AutoCloner

Multiple sequence alignment - TraesCS2D01G246300

Loading Multiple Alignment...

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	TraesCS2D01G246300	chr2D	100.000	2495	0	0	1	2495	286990347	286992841	0.000000e+00	4608
1	TraesCS2D01G246300	chr2D	94.581	978	30	12	7	982	377139584	377138628	0.000000e+00	1491
2	TraesCS2D01G246300	chr2D	91.419	944	28	21	41	984	218024744	218023854	0.000000e+00	1245
3	TraesCS2D01G246300	chr2D	91.069	851	44	8	1	836	39822456	39821623	0.000000e+00	1122
4	TraesCS2D01G246300	chr2D	98.333	180	3	0	1	180	218025072	218024893	1.440000e-82	316
5	TraesCS2D01G246300	chr4D	87.548	1550	149	28	983	2495	275358728	275360270	0.000000e+00	1753
6	TraesCS2D01G246300	chr4D	86.146	1523	156	32	985	2495	191720423	191718944	0.000000e+00	1592
7	TraesCS2D01G246300	chr4D	86.632	389	44	7	2114	2495	266449050	266448663	8.250000e-115	424
8	TraesCS2D01G246300	chr7B	87.254	1522	170	21	985	2493	172328102	172326592	0.000000e+00	1714
9	TraesCS2D01G246300	chr7B	90.121	992	49	20	1	982	340647433	340646481	0.000000e+00	1243
10	TraesCS2D01G246300	chr7B	89.617	992	48	21	1	982	297387095	297386149	0.000000e+00	1210
11	TraesCS2D01G246300	chr7D	97.344	979	14	1	4	982	184175284	184174318	0.000000e+00	1653
12	TraesCS2D01G246300	chr7D	93.890	982	28	18	1	982	5554847	5555796	0.000000e+00	1452
13	TraesCS2D01G246300	chr7D	92.153	994	36	13	1	991	394370648	394369694	0.000000e+00	1365
14	TraesCS2D01G246300	chr7D	85.703	1294	144	32	1220	2495	292077908	292079178	0.000000e+00	1327
15	TraesCS2D01G246300	chr7D	85.626	1294	148	29	1220	2495	292091078	292092351	0.000000e+00	1325
16	TraesCS2D01G246300	chr7D	85.703	1287	145	30	1220	2489	292086685	292087949	0.000000e+00	1321
17	TraesCS2D01G246300	chr7D	85.228	1293	152	30	1220	2495	292082296	292083566	0.000000e+00	1293
18	TraesCS2D01G246300	chr7D	90.598	351	8	2	633	982	394375246	394374920	2.280000e-120	442
19	TraesCS2D01G246300	chr6A	86.358	1554	152	42	985	2495	284424047	284425583	0.000000e+00	1640
20	TraesCS2D01G246300	chr6A	88.034	351	17	6	629	979	33235475	33235800	2.330000e-105	392
21	TraesCS2D01G246300	chr6A	94.083	169	8	2	820	986	94200717	94200549	3.180000e-64	255
22	TraesCS2D01G246300	chr6D	94.512	984	28	12	1	982	338805197	338806156	0.000000e+00	1495
23	TraesCS2D01G246300	chr6D	94.052	992	31	13	1	989	4301687	4300721	0.000000e+00	1480
24	TraesCS2D01G246300	chr6D	95.312	896	31	7	1	892	214545981	214545093	0.000000e+00	1411
25	TraesCS2D01G246300	chr6D	99.387	163	1	0	820	982	214545200	214545038	1.880000e-76	296
26	TraesCS2D01G246300	chr5D	93.103	986	34	15	1	982	334927786	334926831	0.000000e+00	1413
27	TraesCS2D01G246300	chr1B	85.301	1347	171	21	1161	2495	232967898	232969229	0.000000e+00	1365
28	TraesCS2D01G246300	chr1D	96.703	819	20	5	1	815	441022058	441021243	0.000000e+00	1356
29	TraesCS2D01G246300	chr3A	84.524	1260	155	25	1230	2455	407010360	407009107	0.000000e+00	1210
30	TraesCS2D01G246300	chr3A	85.165	182	25	2	1000	1180	167682324	167682144	4.240000e-43	185
31	TraesCS2D01G246300	chr5A	82.221	1378	179	54	1161	2495	444787005	444788359	0.000000e+00	1127
32	TraesCS2D01G246300	chr5A	88.391	982	52	12	1	982	255613462	255614381	0.000000e+00	1125
33	TraesCS2D01G246300	chr5A	86.901	313	35	6	2186	2495	101167616	101167307	1.840000e-91	346
34	TraesCS2D01G246300	chr2B	86.227	1031	77	29	1	999	763814510	763813513	0.000000e+00	1057
35	TraesCS2D01G246300	chr2B	92.727	165	8	4	820	982	227847331	227847493	4.150000e-58	235
36	TraesCS2D01G246300	chr7A	89.916	833	36	15	1	830	82199193	82198406	0.000000e+00	1029
37	TraesCS2D01G246300	chr3B	96.181	419	13	1	1	419	810126061	810125646	0.000000e+00	682
38	TraesCS2D01G246300	chr1A	88.571	350	15	4	633	982	418920630	418920954	3.870000e-108	401
39	TraesCS2D01G246300	chr2A	91.975	162	9	3	820	979	128512083	128512242	8.980000e-55	224
40	TraesCS2D01G246300	chr2A	92.617	149	11	0	1000	1148	140708890	140709038	5.400000e-52	215
41	TraesCS2D01G246300	chr2A	88.235	153	18	0	1000	1152	82413395	82413243	1.520000e-42	183

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	TraesCS2D01G246300	chr2D	286990347	286992841	2494	False	4608.0	4608	100.0000	1	2495	1	chr2D.!!$F1	2494
1	TraesCS2D01G246300	chr2D	377138628	377139584	956	True	1491.0	1491	94.5810	7	982	1	chr2D.!!$R2	975
2	TraesCS2D01G246300	chr2D	39821623	39822456	833	True	1122.0	1122	91.0690	1	836	1	chr2D.!!$R1	835
3	TraesCS2D01G246300	chr2D	218023854	218025072	1218	True	780.5	1245	94.8760	1	984	2	chr2D.!!$R3	983
4	TraesCS2D01G246300	chr4D	275358728	275360270	1542	False	1753.0	1753	87.5480	983	2495	1	chr4D.!!$F1	1512
5	TraesCS2D01G246300	chr4D	191718944	191720423	1479	True	1592.0	1592	86.1460	985	2495	1	chr4D.!!$R1	1510
6	TraesCS2D01G246300	chr7B	172326592	172328102	1510	True	1714.0	1714	87.2540	985	2493	1	chr7B.!!$R1	1508
7	TraesCS2D01G246300	chr7B	340646481	340647433	952	True	1243.0	1243	90.1210	1	982	1	chr7B.!!$R3	981
8	TraesCS2D01G246300	chr7B	297386149	297387095	946	True	1210.0	1210	89.6170	1	982	1	chr7B.!!$R2	981
9	TraesCS2D01G246300	chr7D	184174318	184175284	966	True	1653.0	1653	97.3440	4	982	1	chr7D.!!$R1	978
10	TraesCS2D01G246300	chr7D	5554847	5555796	949	False	1452.0	1452	93.8900	1	982	1	chr7D.!!$F1	981
11	TraesCS2D01G246300	chr7D	394369694	394370648	954	True	1365.0	1365	92.1530	1	991	1	chr7D.!!$R2	990
12	TraesCS2D01G246300	chr7D	292077908	292092351	14443	False	1316.5	1327	85.5650	1220	2495	4	chr7D.!!$F2	1275
13	TraesCS2D01G246300	chr6A	284424047	284425583	1536	False	1640.0	1640	86.3580	985	2495	1	chr6A.!!$F2	1510
14	TraesCS2D01G246300	chr6D	338805197	338806156	959	False	1495.0	1495	94.5120	1	982	1	chr6D.!!$F1	981
15	TraesCS2D01G246300	chr6D	4300721	4301687	966	True	1480.0	1480	94.0520	1	989	1	chr6D.!!$R1	988
16	TraesCS2D01G246300	chr6D	214545038	214545981	943	True	853.5	1411	97.3495	1	982	2	chr6D.!!$R2	981
17	TraesCS2D01G246300	chr5D	334926831	334927786	955	True	1413.0	1413	93.1030	1	982	1	chr5D.!!$R1	981
18	TraesCS2D01G246300	chr1B	232967898	232969229	1331	False	1365.0	1365	85.3010	1161	2495	1	chr1B.!!$F1	1334
19	TraesCS2D01G246300	chr1D	441021243	441022058	815	True	1356.0	1356	96.7030	1	815	1	chr1D.!!$R1	814
20	TraesCS2D01G246300	chr3A	407009107	407010360	1253	True	1210.0	1210	84.5240	1230	2455	1	chr3A.!!$R2	1225
21	TraesCS2D01G246300	chr5A	444787005	444788359	1354	False	1127.0	1127	82.2210	1161	2495	1	chr5A.!!$F2	1334
22	TraesCS2D01G246300	chr5A	255613462	255614381	919	False	1125.0	1125	88.3910	1	982	1	chr5A.!!$F1	981
23	TraesCS2D01G246300	chr2B	763813513	763814510	997	True	1057.0	1057	86.2270	1	999	1	chr2B.!!$R1	998
24	TraesCS2D01G246300	chr7A	82198406	82199193	787	True	1029.0	1029	89.9160	1	830	1	chr7A.!!$R1	829

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
540	888	2.659016	CAGAGGCAGACGGAGCAA	59.341	61.111	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1516	10771	0.321298	GAAACAGCTCACCGGGCTTA	60.321	55.0	6.32	0.0	38.03	3.09	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
540	888	2.659016	CAGAGGCAGACGGAGCAA	59.341	61.111	0.00	0.00	0.00	3.91
647	995	4.772886	ACCACTTGTTAGACCTTTCAGT	57.227	40.909	0.00	0.00	0.00	3.41
995	1433	8.095452	ACTTATCCATCAGATTCTACCTTGTT	57.905	34.615	0.00	0.00	36.33	2.83
1032	1470	9.387123	CAATCACTTAAGCTAGACTTGAAAAAC	57.613	33.333	1.29	0.00	39.58	2.43
1034	1472	8.142994	TCACTTAAGCTAGACTTGAAAAACTG	57.857	34.615	1.29	0.00	39.58	3.16
1061	1499	5.163216	TGCTTGGACATGATCATACATACCA	60.163	40.000	8.15	10.42	35.71	3.25
1067	1505	8.605065	TGGACATGATCATACATACCATGTTAT	58.395	33.333	8.15	0.00	45.20	1.89
1075	1513	8.476064	TCATACATACCATGTTATTGGCATTT	57.524	30.769	0.00	0.00	41.63	2.32
1085	1523	8.415553	CCATGTTATTGGCATTTCTCTCATTTA	58.584	33.333	0.00	0.00	0.00	1.40
1093	1531	7.882179	TGGCATTTCTCTCATTTATGATGATG	58.118	34.615	0.00	0.00	36.02	3.07
1097	1535	9.880064	CATTTCTCTCATTTATGATGATGACAC	57.120	33.333	0.00	0.00	36.02	3.67
1109	1547	9.904198	TTATGATGATGACACTTATTTTCCTCA	57.096	29.630	0.00	0.00	0.00	3.86
1136	1574	7.442364	TGCTAGACCTATGCTTAATGAAACATC	59.558	37.037	0.00	0.00	0.00	3.06
1155	1593	5.845103	ACATCTCATTCTCATGCTAGTCTG	58.155	41.667	0.00	0.00	0.00	3.51
1171	1609	5.755861	GCTAGTCTGGAGGTTAATGATTCAC	59.244	44.000	0.00	0.00	0.00	3.18
1191	1629	5.243207	TCACATCATCCTTATGCTAGCATG	58.757	41.667	35.20	21.53	37.82	4.06
1262	1700	7.040755	TGCTTATGTAATTGGGTATTCGATTGG	60.041	37.037	0.00	0.00	0.00	3.16
1312	1752	6.260936	CACTTGTATTGTCTCTTTGGTGAGTT	59.739	38.462	0.00	0.00	35.68	3.01
1315	1755	6.591935	TGTATTGTCTCTTTGGTGAGTTCTT	58.408	36.000	0.00	0.00	35.68	2.52
1330	1770	5.637387	GTGAGTTCTTTTTCAGGTTTTTGCA	59.363	36.000	0.00	0.00	0.00	4.08
1409	1849	2.295885	GGATTCAGAGCATGGTGAAGG	58.704	52.381	0.00	0.00	36.16	3.46
1412	1852	1.077212	CAGAGCATGGTGAAGGGGG	60.077	63.158	0.00	0.00	0.00	5.40
1485	1930	2.470983	AAGGAGAAGAGCTGCAGTTC	57.529	50.000	21.76	21.76	37.43	3.01
1487	1932	1.696336	AGGAGAAGAGCTGCAGTTCAA	59.304	47.619	29.15	0.00	37.43	2.69
1496	10748	3.484407	AGCTGCAGTTCAAAGAGTGATT	58.516	40.909	16.64	0.00	35.70	2.57
1498	10750	3.004106	GCTGCAGTTCAAAGAGTGATTGT	59.996	43.478	16.64	0.00	35.70	2.71
1504	10756	3.385193	TCAAAGAGTGATTGTGCGAGA	57.615	42.857	0.00	0.00	0.00	4.04
1505	10757	3.059884	TCAAAGAGTGATTGTGCGAGAC	58.940	45.455	0.00	0.00	0.00	3.36
1515	10770	4.340950	TGATTGTGCGAGACCTACATCATA	59.659	41.667	0.00	0.00	0.00	2.15
1516	10771	4.937201	TTGTGCGAGACCTACATCATAT	57.063	40.909	0.00	0.00	0.00	1.78
1617	10874	7.895759	AGTTGCTTAAGCCATTTCTTAAATGA	58.104	30.769	24.30	0.00	46.13	2.57
1691	10949	5.633830	ACTGAATTGTGAATGCCTTGTAG	57.366	39.130	0.00	0.00	0.00	2.74
1776	11034	6.981559	GCTCAAATCCCTAGTACACTAGAAAG	59.018	42.308	16.34	6.41	46.80	2.62
2086	11358	4.471904	TCTGGTAGCTTGGACAGTAATG	57.528	45.455	0.00	0.00	32.92	1.90
2168	11444	3.833559	ATGTTCCTTTGGGGAGACAAT	57.166	42.857	0.00	0.00	46.01	2.71
2169	11445	3.611025	TGTTCCTTTGGGGAGACAATT	57.389	42.857	0.00	0.00	46.01	2.32
2195	11480	5.447624	AAAAACCTAACAATTGGTCGAGG	57.552	39.130	10.29	10.29	38.12	4.63
2245	11530	4.567747	GGTGGTATGTTCCTTTGGTGAGAT	60.568	45.833	0.00	0.00	0.00	2.75
2246	11531	4.636206	GTGGTATGTTCCTTTGGTGAGATC	59.364	45.833	0.00	0.00	0.00	2.75
2290	11577	9.893305	CGAGTTTCAATTTTAATAAGTGGTTCT	57.107	29.630	0.00	0.00	0.00	3.01
2310	11597	8.994500	TGGTTCTACCATAATGTTATGTTCCTA	58.006	33.333	10.82	0.00	44.79	2.94
2489	16208	1.242076	ACCAAGTCTGAAGCATGCAC	58.758	50.000	21.98	13.92	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
296	616	4.074526	GTCGAGGCTGGCTGCAGA	62.075	66.667	20.43	10.87	45.15	4.26
540	888	1.293498	CCAAGTCGGTAGCAGCAGT	59.707	57.895	0.00	0.00	0.00	4.40
647	995	5.164620	TCCACAACTATGAAATGCTCAGA	57.835	39.130	0.00	0.00	37.52	3.27
995	1433	7.395190	AGCTTAAGTGATTGCATCATGTAAA	57.605	32.000	4.02	0.00	42.04	2.01
1032	1470	4.713824	ATGATCATGTCCAAGCAAACAG	57.286	40.909	7.59	0.00	0.00	3.16
1034	1472	5.565592	TGTATGATCATGTCCAAGCAAAC	57.434	39.130	18.72	4.83	0.00	2.93
1061	1499	9.976511	CATAAATGAGAGAAATGCCAATAACAT	57.023	29.630	0.00	0.00	0.00	2.71
1067	1505	7.885009	TCATCATAAATGAGAGAAATGCCAA	57.115	32.000	0.00	0.00	40.64	4.52
1085	1523	8.847196	CATGAGGAAAATAAGTGTCATCATCAT	58.153	33.333	0.00	0.00	39.93	2.45
1093	1531	6.258947	GGTCTAGCATGAGGAAAATAAGTGTC	59.741	42.308	0.00	0.00	0.00	3.67
1097	1535	7.118971	GCATAGGTCTAGCATGAGGAAAATAAG	59.881	40.741	0.00	0.00	0.00	1.73
1101	1539	4.410228	AGCATAGGTCTAGCATGAGGAAAA	59.590	41.667	0.00	0.00	0.00	2.29
1109	1547	7.282585	TGTTTCATTAAGCATAGGTCTAGCAT	58.717	34.615	0.00	0.00	0.00	3.79
1136	1574	4.262121	CCTCCAGACTAGCATGAGAATGAG	60.262	50.000	0.00	0.00	0.00	2.90
1155	1593	6.302269	AGGATGATGTGAATCATTAACCTCC	58.698	40.000	2.91	0.32	39.75	4.30
1171	1609	4.840271	TCCATGCTAGCATAAGGATGATG	58.160	43.478	29.12	15.17	45.31	3.07
1191	1629	7.010339	AGGATGGTATAAATCAGTAAGCTCC	57.990	40.000	0.00	0.00	0.00	4.70
1262	1700	2.484889	GGTCGATGCCCTCTAAATCAC	58.515	52.381	0.00	0.00	0.00	3.06
1312	1752	4.332268	GCACATGCAAAAACCTGAAAAAGA	59.668	37.500	0.00	0.00	41.59	2.52
1330	1770	6.020971	CAGCATATATTGAATGGTGCACAT	57.979	37.500	20.43	7.56	43.47	3.21
1344	1784	3.259374	CCTCGAACCTGGTCAGCATATAT	59.741	47.826	0.00	0.00	0.00	0.86
1409	1849	1.076549	TGTGTCCATTGCTTCCCCC	59.923	57.895	0.00	0.00	0.00	5.40
1412	1852	1.197721	CTTCGTGTGTCCATTGCTTCC	59.802	52.381	0.00	0.00	0.00	3.46
1423	1864	2.625790	AGCTTCTCTCTTCTTCGTGTGT	59.374	45.455	0.00	0.00	0.00	3.72
1450	1895	2.101249	CTCCTTTTGCTTCCACTTGCAA	59.899	45.455	0.00	0.00	45.83	4.08
1455	1900	3.749226	CTCTTCTCCTTTTGCTTCCACT	58.251	45.455	0.00	0.00	0.00	4.00
1485	1930	2.158449	GGTCTCGCACAATCACTCTTTG	59.842	50.000	0.00	0.00	0.00	2.77
1487	1932	1.620819	AGGTCTCGCACAATCACTCTT	59.379	47.619	0.00	0.00	0.00	2.85
1496	10748	5.564848	GCTTATATGATGTAGGTCTCGCACA	60.565	44.000	0.00	0.00	0.00	4.57
1498	10750	4.082190	GGCTTATATGATGTAGGTCTCGCA	60.082	45.833	0.00	0.00	0.00	5.10
1504	10756	3.260884	CACCGGGCTTATATGATGTAGGT	59.739	47.826	6.32	0.00	0.00	3.08
1505	10757	3.513912	TCACCGGGCTTATATGATGTAGG	59.486	47.826	6.32	0.00	0.00	3.18
1515	10770	0.328258	AAACAGCTCACCGGGCTTAT	59.672	50.000	6.32	0.00	38.03	1.73
1516	10771	0.321298	GAAACAGCTCACCGGGCTTA	60.321	55.000	6.32	0.00	38.03	3.09
1592	10849	7.895759	TCATTTAAGAAATGGCTTAAGCAACT	58.104	30.769	27.83	15.33	46.40	3.16
1617	10874	7.507616	TGTCAAAGGTAAAATTTAGTGGGACAT	59.492	33.333	0.00	0.00	44.52	3.06
1627	10884	7.906327	AGCACCATATGTCAAAGGTAAAATTT	58.094	30.769	1.24	0.00	32.01	1.82
1691	10949	5.918011	GCAAGCACTATGTAGATCACTAGTC	59.082	44.000	0.00	0.00	0.00	2.59
1708	10966	4.149396	CACTAATTTCAGCAAAGCAAGCAC	59.851	41.667	0.00	0.00	0.00	4.40
1776	11034	5.899299	AGTAAATGCAGAAAATGATGGAGC	58.101	37.500	0.00	0.00	0.00	4.70
2115	11391	4.162320	CCAGAGAACATGGTATACACCTGT	59.838	45.833	5.01	2.07	45.98	4.00
2183	11468	0.606401	ACACCTGCCTCGACCAATTG	60.606	55.000	0.00	0.00	0.00	2.32
2195	11480	3.123804	CGAGAACATGGTATACACCTGC	58.876	50.000	5.01	0.00	45.98	4.85
2262	11547	7.882179	ACCACTTATTAAAATTGAAACTCGCT	58.118	30.769	0.00	0.00	0.00	4.93
2263	11548	8.515473	AACCACTTATTAAAATTGAAACTCGC	57.485	30.769	0.00	0.00	0.00	5.03
2264	11549	9.893305	AGAACCACTTATTAAAATTGAAACTCG	57.107	29.630	0.00	0.00	0.00	4.18
2310	11597	5.529289	TGATCCCAAGAGACACCTATTACT	58.471	41.667	0.00	0.00	0.00	2.24
2317	11604	1.211457	AGCATGATCCCAAGAGACACC	59.789	52.381	0.00	0.00	0.00	4.16
2322	11609	3.842007	AAGAGAGCATGATCCCAAGAG	57.158	47.619	7.49	0.00	0.00	2.85
2410	16127	9.653287	CAATAGGACACTAGTAAACTCAATCAA	57.347	33.333	0.00	0.00	31.54	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.