AutoCloner

Multiple sequence alignment - TraesCS6A01G189500

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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	TraesCS6A01G189500	chr6A	100.000	2484	0	0	1	2484	242010628	242008145	0.000000e+00	4588
1	TraesCS6A01G189500	chr6A	92.842	461	30	3	2024	2484	180952684	180952227	0.000000e+00	665
2	TraesCS6A01G189500	chr7A	96.261	2487	77	7	1	2484	347383184	347385657	0.000000e+00	4063
3	TraesCS6A01G189500	chr7A	95.974	2484	99	1	1	2484	401494982	401497464	0.000000e+00	4032
4	TraesCS6A01G189500	chr7A	89.524	420	42	2	1476	1894	458555683	458555265	4.700000e-147	531
5	TraesCS6A01G189500	chr7A	87.906	339	31	7	1	329	458556519	458556181	8.330000e-105	390
6	TraesCS6A01G189500	chr2A	96.055	2484	98	0	1	2484	284782265	284784748	0.000000e+00	4045
7	TraesCS6A01G189500	chr2A	93.074	462	29	3	2024	2484	528783399	528782940	0.000000e+00	673
8	TraesCS6A01G189500	chr2A	92.391	460	32	3	2023	2481	482546045	482546502	0.000000e+00	652
9	TraesCS6A01G189500	chr2A	95.890	73	3	0	1892	1964	284784086	284784158	4.340000e-23	119
10	TraesCS6A01G189500	chr2D	93.593	874	54	2	1025	1898	64941660	64940789	0.000000e+00	1303
11	TraesCS6A01G189500	chr2D	92.027	740	32	6	28	767	64942371	64941659	0.000000e+00	1014
12	TraesCS6A01G189500	chr2D	86.891	267	33	2	1884	2150	64940615	64940351	5.190000e-77	298
13	TraesCS6A01G189500	chr1B	92.978	769	46	5	1	764	226904477	226905242	0.000000e+00	1114
14	TraesCS6A01G189500	chr1B	89.740	809	56	10	1032	1839	227793850	227794632	0.000000e+00	1009
15	TraesCS6A01G189500	chr1B	90.947	718	40	4	50	767	227793151	227793843	0.000000e+00	942
16	TraesCS6A01G189500	chr1B	93.250	637	40	3	1024	1659	226905242	226905876	0.000000e+00	935
17	TraesCS6A01G189500	chr1B	88.221	416	46	3	1480	1894	310676592	310676179	6.170000e-136	494
18	TraesCS6A01G189500	chr1B	88.496	339	29	7	1	329	412240626	412240288	3.850000e-108	401
19	TraesCS6A01G189500	chr1B	86.992	246	28	4	1884	2128	412239684	412239442	8.750000e-70	274
20	TraesCS6A01G189500	chr1B	84.454	238	34	3	1892	2128	390091084	390090849	5.340000e-57	231
21	TraesCS6A01G189500	chr1B	85.446	213	29	1	317	527	197788773	197788985	1.160000e-53	220
22	TraesCS6A01G189500	chr5B	95.298	553	24	2	930	1481	675081279	675081830	0.000000e+00	876
23	TraesCS6A01G189500	chr5B	94.937	553	26	2	930	1481	674893310	674893861	0.000000e+00	865
24	TraesCS6A01G189500	chr5B	88.249	417	32	11	317	732	675079413	675079813	1.340000e-132	483
25	TraesCS6A01G189500	chr5B	90.594	202	14	4	735	935	675080110	675080307	1.890000e-66	263
26	TraesCS6A01G189500	chr5B	88.591	149	17	0	787	935	675423345	675423493	5.460000e-42	182
27	TraesCS6A01G189500	chr5B	93.684	95	5	1	673	767	280176329	280176422	9.260000e-30	141
28	TraesCS6A01G189500	chr5D	95.118	553	25	2	930	1481	534638093	534638644	0.000000e+00	870
29	TraesCS6A01G189500	chr5D	95.118	553	25	2	930	1481	534857986	534858537	0.000000e+00	870
30	TraesCS6A01G189500	chr5D	87.419	620	47	17	317	935	534856425	534857014	0.000000e+00	684
31	TraesCS6A01G189500	chr5D	92.663	368	24	3	1476	1842	198493533	198493168	6.080000e-146	527
32	TraesCS6A01G189500	chr5D	94.007	267	16	0	1	267	198494340	198494074	2.970000e-109	405
33	TraesCS6A01G189500	chr5D	76.815	496	83	25	460	935	534864655	534865138	1.480000e-62	250
34	TraesCS6A01G189500	chr5D	87.324	213	25	1	317	527	228445898	228445686	2.470000e-60	243
35	TraesCS6A01G189500	chr5D	89.000	100	11	0	836	935	534637022	534637121	9.330000e-25	124
36	TraesCS6A01G189500	chr4A	93.074	462	29	3	2024	2484	123476644	123477103	0.000000e+00	673
37	TraesCS6A01G189500	chr4A	86.986	292	28	6	646	935	636687360	636687077	1.110000e-83	320
38	TraesCS6A01G189500	chr4A	87.456	287	23	2	317	602	636687636	636687362	3.990000e-83	318
39	TraesCS6A01G189500	chr4A	76.506	498	86	19	462	935	636965290	636964800	2.470000e-60	243
40	TraesCS6A01G189500	chr4A	80.615	325	43	18	623	935	636680302	636679986	1.490000e-57	233
41	TraesCS6A01G189500	chr1A	93.074	462	28	4	2024	2484	534671675	534672133	0.000000e+00	673
42	TraesCS6A01G189500	chr1A	92.424	462	33	1	2023	2484	288306435	288306894	0.000000e+00	658
43	TraesCS6A01G189500	chr2B	90.231	389	37	1	1506	1894	51451681	51451294	7.930000e-140	507
44	TraesCS6A01G189500	chr3B	89.879	247	25	0	1	247	410850478	410850232	3.990000e-83	318
45	TraesCS6A01G189500	chr3B	88.571	245	26	2	1884	2128	410849468	410849226	1.870000e-76	296
46	TraesCS6A01G189500	chr3B	86.498	237	27	5	1884	2119	529269708	529269940	3.170000e-64	255
47	TraesCS6A01G189500	chr7D	77.800	500	75	26	457	935	568598107	568598591	2.430000e-70	276
48	TraesCS6A01G189500	chr4B	86.854	213	26	1	317	527	426877414	426877626	1.150000e-58	237
49	TraesCS6A01G189500	chr7B	80.063	316	49	11	623	935	624350911	624351215	3.220000e-54	222
50	TraesCS6A01G189500	chr4D	83.221	149	23	2	317	464	280924958	280925105	4.310000e-28	135

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	TraesCS6A01G189500	chr6A	242008145	242010628	2483	True	4588.000000	4588	100.000000	1	2484	1	chr6A.!!$R2	2483
1	TraesCS6A01G189500	chr7A	347383184	347385657	2473	False	4063.000000	4063	96.261000	1	2484	1	chr7A.!!$F1	2483
2	TraesCS6A01G189500	chr7A	401494982	401497464	2482	False	4032.000000	4032	95.974000	1	2484	1	chr7A.!!$F2	2483
3	TraesCS6A01G189500	chr7A	458555265	458556519	1254	True	460.500000	531	88.715000	1	1894	2	chr7A.!!$R1	1893
4	TraesCS6A01G189500	chr2A	284782265	284784748	2483	False	2082.000000	4045	95.972500	1	2484	2	chr2A.!!$F2	2483
5	TraesCS6A01G189500	chr2D	64940351	64942371	2020	True	871.666667	1303	90.837000	28	2150	3	chr2D.!!$R1	2122
6	TraesCS6A01G189500	chr1B	226904477	226905876	1399	False	1024.500000	1114	93.114000	1	1659	2	chr1B.!!$F2	1658
7	TraesCS6A01G189500	chr1B	227793151	227794632	1481	False	975.500000	1009	90.343500	50	1839	2	chr1B.!!$F3	1789
8	TraesCS6A01G189500	chr1B	412239442	412240626	1184	True	337.500000	401	87.744000	1	2128	2	chr1B.!!$R3	2127
9	TraesCS6A01G189500	chr5B	674893310	674893861	551	False	865.000000	865	94.937000	930	1481	1	chr5B.!!$F2	551
10	TraesCS6A01G189500	chr5B	675079413	675081830	2417	False	540.666667	876	91.380333	317	1481	3	chr5B.!!$F4	1164
11	TraesCS6A01G189500	chr5D	534856425	534858537	2112	False	777.000000	870	91.268500	317	1481	2	chr5D.!!$F3	1164
12	TraesCS6A01G189500	chr5D	534637022	534638644	1622	False	497.000000	870	92.059000	836	1481	2	chr5D.!!$F2	645
13	TraesCS6A01G189500	chr5D	198493168	198494340	1172	True	466.000000	527	93.335000	1	1842	2	chr5D.!!$R2	1841
14	TraesCS6A01G189500	chr4A	636687077	636687636	559	True	319.000000	320	87.221000	317	935	2	chr4A.!!$R3	618
15	TraesCS6A01G189500	chr3B	410849226	410850478	1252	True	307.000000	318	89.225000	1	2128	2	chr3B.!!$R1	2127

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
912	1354	0.178068	TATCGCCCAGGAAGTTGCTC	59.822	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2460	4398	0.935196	GCGGACACTCTGTTTTTCGT	59.065	50.0	0.0	0.0	0.0	3.85	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
561	701	2.169832	TGCTCCTGTTAGTTGCTGAC	57.830	50.000	0.00	0.00	0.00	3.51
589	729	9.532697	GTATTACAATTTACACGGTTGTACTTG	57.467	33.333	0.00	0.00	37.97	3.16
912	1354	0.178068	TATCGCCCAGGAAGTTGCTC	59.822	55.000	0.00	0.00	0.00	4.26
918	1360	1.363744	CCAGGAAGTTGCTCGTGATC	58.636	55.000	0.00	0.00	33.92	2.92
921	1363	3.070018	CAGGAAGTTGCTCGTGATCTTT	58.930	45.455	0.00	0.00	33.92	2.52
933	2352	5.009854	TCGTGATCTTTGCATGACTGATA	57.990	39.130	0.00	0.00	0.00	2.15
941	2360	7.054491	TCTTTGCATGACTGATACTAGCATA	57.946	36.000	0.00	0.00	0.00	3.14
1127	2657	1.351017	GGTTGAGGATGTTCCCTGTGA	59.649	52.381	0.00	0.00	37.19	3.58
1193	2849	1.619654	TGCAACCCTGACAAATGAGG	58.380	50.000	0.00	0.00	0.00	3.86
1297	2953	4.570369	GCTTCTGATCTTCCTAAGCTTGTC	59.430	45.833	9.86	0.00	39.51	3.18
1331	2987	0.101579	GCTAGCGAAGTCTGACCCTC	59.898	60.000	0.00	0.90	0.00	4.30
1457	3118	6.165577	GGTGGTGCTGAAATTATTGTTTCAT	58.834	36.000	2.91	0.00	44.48	2.57
1465	3139	8.031277	GCTGAAATTATTGTTTCATCTCCTGTT	58.969	33.333	2.91	0.00	44.48	3.16
1466	3140	9.350357	CTGAAATTATTGTTTCATCTCCTGTTG	57.650	33.333	2.91	0.00	44.48	3.33
1467	3141	8.859090	TGAAATTATTGTTTCATCTCCTGTTGT	58.141	29.630	0.00	0.00	41.70	3.32
1468	3142	9.346725	GAAATTATTGTTTCATCTCCTGTTGTC	57.653	33.333	0.00	0.00	37.87	3.18
1469	3143	8.641498	AATTATTGTTTCATCTCCTGTTGTCT	57.359	30.769	0.00	0.00	0.00	3.41
1470	3144	7.672983	TTATTGTTTCATCTCCTGTTGTCTC	57.327	36.000	0.00	0.00	0.00	3.36
1471	3145	4.008074	TGTTTCATCTCCTGTTGTCTCC	57.992	45.455	0.00	0.00	0.00	3.71
1472	3146	3.648067	TGTTTCATCTCCTGTTGTCTCCT	59.352	43.478	0.00	0.00	0.00	3.69
1473	3147	4.103153	TGTTTCATCTCCTGTTGTCTCCTT	59.897	41.667	0.00	0.00	0.00	3.36
1474	3148	4.543590	TTCATCTCCTGTTGTCTCCTTC	57.456	45.455	0.00	0.00	0.00	3.46
1475	3149	3.784178	TCATCTCCTGTTGTCTCCTTCT	58.216	45.455	0.00	0.00	0.00	2.85
1476	3150	3.513119	TCATCTCCTGTTGTCTCCTTCTG	59.487	47.826	0.00	0.00	0.00	3.02
1477	3151	2.964209	TCTCCTGTTGTCTCCTTCTGT	58.036	47.619	0.00	0.00	0.00	3.41
1486	3160	6.925211	TGTTGTCTCCTTCTGTAGATAACTG	58.075	40.000	11.51	0.00	41.64	3.16
1506	3180	5.299949	ACTGAAAAGAATGATGGCCAAAAC	58.700	37.500	10.96	5.13	0.00	2.43
1534	3210	5.586643	TGCAGTACACTTTTTATGTGTGTGA	59.413	36.000	9.42	0.00	46.54	3.58
1564	3240	4.577875	CTTTGAACTCTCTGGAAGCTCAT	58.422	43.478	0.00	0.00	0.00	2.90
1581	3257	2.417933	CTCATTCGGGCTCAAGAACAAG	59.582	50.000	0.00	0.00	0.00	3.16
1682	3617	5.294060	ACATTGCAGTGTGGTTTTTGATTTC	59.706	36.000	14.74	0.00	0.00	2.17
1934	3871	9.990888	CGCTCGTAGAAAAATATTAAGTATGAC	57.009	33.333	0.00	0.00	34.09	3.06
1992	3929	1.559149	GCGGTGCGGTTTAGTTTCGA	61.559	55.000	0.00	0.00	0.00	3.71
2106	4043	3.251729	CACTTGTCTGTCCAATGAAGTGG	59.748	47.826	0.00	0.00	37.64	4.00
2152	4089	3.934457	TTTCTGTCTGATGCAGTACGA	57.066	42.857	0.00	0.00	35.60	3.43
2154	4091	2.437413	TCTGTCTGATGCAGTACGACT	58.563	47.619	0.00	0.00	35.60	4.18
2195	4132	5.625150	AGGTTCACTTTTCATAGTCTTGCT	58.375	37.500	0.00	0.00	0.00	3.91
2289	4226	4.927425	GCGGTTCACTTCTTGATAGTGTTA	59.073	41.667	0.00	0.00	42.77	2.41
2331	4268	4.621991	GTGAAGTGCACTCTACTTTCTCA	58.378	43.478	21.95	14.47	44.27	3.27
2385	4322	2.862536	CCATGCAGTTCTCTATCACGTG	59.137	50.000	9.94	9.94	0.00	4.49
2460	4398	0.601576	CCACGTCGATTTGGGTGTCA	60.602	55.000	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
259	295	3.503363	GAGATGCACTGCACGCCC	61.503	66.667	5.67	0.00	43.04	6.13
273	409	2.202919	CCGCATGCATGGACGAGA	60.203	61.111	27.34	0.00	0.00	4.04
435	571	5.683876	AAGCAGTAAGAATAAGCTCCAGA	57.316	39.130	0.00	0.00	33.83	3.86
561	701	8.928733	AGTACAACCGTGTAAATTGTAATACAG	58.071	33.333	0.00	0.00	41.89	2.74
589	729	3.317993	AGGACATGTGTTTTTGTGCTACC	59.682	43.478	1.15	0.00	41.90	3.18
850	1292	3.428589	GGAATCCGTAAGCGTAGAGTTGT	60.429	47.826	0.00	0.00	36.15	3.32
912	1354	4.807834	AGTATCAGTCATGCAAAGATCACG	59.192	41.667	0.00	0.00	0.00	4.35
918	1360	7.601508	TCATATGCTAGTATCAGTCATGCAAAG	59.398	37.037	0.00	0.00	32.66	2.77
921	1363	6.015180	TGTCATATGCTAGTATCAGTCATGCA	60.015	38.462	0.00	0.00	0.00	3.96
933	2352	6.784969	AGAATCTACCCTTGTCATATGCTAGT	59.215	38.462	0.00	0.00	0.00	2.57
941	2360	4.018050	AGGCAAAGAATCTACCCTTGTCAT	60.018	41.667	0.71	0.00	0.00	3.06
1127	2657	3.704061	ACCAACCAAAGCAACAGTGTTAT	59.296	39.130	8.49	0.00	0.00	1.89
1193	2849	1.034292	GGGCAGGCATCAACTTCCTC	61.034	60.000	0.00	0.00	0.00	3.71
1297	2953	1.079405	TAGCCGCTTCAAACCCTCG	60.079	57.895	0.00	0.00	0.00	4.63
1331	2987	4.825422	TCTTCAATGCTACAGAGAACCAG	58.175	43.478	0.00	0.00	0.00	4.00
1457	3118	2.964209	ACAGAAGGAGACAACAGGAGA	58.036	47.619	0.00	0.00	0.00	3.71
1465	3139	7.776618	TTTCAGTTATCTACAGAAGGAGACA	57.223	36.000	0.00	0.00	34.30	3.41
1466	3140	8.524487	TCTTTTCAGTTATCTACAGAAGGAGAC	58.476	37.037	0.00	0.00	34.30	3.36
1467	3141	8.651589	TCTTTTCAGTTATCTACAGAAGGAGA	57.348	34.615	0.00	0.00	34.30	3.71
1468	3142	9.883142	ATTCTTTTCAGTTATCTACAGAAGGAG	57.117	33.333	0.00	0.00	34.30	3.69
1469	3143	9.658799	CATTCTTTTCAGTTATCTACAGAAGGA	57.341	33.333	0.00	0.00	34.30	3.36
1470	3144	9.658799	TCATTCTTTTCAGTTATCTACAGAAGG	57.341	33.333	0.00	0.00	34.30	3.46
1473	3147	9.605275	CCATCATTCTTTTCAGTTATCTACAGA	57.395	33.333	0.00	0.00	0.00	3.41
1474	3148	8.341173	GCCATCATTCTTTTCAGTTATCTACAG	58.659	37.037	0.00	0.00	0.00	2.74
1475	3149	7.283127	GGCCATCATTCTTTTCAGTTATCTACA	59.717	37.037	0.00	0.00	0.00	2.74
1476	3150	7.283127	TGGCCATCATTCTTTTCAGTTATCTAC	59.717	37.037	0.00	0.00	0.00	2.59
1477	3151	7.345691	TGGCCATCATTCTTTTCAGTTATCTA	58.654	34.615	0.00	0.00	0.00	1.98
1486	3160	5.759763	AGTTGTTTTGGCCATCATTCTTTTC	59.240	36.000	6.09	0.00	0.00	2.29
1506	3180	6.974677	CACATAAAAAGTGTACTGCAGTTG	57.025	37.500	27.06	15.09	40.38	3.16
1564	3240	1.227999	CGCTTGTTCTTGAGCCCGAA	61.228	55.000	0.00	0.00	35.49	4.30
1682	3617	4.023792	ACAACATATCACACACACTGCTTG	60.024	41.667	0.00	0.00	0.00	4.01
1934	3871	6.791299	CCGCATGACATTTTTGTTAACATTTG	59.209	34.615	9.56	7.46	0.00	2.32
1938	3875	4.938080	ACCGCATGACATTTTTGTTAACA	58.062	34.783	3.59	3.59	0.00	2.41
1971	3908	2.191354	GAAACTAAACCGCACCGCCC	62.191	60.000	0.00	0.00	0.00	6.13
2106	4043	8.400184	ACCACACTTATTTAGACTAAAAACCC	57.600	34.615	11.57	0.00	0.00	4.11
2152	4089	3.626670	CCTCGAGACTACCGTAAATGAGT	59.373	47.826	15.71	0.00	0.00	3.41
2154	4091	3.614092	ACCTCGAGACTACCGTAAATGA	58.386	45.455	15.71	0.00	0.00	2.57
2195	4132	5.650266	ACTTCATGTTAAGTGTTGGTGAACA	59.350	36.000	0.00	0.00	38.28	3.18
2289	4226	3.694072	CACATCGGGTGTAAATGAACCAT	59.306	43.478	0.00	0.00	42.75	3.55
2345	4282	8.218338	TGCATGGTTTATTTTGTTCAAACATT	57.782	26.923	0.00	0.00	38.95	2.71
2385	4322	1.408422	GAAAAACCGCACTGCATCAC	58.592	50.000	1.11	0.00	0.00	3.06
2460	4398	0.935196	GCGGACACTCTGTTTTTCGT	59.065	50.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.