATGGAGTTTGACAAAACAATTA	59.011	36.000	1.27	0.00	46.80	1.40
2119	2605	1.142688	ACCCAGGAGGCATGGAGTTT	61.143	55.000	0.00	0.00	40.51	2.66
2125	2611	0.040204	AAAGGAACCCAGGAGGCATG	59.960	55.000	0.00	0.00	40.58	4.06
2135	2621	3.227614	TCAGCCAAACTAAAAGGAACCC	58.772	45.455	0.00	0.00	0.00	4.11
2152	2638	8.903820	AGATAAAAATACACCTTGGTTATCAGC	58.096	33.333	0.00	0.00	31.76	4.26
2161	2647	9.667107	TCCTTCTACAGATAAAAATACACCTTG	57.333	33.333	0.00	0.00	0.00	3.61
2340	3111	8.686334	CCAAGCTGTATATCCACTAACAAAAAT	58.314	33.333	0.00	0.00	0.00	1.82
2403	3177	0.457851	ATTCTCTCGGTGCTTCCTCG	59.542	55.000	0.00	0.00	0.00	4.63
2419	3193	7.175119	AGTCCAAGGCTTCTTGTTTAAGTATTC	59.825	37.037	0.00	0.00	44.71	1.75
2420	3194	7.004691	AGTCCAAGGCTTCTTGTTTAAGTATT	58.995	34.615	0.00	0.00	44.71	1.89
2443	3217	1.401761	TGGTTTGCAGCAACATGAGT	58.598	45.000	7.54	0.00	0.00	3.41
2511	3286	2.938451	TCTCAAGCATCTGCCAATAACG	59.062	45.455	0.00	0.00	43.38	3.18
2624	3399	6.635030	AGGAACATGTACCAAGAAAAGAAC	57.365	37.500	0.00	0.00	0.00	3.01
2642	3417	4.767409	ACTCCTGGAATTAGCAAAAGGAAC	59.233	41.667	0.00	0.00	33.57	3.62
2667	3442	3.779444	AGTAGACCAGTTGATCCAGTCA	58.221	45.455	0.00	0.00	34.25	3.41
2737	3512	4.130118	GGTGTGTGACAGACAGAATTTCT	58.870	43.478	14.98	0.00	34.28	2.52
2738	3513	3.876914	TGGTGTGTGACAGACAGAATTTC	59.123	43.478	14.98	0.00	34.28	2.17
2804	3579	5.187967	AGAAGTAATCCCACGAGTGAAGAAT	59.812	40.000	4.59	0.00	0.00	2.40
2849	3624	3.120041	CCAAAATGAAACAACCGACCAC	58.880	45.455	0.00	0.00	0.00	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.