AutoCloner

Multiple sequence alignment - TraesCS5D01G348500

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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	TraesCS5D01G348500	chr5D	100.000	2270	0	0	1	2270	434327372	434325103	0.000000e+00	4193.0
1	TraesCS5D01G348500	chr5D	93.072	1660	93	15	1	1649	434396396	434398044	0.000000e+00	2409.0
2	TraesCS5D01G348500	chr5D	83.163	1663	206	45	1	1615	433018288	433019924	0.000000e+00	1452.0
3	TraesCS5D01G348500	chr5D	82.657	1701	209	49	1	1645	435249481	435247811	0.000000e+00	1428.0
4	TraesCS5D01G348500	chr5D	91.022	1047	78	11	614	1649	435251867	435250826	0.000000e+00	1399.0
5	TraesCS5D01G348500	chr5D	89.303	617	50	9	1670	2270	435250438	435249822	0.000000e+00	760.0
6	TraesCS5D01G348500	chr5D	81.279	657	93	19	66	698	434399344	434399994	2.600000e-139	505.0
7	TraesCS5D01G348500	chr5D	92.361	288	19	3	1670	1955	434398453	434398739	7.550000e-110	407.0
8	TraesCS5D01G348500	chr5D	93.625	251	15	1	2021	2270	434398741	434398991	7.660000e-100	374.0
9	TraesCS5D01G348500	chr5D	83.333	414	54	10	1	413	435252431	435252032	3.560000e-98	368.0
10	TraesCS5D01G348500	chr5D	85.660	265	36	2	1670	1934	433017797	433018059	6.180000e-71	278.0
11	TraesCS5D01G348500	chr5D	92.857	56	3	1	2151	2205	434395932	434395987	1.870000e-11	80.5
12	TraesCS5D01G348500	chr5D	96.970	33	1	0	1644	1676	434398340	434398372	3.150000e-04	56.5
13	TraesCS5D01G348500	chr5D	100.000	30	0	0	1647	1676	435250538	435250509	3.150000e-04	56.5
14	TraesCS5D01G348500	chr5A	93.068	1659	82	15	1	1649	548233481	548235116	0.000000e+00	2396.0
15	TraesCS5D01G348500	chr5A	85.689	1698	168	37	1	1649	549161273	549159602	0.000000e+00	1720.0
16	TraesCS5D01G348500	chr5A	83.667	1647	198	49	3	1612	549158338	549156726	0.000000e+00	1485.0
17	TraesCS5D01G348500	chr5A	90.089	898	66	12	760	1649	549163518	549162636	0.000000e+00	1144.0
18	TraesCS5D01G348500	chr5A	82.826	1019	133	23	559	1559	547636346	547637340	0.000000e+00	874.0
19	TraesCS5D01G348500	chr5A	92.920	339	19	4	1926	2259	549159029	549158691	2.620000e-134	488.0
20	TraesCS5D01G348500	chr5A	90.625	352	25	6	1926	2270	549161962	549161612	5.710000e-126	460.0
21	TraesCS5D01G348500	chr5A	92.042	289	20	3	1670	1955	548235510	548235798	9.770000e-109	403.0
22	TraesCS5D01G348500	chr5A	81.727	498	62	20	253	731	549163997	549163510	2.730000e-104	388.0
23	TraesCS5D01G348500	chr5A	91.633	251	20	1	2021	2270	548235800	548236050	1.670000e-91	346.0
24	TraesCS5D01G348500	chr5A	85.196	331	39	3	744	1073	549196673	549196352	4.670000e-87	331.0
25	TraesCS5D01G348500	chr5A	88.393	224	13	6	1670	1891	549162175	549161963	8.050000e-65	257.0
26	TraesCS5D01G348500	chr5A	86.486	222	18	5	1670	1890	549159241	549159031	1.360000e-57	233.0
27	TraesCS5D01G348500	chr5A	88.312	154	16	2	1948	2099	549164931	549164778	1.380000e-42	183.0
28	TraesCS5D01G348500	chr5A	82.028	217	33	1	64	274	547599789	547600005	1.790000e-41	180.0
29	TraesCS5D01G348500	chr5B	87.160	1690	163	35	1	1649	528545687	528544011	0.000000e+00	1869.0
30	TraesCS5D01G348500	chr5B	91.464	1277	64	17	384	1649	527052759	527054001	0.000000e+00	1712.0
31	TraesCS5D01G348500	chr5B	82.229	1705	210	58	1	1645	527055307	527056978	0.000000e+00	1384.0
32	TraesCS5D01G348500	chr5B	83.253	1445	173	52	253	1645	528541904	528540477	0.000000e+00	1264.0
33	TraesCS5D01G348500	chr5B	85.197	608	48	16	1670	2270	528543611	528543039	9.030000e-164	586.0
34	TraesCS5D01G348500	chr5B	95.963	322	13	0	1	322	527052434	527052755	7.180000e-145	523.0
35	TraesCS5D01G348500	chr5B	85.584	437	46	8	1	436	528542719	528542299	2.070000e-120	442.0
36	TraesCS5D01G348500	chr5B	91.304	253	19	3	2021	2270	527054717	527054969	2.160000e-90	342.0
37	TraesCS5D01G348500	chr5B	82.512	406	53	9	1670	2057	528546879	528546474	7.770000e-90	340.0
38	TraesCS5D01G348500	chr5B	86.230	305	23	4	1670	1955	527054411	527054715	1.690000e-81	313.0
39	TraesCS5D01G348500	chr5B	85.338	266	36	3	1670	1934	526583984	526584247	2.870000e-69	272.0
40	TraesCS5D01G348500	chr5B	86.066	122	12	2	1669	1785	528560745	528560624	2.370000e-25	126.0
41	TraesCS5D01G348500	chr5B	96.970	33	1	0	1644	1676	527054298	527054330	3.150000e-04	56.5

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	TraesCS5D01G348500	chr5D	434325103	434327372	2269	True	4193.000000	4193	100.000000	1	2270	1	chr5D.!!$R1	2269
1	TraesCS5D01G348500	chr5D	433017797	433019924	2127	False	865.000000	1452	84.411500	1	1934	2	chr5D.!!$F1	1933
2	TraesCS5D01G348500	chr5D	435247811	435252431	4620	True	802.300000	1428	89.263000	1	2270	5	chr5D.!!$R2	2269
3	TraesCS5D01G348500	chr5D	434395932	434399994	4062	False	638.666667	2409	91.694000	1	2270	6	chr5D.!!$F2	2269
4	TraesCS5D01G348500	chr5A	548233481	548236050	2569	False	1048.333333	2396	92.247667	1	2270	3	chr5A.!!$F3	2269
5	TraesCS5D01G348500	chr5A	547636346	547637340	994	False	874.000000	874	82.826000	559	1559	1	chr5A.!!$F2	1000
6	TraesCS5D01G348500	chr5A	549156726	549164931	8205	True	706.444444	1720	87.545333	1	2270	9	chr5A.!!$R2	2269
7	TraesCS5D01G348500	chr5B	528540477	528546879	6402	True	900.200000	1869	84.741200	1	2270	5	chr5B.!!$R2	2269
8	TraesCS5D01G348500	chr5B	527052434	527056978	4544	False	721.750000	1712	90.693333	1	2270	6	chr5B.!!$F2	2269

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
550	1877	0.108615	GGAGGTGACTGTGATGGACG	60.109	60.0	0.0	0.0	44.43	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1856	3706	1.351017	CCTAGAAACCCTCAACTGCCA	59.649	52.381	0.0	0.0	0.0	4.92	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
33	1239	4.442401	TGGCATACTCCATCATTGATGT	57.558	40.909	21.95	9.13	38.28	3.06
63	1269	0.250467	AGCGTGATTCTGCCACTGTT	60.250	50.000	0.00	0.00	32.64	3.16
103	1309	1.909302	TCCTCTTGGGACATCCTCAAC	59.091	52.381	0.00	0.00	39.58	3.18
391	1677	2.025037	TGCTAATTGGAGGCTGGAATGT	60.025	45.455	0.00	0.00	0.00	2.71
395	1681	2.496899	TTGGAGGCTGGAATGTCTTC	57.503	50.000	0.00	0.00	0.00	2.87
433	1733	3.010420	GGTGGTGTTAGGAGAGCATTTC	58.990	50.000	0.00	0.00	0.00	2.17
493	1812	2.742348	ACGGTGGACTGTGATGGTATA	58.258	47.619	0.00	0.00	33.47	1.47
494	1813	3.305720	ACGGTGGACTGTGATGGTATAT	58.694	45.455	0.00	0.00	33.47	0.86
495	1814	4.476297	ACGGTGGACTGTGATGGTATATA	58.524	43.478	0.00	0.00	33.47	0.86
496	1815	5.084519	ACGGTGGACTGTGATGGTATATAT	58.915	41.667	0.00	0.00	33.47	0.86
538	1865	1.896660	GCTGCGGTTTTGGAGGTGA	60.897	57.895	0.00	0.00	0.00	4.02
541	1868	0.817634	TGCGGTTTTGGAGGTGACTG	60.818	55.000	0.00	0.00	44.43	3.51
542	1869	0.818040	GCGGTTTTGGAGGTGACTGT	60.818	55.000	0.00	0.00	44.43	3.55
544	1871	1.474320	CGGTTTTGGAGGTGACTGTGA	60.474	52.381	0.00	0.00	44.43	3.58
545	1872	2.810400	CGGTTTTGGAGGTGACTGTGAT	60.810	50.000	0.00	0.00	44.43	3.06
546	1873	2.554032	GGTTTTGGAGGTGACTGTGATG	59.446	50.000	0.00	0.00	44.43	3.07
549	1876	0.976641	TGGAGGTGACTGTGATGGAC	59.023	55.000	0.00	0.00	44.43	4.02
550	1877	0.108615	GGAGGTGACTGTGATGGACG	60.109	60.000	0.00	0.00	44.43	4.79
551	1878	0.108615	GAGGTGACTGTGATGGACGG	60.109	60.000	0.00	0.00	44.43	4.79
569	1899	2.611800	TGATGGTCTGCTGGGGCT	60.612	61.111	0.00	0.00	39.59	5.19
653	1997	1.264749	TGCTAGGGAATGGCACGAGT	61.265	55.000	0.00	0.00	41.01	4.18
659	2003	0.172803	GGAATGGCACGAGTACGAGT	59.827	55.000	0.00	0.00	42.66	4.18
736	2083	7.778382	TGGAAGTCTCATCAAAATCATCATCAT	59.222	33.333	0.00	0.00	0.00	2.45
806	2162	0.541764	GCATTGTCCCCTTCCCAACA	60.542	55.000	0.00	0.00	0.00	3.33
846	2202	1.220529	CTACCCACACGCATATGCAG	58.779	55.000	26.52	19.77	42.21	4.41
949	2308	5.049405	CACAATCTAAACACACCTTCAGACC	60.049	44.000	0.00	0.00	0.00	3.85
1096	2467	2.110757	TTGGCATGCCTCAGACACGA	62.111	55.000	35.53	11.01	36.94	4.35
1100	2471	3.006756	ATGCCTCAGACACGACCGG	62.007	63.158	0.00	0.00	0.00	5.28
1137	2514	1.417517	TCAGTGTCATCTGTGGTTGCT	59.582	47.619	0.00	0.00	36.85	3.91
1158	2535	2.512515	GAGGGCCACTGCGTGATC	60.513	66.667	6.18	0.00	38.85	2.92
1410	2787	3.694043	TGCCACAACTACAATGCTAGA	57.306	42.857	0.00	0.00	0.00	2.43
1413	2790	3.941483	GCCACAACTACAATGCTAGATGT	59.059	43.478	0.00	0.00	31.73	3.06
1569	2950	7.546667	CAGGAAATGATACAAAGGGACAATTTG	59.453	37.037	0.00	0.00	42.17	2.32
1726	3574	5.689961	GCATGTTAGGTGTTTGTTGGTTTAG	59.310	40.000	0.00	0.00	0.00	1.85
1765	3613	0.610232	GATCTGGCAAGTTGCTGGGT	60.610	55.000	26.16	15.54	44.28	4.51
1793	3641	1.275666	ATCTCATTGTCCACCCACGA	58.724	50.000	0.00	0.00	0.00	4.35
1810	3658	3.430790	CCACGATCTGCATGGTTTCTAGA	60.431	47.826	0.00	0.00	0.00	2.43
1814	3662	6.648310	CACGATCTGCATGGTTTCTAGAATAT	59.352	38.462	5.89	0.00	0.00	1.28
1833	3682	6.832384	AGAATATCATGTGTCAGCCATTTTCT	59.168	34.615	0.00	0.00	0.00	2.52
1834	3683	4.713824	ATCATGTGTCAGCCATTTTCTG	57.286	40.909	0.00	0.00	0.00	3.02
1856	3706	3.131755	GGCATCTTCCTTGCATTTAGCTT	59.868	43.478	0.00	0.00	45.94	3.74
2019	3890	3.950395	AGCCTTGCCTGATGATTTACTTC	59.050	43.478	0.00	0.00	0.00	3.01
2048	3919	5.124297	TCCATGACACAAACATAGCATGAAG	59.876	40.000	0.00	0.00	36.20	3.02
2069	3944	8.810652	TGAAGATTTATTTGCCAAGTACAAAC	57.189	30.769	0.00	0.00	39.65	2.93
2095	3977	5.187687	TGATGAGCTTATTCTGCATGACAA	58.812	37.500	0.00	0.00	0.00	3.18
2100	3982	3.193267	GCTTATTCTGCATGACAAACCCA	59.807	43.478	0.00	0.00	0.00	4.51
2223	4110	2.569404	CCCTAATCCATCTGCTAGGACC	59.431	54.545	0.00	0.00	36.60	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	1239	2.395988	AATCACGCTGCCCTGTGACA	62.396	55.000	10.34	0.00	46.87	3.58
375	1661	2.579860	AGAAGACATTCCAGCCTCCAAT	59.420	45.455	0.00	0.00	35.94	3.16
391	1677	3.007290	CCACTTCATCCACAGACAGAAGA	59.993	47.826	7.40	0.00	38.70	2.87
395	1681	2.420642	CACCACTTCATCCACAGACAG	58.579	52.381	0.00	0.00	0.00	3.51
433	1733	4.684703	CCCTTGAACTATAAATCCGTAGCG	59.315	45.833	0.00	0.00	0.00	4.26
436	1736	7.712205	GCTTTACCCTTGAACTATAAATCCGTA	59.288	37.037	0.00	0.00	0.00	4.02
438	1738	6.766467	AGCTTTACCCTTGAACTATAAATCCG	59.234	38.462	0.00	0.00	0.00	4.18
493	1812	2.976882	ACGTACCCTACCCATTGCATAT	59.023	45.455	0.00	0.00	0.00	1.78
494	1813	2.103432	CACGTACCCTACCCATTGCATA	59.897	50.000	0.00	0.00	0.00	3.14
495	1814	1.134220	CACGTACCCTACCCATTGCAT	60.134	52.381	0.00	0.00	0.00	3.96
496	1815	0.250793	CACGTACCCTACCCATTGCA	59.749	55.000	0.00	0.00	0.00	4.08
538	1865	0.250234	CCATCACCGTCCATCACAGT	59.750	55.000	0.00	0.00	0.00	3.55
540	1867	0.249120	GACCATCACCGTCCATCACA	59.751	55.000	0.00	0.00	0.00	3.58
541	1868	0.537188	AGACCATCACCGTCCATCAC	59.463	55.000	0.00	0.00	0.00	3.06
542	1869	0.536724	CAGACCATCACCGTCCATCA	59.463	55.000	0.00	0.00	0.00	3.07
544	1871	1.221840	GCAGACCATCACCGTCCAT	59.778	57.895	0.00	0.00	0.00	3.41
545	1872	1.913262	AGCAGACCATCACCGTCCA	60.913	57.895	0.00	0.00	0.00	4.02
546	1873	1.448540	CAGCAGACCATCACCGTCC	60.449	63.158	0.00	0.00	0.00	4.79
549	1876	2.124983	CCCAGCAGACCATCACCG	60.125	66.667	0.00	0.00	0.00	4.94
550	1877	2.273449	CCCCAGCAGACCATCACC	59.727	66.667	0.00	0.00	0.00	4.02
551	1878	1.626356	TAGCCCCAGCAGACCATCAC	61.626	60.000	0.00	0.00	43.56	3.06
552	1879	0.913934	TTAGCCCCAGCAGACCATCA	60.914	55.000	0.00	0.00	43.56	3.07
600	1931	1.217511	CTGTGCAGGCGAGATGTCT	59.782	57.895	0.00	0.00	0.00	3.41
653	1997	1.826720	GAACCACATGGGGTACTCGTA	59.173	52.381	22.88	0.00	41.32	3.43
736	2083	1.140852	ACTAGCTGCAGACACCAAACA	59.859	47.619	20.43	0.00	0.00	2.83
806	2162	3.766591	AGTGTGTAGCTATCAGCAAGAGT	59.233	43.478	0.00	0.00	45.56	3.24
846	2202	0.037447	AAGAAAGGACTCAGGGCAGC	59.963	55.000	0.00	0.00	0.00	5.25
949	2308	4.861102	AAATTTCACTTTGGCTCTGGAG	57.139	40.909	0.00	0.00	0.00	3.86
1078	2449	2.046988	CGTGTCTGAGGCATGCCA	60.047	61.111	37.18	18.01	38.92	4.92
1117	2494	1.417517	AGCAACCACAGATGACACTGA	59.582	47.619	10.71	0.00	40.63	3.41
1137	2514	3.321648	ACGCAGTGGCCCTCATCA	61.322	61.111	0.00	0.00	42.51	3.07
1158	2535	1.520787	GGTTCCATCGGCGGTGTAG	60.521	63.158	20.02	4.61	0.00	2.74
1183	2560	0.252284	AGGTACACCAGAGGGACCTG	60.252	60.000	0.00	0.00	39.09	4.00
1227	2604	1.925959	TCCTCCTCAGACATCCTCAGA	59.074	52.381	0.00	0.00	0.00	3.27
1267	2644	2.263545	CATGATCCTGCCTCCATCCTA	58.736	52.381	0.00	0.00	0.00	2.94
1268	2645	1.065647	CATGATCCTGCCTCCATCCT	58.934	55.000	0.00	0.00	0.00	3.24
1269	2646	0.608582	GCATGATCCTGCCTCCATCC	60.609	60.000	11.56	0.00	36.10	3.51
1336	2713	2.445654	CTCCTCAGGGGCCTCTCC	60.446	72.222	0.00	0.00	34.39	3.71
1410	2787	2.177451	TCCCATTGATGGTGCCATACAT	59.823	45.455	9.07	0.00	46.65	2.29
1413	2790	1.852309	AGTCCCATTGATGGTGCCATA	59.148	47.619	9.07	0.00	46.65	2.74
1434	2811	1.891150	CAAAGAGCAAACTGATGGCCT	59.109	47.619	3.32	0.00	0.00	5.19
1569	2950	7.713073	TGTAAAACAATCCAATTTCTCCCAAAC	59.287	33.333	0.00	0.00	0.00	2.93
1726	3574	2.442084	GCAGCAATCAAAGCACTGC	58.558	52.632	0.00	0.00	45.95	4.40
1765	3613	5.246203	GGGTGGACAATGAGATACATAGCTA	59.754	44.000	0.00	0.00	38.38	3.32
1771	3619	2.093711	CGTGGGTGGACAATGAGATACA	60.094	50.000	0.00	0.00	0.00	2.29
1772	3620	2.167693	TCGTGGGTGGACAATGAGATAC	59.832	50.000	0.00	0.00	0.00	2.24
1793	3641	8.162085	ACATGATATTCTAGAAACCATGCAGAT	58.838	33.333	27.17	15.56	0.00	2.90
1810	3658	6.183360	CCAGAAAATGGCTGACACATGATATT	60.183	38.462	0.00	0.00	43.83	1.28
1814	3662	2.821378	CCAGAAAATGGCTGACACATGA	59.179	45.455	0.00	0.00	43.83	3.07
1833	3682	2.428171	GCTAAATGCAAGGAAGATGCCA	59.572	45.455	0.00	0.00	43.16	4.92
1834	3683	2.692041	AGCTAAATGCAAGGAAGATGCC	59.308	45.455	0.00	0.00	45.94	4.40
1836	3686	4.679662	CCAAGCTAAATGCAAGGAAGATG	58.320	43.478	0.00	0.00	45.94	2.90
1856	3706	1.351017	CCTAGAAACCCTCAACTGCCA	59.649	52.381	0.00	0.00	0.00	4.92
1984	3853	1.683385	GCAAGGCTGGGTTCATTATCC	59.317	52.381	0.00	0.00	0.00	2.59
2019	3890	4.494690	GCTATGTTTGTGTCATGGATGTCG	60.495	45.833	0.00	0.00	0.00	4.35
2048	3919	7.816995	TCATGGTTTGTACTTGGCAAATAAATC	59.183	33.333	0.00	0.00	38.00	2.17
2069	3944	4.760204	TCATGCAGAATAAGCTCATCATGG	59.240	41.667	0.00	0.00	32.63	3.66
2095	3977	5.309806	ACCTACTAGTGTTCAGAATTGGGTT	59.690	40.000	5.39	0.00	0.00	4.11
2100	3982	6.428159	CAGCAAACCTACTAGTGTTCAGAATT	59.572	38.462	5.39	0.00	0.00	2.17
2223	4110	3.434940	AAGTTTAGGTTGGGCAGGTAG	57.565	47.619	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.