AutoCloner

Multiple sequence alignment - TraesCS4A01G174800

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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	TraesCS4A01G174800	chr4A	100.000	2277	0	0	1	2277	445166933	445169209	0.000000e+00	4205.0
1	TraesCS4A01G174800	chr4A	93.733	1484	60	16	775	2241	445175587	445177054	0.000000e+00	2194.0
2	TraesCS4A01G174800	chr4A	96.070	229	6	3	1401	1628	275583179	275582953	9.940000e-99	370.0
3	TraesCS4A01G174800	chr4A	89.744	117	11	1	1222	1337	151224337	151224221	5.070000e-32	148.0
4	TraesCS4A01G174800	chr4A	84.247	146	16	6	1225	1368	422408764	422408624	3.950000e-28	135.0
5	TraesCS4A01G174800	chr4A	84.138	145	17	5	1226	1368	422427435	422427295	3.950000e-28	135.0
6	TraesCS4A01G174800	chr4A	91.379	58	3	1	1400	1455	171994765	171994708	6.740000e-11	78.7
7	TraesCS4A01G174800	chr4A	92.500	40	3	0	1337	1376	151224205	151224166	8.790000e-05	58.4
8	TraesCS4A01G174800	chr1A	97.792	770	14	2	1	767	562150879	562151648	0.000000e+00	1325.0
9	TraesCS4A01G174800	chr1A	95.596	772	26	6	1	767	38872682	38873450	0.000000e+00	1230.0
10	TraesCS4A01G174800	chr1A	86.986	146	12	6	1226	1368	369287569	369287710	8.420000e-35	158.0
11	TraesCS4A01G174800	chr1A	81.818	88	8	6	1399	1481	236551609	236551693	1.460000e-07	67.6
12	TraesCS4A01G174800	chr2B	97.399	769	18	1	1	767	30416795	30417563	0.000000e+00	1308.0
13	TraesCS4A01G174800	chr2B	94.293	771	36	5	1	768	799114871	799115636	0.000000e+00	1173.0
14	TraesCS4A01G174800	chr5B	95.882	777	24	5	1	771	94263695	94262921	0.000000e+00	1251.0
15	TraesCS4A01G174800	chr5B	94.156	770	38	5	1	767	702416088	702415323	0.000000e+00	1166.0
16	TraesCS4A01G174800	chr5B	93.661	773	36	6	1	768	592199853	592200617	0.000000e+00	1144.0
17	TraesCS4A01G174800	chr5A	89.406	774	70	11	1	767	8096678	8095910	0.000000e+00	965.0
18	TraesCS4A01G174800	chr5A	91.088	662	34	14	1637	2277	270631293	270630636	0.000000e+00	872.0
19	TraesCS4A01G174800	chr5A	94.414	555	20	8	1637	2185	270622913	270622364	0.000000e+00	843.0
20	TraesCS4A01G174800	chr5A	88.326	651	61	11	1635	2277	65908141	65907498	0.000000e+00	767.0
21	TraesCS4A01G174800	chr5A	84.545	660	75	22	1639	2277	521587399	521586746	1.480000e-176	628.0
22	TraesCS4A01G174800	chr5A	95.062	162	4	4	1462	1622	270631429	270631271	3.750000e-63	252.0
23	TraesCS4A01G174800	chr5A	92.135	178	9	5	1448	1622	270623066	270622891	1.750000e-61	246.0
24	TraesCS4A01G174800	chr5A	87.097	124	7	7	1504	1620	350685028	350685149	5.100000e-27	132.0
25	TraesCS4A01G174800	chr5A	94.366	71	4	0	1481	1551	488611100	488611170	2.390000e-20	110.0
26	TraesCS4A01G174800	chr6B	89.231	780	67	13	1	768	704558907	704559681	0.000000e+00	959.0
27	TraesCS4A01G174800	chr2A	93.654	520	28	4	1628	2143	570204935	570204417	0.000000e+00	773.0
28	TraesCS4A01G174800	chr2A	87.852	675	51	22	1628	2277	570225072	570224404	0.000000e+00	763.0
29	TraesCS4A01G174800	chr2A	83.994	656	82	20	1635	2277	309565231	309565876	1.930000e-170	608.0
30	TraesCS4A01G174800	chr2A	85.811	148	14	6	1223	1368	657832043	657832185	1.410000e-32	150.0
31	TraesCS4A01G174800	chr2A	98.592	71	1	0	1481	1551	581109240	581109170	2.370000e-25	126.0
32	TraesCS4A01G174800	chr6A	92.514	521	33	5	1627	2143	145123586	145124104	0.000000e+00	741.0
33	TraesCS4A01G174800	chr6A	84.049	163	7	12	1223	1367	417066181	417066342	3.050000e-29	139.0
34	TraesCS4A01G174800	chr6A	95.082	61	0	2	1398	1455	513617507	513617447	2.410000e-15	93.5
35	TraesCS4A01G174800	chr3A	90.586	563	37	1	923	1469	226637219	226636657	0.000000e+00	732.0
36	TraesCS4A01G174800	chr3A	88.099	563	38	9	923	1469	226629407	226628858	1.910000e-180	641.0
37	TraesCS4A01G174800	chr3A	90.159	315	30	1	900	1214	334154359	334154672	2.110000e-110	409.0
38	TraesCS4A01G174800	chr3A	89.841	315	31	1	900	1214	334052628	334052941	9.800000e-109	403.0
39	TraesCS4A01G174800	chr3A	89.841	315	31	1	900	1214	334082056	334082369	9.800000e-109	403.0
40	TraesCS4A01G174800	chr3A	89.841	315	30	2	900	1214	334103398	334103710	9.800000e-109	403.0
41	TraesCS4A01G174800	chr3A	89.524	315	32	1	900	1214	623272109	623272422	4.560000e-107	398.0
42	TraesCS4A01G174800	chr3A	88.254	315	36	1	900	1214	623262238	623262551	2.140000e-100	375.0
43	TraesCS4A01G174800	chr7A	89.916	119	10	2	1222	1339	550694344	550694227	3.920000e-33	152.0
44	TraesCS4A01G174800	chr7A	84.404	109	11	5	1448	1551	193157677	193157570	4.000000e-18	102.0
45	TraesCS4A01G174800	chr7A	84.404	109	11	5	1448	1551	193173417	193173310	4.000000e-18	102.0
46	TraesCS4A01G174800	chr7A	95.082	61	0	2	1398	1455	354070449	354070389	2.410000e-15	93.5
47	TraesCS4A01G174800	chr7A	80.220	91	11	7	1398	1484	374366877	374366790	6.790000e-06	62.1

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	TraesCS4A01G174800	chr4A	445166933	445169209	2276	False	4205.0	4205	100.0000	1	2277	1	chr4A.!!$F1	2276
1	TraesCS4A01G174800	chr4A	445175587	445177054	1467	False	2194.0	2194	93.7330	775	2241	1	chr4A.!!$F2	1466
2	TraesCS4A01G174800	chr1A	562150879	562151648	769	False	1325.0	1325	97.7920	1	767	1	chr1A.!!$F4	766
3	TraesCS4A01G174800	chr1A	38872682	38873450	768	False	1230.0	1230	95.5960	1	767	1	chr1A.!!$F1	766
4	TraesCS4A01G174800	chr2B	30416795	30417563	768	False	1308.0	1308	97.3990	1	767	1	chr2B.!!$F1	766
5	TraesCS4A01G174800	chr2B	799114871	799115636	765	False	1173.0	1173	94.2930	1	768	1	chr2B.!!$F2	767
6	TraesCS4A01G174800	chr5B	94262921	94263695	774	True	1251.0	1251	95.8820	1	771	1	chr5B.!!$R1	770
7	TraesCS4A01G174800	chr5B	702415323	702416088	765	True	1166.0	1166	94.1560	1	767	1	chr5B.!!$R2	766
8	TraesCS4A01G174800	chr5B	592199853	592200617	764	False	1144.0	1144	93.6610	1	768	1	chr5B.!!$F1	767
9	TraesCS4A01G174800	chr5A	8095910	8096678	768	True	965.0	965	89.4060	1	767	1	chr5A.!!$R1	766
10	TraesCS4A01G174800	chr5A	65907498	65908141	643	True	767.0	767	88.3260	1635	2277	1	chr5A.!!$R2	642
11	TraesCS4A01G174800	chr5A	521586746	521587399	653	True	628.0	628	84.5450	1639	2277	1	chr5A.!!$R3	638
12	TraesCS4A01G174800	chr5A	270630636	270631429	793	True	562.0	872	93.0750	1462	2277	2	chr5A.!!$R5	815
13	TraesCS4A01G174800	chr5A	270622364	270623066	702	True	544.5	843	93.2745	1448	2185	2	chr5A.!!$R4	737
14	TraesCS4A01G174800	chr6B	704558907	704559681	774	False	959.0	959	89.2310	1	768	1	chr6B.!!$F1	767
15	TraesCS4A01G174800	chr2A	570204417	570204935	518	True	773.0	773	93.6540	1628	2143	1	chr2A.!!$R1	515
16	TraesCS4A01G174800	chr2A	570224404	570225072	668	True	763.0	763	87.8520	1628	2277	1	chr2A.!!$R2	649
17	TraesCS4A01G174800	chr2A	309565231	309565876	645	False	608.0	608	83.9940	1635	2277	1	chr2A.!!$F1	642
18	TraesCS4A01G174800	chr6A	145123586	145124104	518	False	741.0	741	92.5140	1627	2143	1	chr6A.!!$F1	516
19	TraesCS4A01G174800	chr3A	226636657	226637219	562	True	732.0	732	90.5860	923	1469	1	chr3A.!!$R2	546
20	TraesCS4A01G174800	chr3A	226628858	226629407	549	True	641.0	641	88.0990	923	1469	1	chr3A.!!$R1	546

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
914	933	0.60864	ACTAGGCAGGAAAGTGACGG	59.391	55.0	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
1905	1949	1.228154	ACCTCCAAACCTTGCCGAC	60.228	57.895	0.0	0.0	0.0	4.79	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
399	403	1.135053	GGTAGAAGTCCTCCTCAACGC	60.135	57.143	0.00	0.00	0.00	4.84
591	598	1.378531	CCTTTTATGTAGCGCTGGCA	58.621	50.000	22.90	19.22	43.41	4.92
768	787	3.821841	CCGTCAGATTAAAACCAACAGC	58.178	45.455	0.00	0.00	0.00	4.40
770	789	3.666902	CGTCAGATTAAAACCAACAGCCG	60.667	47.826	0.00	0.00	0.00	5.52
772	791	1.544246	AGATTAAAACCAACAGCCGGC	59.456	47.619	21.89	21.89	0.00	6.13
773	792	1.271102	GATTAAAACCAACAGCCGGCA	59.729	47.619	31.54	2.48	0.00	5.69
802	821	3.485431	CTGCAGCGAGGTGAAGCG	61.485	66.667	0.00	0.00	38.61	4.68
806	825	4.443266	AGCGAGGTGAAGCGAGGC	62.443	66.667	0.00	0.00	38.61	4.70
859	878	2.225066	GGTAGTAGAGGGGATCGACCAT	60.225	54.545	7.69	0.00	41.20	3.55
861	880	0.969894	GTAGAGGGGATCGACCATGG	59.030	60.000	11.19	11.19	41.20	3.66
869	888	1.739338	GATCGACCATGGAGCTCGGT	61.739	60.000	21.47	14.27	35.12	4.69
872	891	1.742768	GACCATGGAGCTCGGTAGG	59.257	63.158	21.47	10.84	31.63	3.18
883	902	0.970937	CTCGGTAGGGCTGGAGAACA	60.971	60.000	0.00	0.00	0.00	3.18
904	923	2.423446	GGCGATGGACTAGGCAGG	59.577	66.667	0.00	0.00	0.00	4.85
909	928	1.482593	CGATGGACTAGGCAGGAAAGT	59.517	52.381	0.00	0.00	0.00	2.66
913	932	1.404315	GGACTAGGCAGGAAAGTGACG	60.404	57.143	0.00	0.00	0.00	4.35
914	933	0.608640	ACTAGGCAGGAAAGTGACGG	59.391	55.000	0.00	0.00	0.00	4.79
968	987	1.000283	CTGACAGAGAACAGCGAGGTT	60.000	52.381	0.00	0.00	0.00	3.50
969	988	1.412710	TGACAGAGAACAGCGAGGTTT	59.587	47.619	0.00	0.00	0.00	3.27
1114	1133	1.234821	GTTGTTTGTCGATCTGGCCA	58.765	50.000	4.71	4.71	0.00	5.36
1132	1151	1.265236	CAGAGTTGAGGCAGAGGAGT	58.735	55.000	0.00	0.00	0.00	3.85
1181	1200	1.003839	GTCTGGTGGGCGTTCATGA	60.004	57.895	0.00	0.00	0.00	3.07
1183	1202	1.302431	CTGGTGGGCGTTCATGACA	60.302	57.895	0.00	0.00	0.00	3.58
1188	1207	1.302511	GGGCGTTCATGACAGTGGT	60.303	57.895	0.00	0.00	0.00	4.16
1254	1273	2.691252	GGGGAATGGGACGAGGGT	60.691	66.667	0.00	0.00	0.00	4.34
1283	1302	3.823330	CGGCGGCTTAGACTCCGT	61.823	66.667	8.53	0.00	46.79	4.69
1618	1657	3.244044	GCTCCTCTCTCTCTCTCTCTCTC	60.244	56.522	0.00	0.00	0.00	3.20
1619	1658	4.222336	CTCCTCTCTCTCTCTCTCTCTCT	58.778	52.174	0.00	0.00	0.00	3.10
1620	1659	4.219115	TCCTCTCTCTCTCTCTCTCTCTC	58.781	52.174	0.00	0.00	0.00	3.20
1621	1660	4.078922	TCCTCTCTCTCTCTCTCTCTCTCT	60.079	50.000	0.00	0.00	0.00	3.10
1622	1661	4.280677	CCTCTCTCTCTCTCTCTCTCTCTC	59.719	54.167	0.00	0.00	0.00	3.20
1623	1662	5.136068	TCTCTCTCTCTCTCTCTCTCTCT	57.864	47.826	0.00	0.00	0.00	3.10
1624	1663	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1625	1664	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1626	1665	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1627	1666	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1628	1667	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1629	1668	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1630	1669	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1631	1670	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1706	1750	5.372066	AGATTTAAGAGAAGAGGCCATGGAT	59.628	40.000	18.40	1.89	0.00	3.41
1905	1949	6.151144	ACCCTCGATAAAAGGAGAAACAATTG	59.849	38.462	3.24	3.24	35.83	2.32
2098	2149	8.530269	ACCGAAGATCCATACGATTTATTTAC	57.470	34.615	0.00	0.00	0.00	2.01
2158	2220	7.519032	TGACATGATATGAAATGCATGACAT	57.481	32.000	18.34	18.34	40.58	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
455	459	2.017559	GCAGCGACGGGAAGACCTAT	62.018	60.000	0.00	0.00	36.97	2.57
591	598	2.354328	TGATGGTTTAGGTCCCCTGTT	58.646	47.619	0.00	0.00	34.61	3.16
637	646	3.751698	GCTTTTTATCCCAACTGAGACGT	59.248	43.478	0.00	0.00	0.00	4.34
640	649	3.697166	GGGCTTTTTATCCCAACTGAGA	58.303	45.455	0.00	0.00	42.18	3.27
756	775	0.466555	ACTGCCGGCTGTTGGTTTTA	60.467	50.000	30.90	4.25	0.00	1.52
768	787	2.125350	GCTCCTTCTCACTGCCGG	60.125	66.667	0.00	0.00	0.00	6.13
770	789	4.613929	CAGCTCCTTCTCACTGCC	57.386	61.111	0.00	0.00	0.00	4.85
772	791	1.020333	GCTGCAGCTCCTTCTCACTG	61.020	60.000	31.33	0.00	38.21	3.66
773	792	1.296068	GCTGCAGCTCCTTCTCACT	59.704	57.895	31.33	0.00	38.21	3.41
859	878	2.759973	CAGCCCTACCGAGCTCCA	60.760	66.667	8.47	0.00	37.18	3.86
861	880	2.442272	TCCAGCCCTACCGAGCTC	60.442	66.667	2.73	2.73	37.18	4.09
869	888	0.909610	CCACCTGTTCTCCAGCCCTA	60.910	60.000	0.00	0.00	40.06	3.53
872	891	2.360475	GCCACCTGTTCTCCAGCC	60.360	66.667	0.00	0.00	40.06	4.85
883	902	2.435693	GCCTAGTCCATCGCCACCT	61.436	63.158	0.00	0.00	0.00	4.00
889	908	1.482593	ACTTTCCTGCCTAGTCCATCG	59.517	52.381	0.00	0.00	0.00	3.84
904	923	3.119096	GCCCGAGCCGTCACTTTC	61.119	66.667	0.00	0.00	0.00	2.62
968	987	1.550130	CCCCGCCTTCCTGTGTCTAA	61.550	60.000	0.00	0.00	0.00	2.10
969	988	1.987855	CCCCGCCTTCCTGTGTCTA	60.988	63.158	0.00	0.00	0.00	2.59
1114	1133	2.733956	CTACTCCTCTGCCTCAACTCT	58.266	52.381	0.00	0.00	0.00	3.24
1132	1151	1.961180	GCCTCTCCTTCGCCTTGCTA	61.961	60.000	0.00	0.00	0.00	3.49
1181	1200	3.958860	GCAGGAGGCCACCACTGT	61.959	66.667	22.29	0.00	34.68	3.55
1183	1202	3.644606	CAGCAGGAGGCCACCACT	61.645	66.667	22.29	14.99	46.50	4.00
1331	1350	3.147595	CCATCCTCGCGTCTCCCA	61.148	66.667	5.77	0.00	0.00	4.37
1618	1657	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1619	1658	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1620	1659	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1621	1660	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1622	1661	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1623	1662	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1624	1663	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1625	1664	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1626	1665	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1627	1666	5.136068	AGAGAGAGAGAGAGAGAGAGAGA	57.864	47.826	0.00	0.00	0.00	3.10
1628	1667	5.867903	AAGAGAGAGAGAGAGAGAGAGAG	57.132	47.826	0.00	0.00	0.00	3.20
1629	1668	7.786943	AGAATAAGAGAGAGAGAGAGAGAGAGA	59.213	40.741	0.00	0.00	0.00	3.10
1630	1669	7.961351	AGAATAAGAGAGAGAGAGAGAGAGAG	58.039	42.308	0.00	0.00	0.00	3.20
1631	1670	7.786943	AGAGAATAAGAGAGAGAGAGAGAGAGA	59.213	40.741	0.00	0.00	0.00	3.10
1756	1800	5.461032	TGTTGAAACCACTTTTGTTGAGT	57.539	34.783	0.00	0.00	0.00	3.41
1905	1949	1.228154	ACCTCCAAACCTTGCCGAC	60.228	57.895	0.00	0.00	0.00	4.79
2158	2220	2.935201	GTTGCCTTGTCATTTGTTTGCA	59.065	40.909	0.00	0.00	0.00	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.