AutoCloner

Multiple sequence alignment - TraesCS1B01G015100

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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	TraesCS1B01G015100	chr1B	100.000	2462	0	0	1	2462	7303930	7306391	0.000000e+00	4547
1	TraesCS1B01G015100	chr1B	98.506	1004	15	0	1459	2462	22204516	22203513	0.000000e+00	1772
2	TraesCS1B01G015100	chr1B	85.543	1584	173	26	849	2418	6426186	6427727	0.000000e+00	1605
3	TraesCS1B01G015100	chr1B	85.473	1363	121	39	275	1608	7885013	7883699	0.000000e+00	1349
4	TraesCS1B01G015100	chr1B	86.737	754	83	11	1	745	6425442	6426187	0.000000e+00	822
5	TraesCS1B01G015100	chr1B	77.218	1071	149	59	685	1705	22274971	22273946	2.790000e-149	538
6	TraesCS1B01G015100	chr1B	76.851	1067	149	60	685	1701	7364441	7365459	1.690000e-141	512
7	TraesCS1B01G015100	chr1B	76.751	1071	156	53	685	1705	7552976	7551949	1.690000e-141	512
8	TraesCS1B01G015100	chr1B	77.098	1013	140	53	685	1650	17254596	17255563	3.660000e-138	501
9	TraesCS1B01G015100	chr1B	76.449	1070	160	56	685	1705	7548706	7547680	1.700000e-136	496
10	TraesCS1B01G015100	chr1B	76.355	1070	161	58	685	1705	7544444	7543418	7.910000e-135	490
11	TraesCS1B01G015100	chr1B	86.577	149	17	3	1941	2088	199579664	199579518	7.050000e-36	161
12	TraesCS1B01G015100	chr1B	92.000	100	7	1	1	99	7885110	7885011	3.300000e-29	139
13	TraesCS1B01G015100	chr1D	85.082	1401	138	26	849	2238	4354948	4353608	0.000000e+00	1363
14	TraesCS1B01G015100	chr1D	87.959	789	81	10	962	1744	3465909	3466689	0.000000e+00	918
15	TraesCS1B01G015100	chr1D	86.100	741	78	10	24	748	4355675	4354944	0.000000e+00	774
16	TraesCS1B01G015100	chr1D	86.163	701	81	11	1	695	3464824	3465514	0.000000e+00	743
17	TraesCS1B01G015100	chr1D	77.718	929	123	55	747	1635	3451893	3452777	2.200000e-135	492
18	TraesCS1B01G015100	chr1D	84.071	226	21	12	698	923	3465700	3465910	1.150000e-48	204
19	TraesCS1B01G015100	chr1A	76.309	1127	175	57	747	1822	6023651	6022566	3.630000e-143	518
20	TraesCS1B01G015100	chr7B	81.214	527	74	13	1948	2462	524041463	524041976	3.810000e-108	401
21	TraesCS1B01G015100	chr6D	79.271	521	87	14	1952	2457	19292990	19292476	6.520000e-91	344
22	TraesCS1B01G015100	chr5D	79.508	244	33	13	1948	2178	452286328	452286089	9.110000e-35	158
23	TraesCS1B01G015100	chr4A	90.000	120	10	2	1948	2066	200947370	200947488	1.180000e-33	154

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	TraesCS1B01G015100	chr1B	7303930	7306391	2461	False	4547.000000	4547	100.000000	1	2462	1	chr1B.!!$F1	2461
1	TraesCS1B01G015100	chr1B	22203513	22204516	1003	True	1772.000000	1772	98.506000	1459	2462	1	chr1B.!!$R1	1003
2	TraesCS1B01G015100	chr1B	6425442	6427727	2285	False	1213.500000	1605	86.140000	1	2418	2	chr1B.!!$F4	2417
3	TraesCS1B01G015100	chr1B	7883699	7885110	1411	True	744.000000	1349	88.736500	1	1608	2	chr1B.!!$R5	1607
4	TraesCS1B01G015100	chr1B	22273946	22274971	1025	True	538.000000	538	77.218000	685	1705	1	chr1B.!!$R2	1020
5	TraesCS1B01G015100	chr1B	7364441	7365459	1018	False	512.000000	512	76.851000	685	1701	1	chr1B.!!$F2	1016
6	TraesCS1B01G015100	chr1B	17254596	17255563	967	False	501.000000	501	77.098000	685	1650	1	chr1B.!!$F3	965
7	TraesCS1B01G015100	chr1B	7543418	7552976	9558	True	499.333333	512	76.518333	685	1705	3	chr1B.!!$R4	1020
8	TraesCS1B01G015100	chr1D	4353608	4355675	2067	True	1068.500000	1363	85.591000	24	2238	2	chr1D.!!$R1	2214
9	TraesCS1B01G015100	chr1D	3464824	3466689	1865	False	621.666667	918	86.064333	1	1744	3	chr1D.!!$F2	1743
10	TraesCS1B01G015100	chr1D	3451893	3452777	884	False	492.000000	492	77.718000	747	1635	1	chr1D.!!$F1	888
11	TraesCS1B01G015100	chr1A	6022566	6023651	1085	True	518.000000	518	76.309000	747	1822	1	chr1A.!!$R1	1075
12	TraesCS1B01G015100	chr7B	524041463	524041976	513	False	401.000000	401	81.214000	1948	2462	1	chr7B.!!$F1	514
13	TraesCS1B01G015100	chr6D	19292476	19292990	514	True	344.000000	344	79.271000	1952	2457	1	chr6D.!!$R1	505

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
617	636	0.040692	GACACGTGCGAGTGAGTGTA	60.041	55.0	17.22	0.0	46.34	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1857	10720	0.191563	TAGGTAGTGGTGGTGGTGGT	59.808	55.0	0.0	0.0	0.0	4.16	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
34	36	5.710984	ACAGGTGACTAGATTTGTTCTACG	58.289	41.667	0.00	0.00	40.21	3.51
36	38	4.771054	AGGTGACTAGATTTGTTCTACGGT	59.229	41.667	0.00	0.00	40.61	4.83
64	66	3.562973	GTGATTGTCCTGCATGTATCTGG	59.437	47.826	0.00	0.00	0.00	3.86
85	87	2.836636	ATCTCCTCTGTAGCCTGTCA	57.163	50.000	0.00	0.00	0.00	3.58
125	127	3.567585	TGCACTACACAATAGCAAAAGCA	59.432	39.130	0.00	0.00	31.42	3.91
135	145	9.613428	ACACAATAGCAAAAGCAATACTAGATA	57.387	29.630	0.00	0.00	0.00	1.98
240	250	9.988815	AAGTTATATACTAAAGAGTGAGCATGG	57.011	33.333	0.00	0.00	35.54	3.66
250	260	5.939764	AGAGTGAGCATGGTTTAGTCATA	57.060	39.130	15.75	0.00	0.00	2.15
330	340	2.030412	TTGCGTGGATGAGTGCGT	59.970	55.556	0.00	0.00	0.00	5.24
355	368	1.752833	GACTGGTTTCTCCCGTGGT	59.247	57.895	0.00	0.00	33.84	4.16
364	377	0.459899	TCTCCCGTGGTGAATCGATG	59.540	55.000	0.00	0.00	0.00	3.84
369	382	2.418197	CCCGTGGTGAATCGATGTAGTT	60.418	50.000	0.00	0.00	0.00	2.24
406	421	2.104792	AGTGTTTGAGAGCTTGGCTGTA	59.895	45.455	0.00	0.00	39.88	2.74
440	456	7.675619	AGAGGTGGGAAATATGTCATTTTTCTT	59.324	33.333	20.97	8.31	32.87	2.52
467	484	5.476945	GTGGATCAAATGTCCCTTGTAAAGT	59.523	40.000	0.00	0.00	44.25	2.66
481	498	8.877195	TCCCTTGTAAAGTGTTATCTTTCTACT	58.123	33.333	0.00	0.00	44.25	2.57
567	584	2.819019	TCTATTGGTGGCACATGTGTTG	59.181	45.455	26.01	6.59	44.52	3.33
568	585	1.412079	ATTGGTGGCACATGTGTTGT	58.588	45.000	26.01	4.27	44.52	3.32
569	586	0.743688	TTGGTGGCACATGTGTTGTC	59.256	50.000	26.01	14.27	44.52	3.18
570	587	0.106769	TGGTGGCACATGTGTTGTCT	60.107	50.000	26.01	0.00	44.52	3.41
571	588	0.593128	GGTGGCACATGTGTTGTCTC	59.407	55.000	26.01	8.87	44.52	3.36
572	589	0.235665	GTGGCACATGTGTTGTCTCG	59.764	55.000	26.01	0.00	44.52	4.04
573	590	0.179059	TGGCACATGTGTTGTCTCGT	60.179	50.000	26.01	0.00	36.00	4.18
574	591	0.512952	GGCACATGTGTTGTCTCGTC	59.487	55.000	26.01	6.73	36.00	4.20
575	592	0.161658	GCACATGTGTTGTCTCGTCG	59.838	55.000	26.01	0.00	36.00	5.12
605	622	0.742990	ACCAGTGGTTGTGACACGTG	60.743	55.000	15.48	15.48	43.41	4.49
617	636	0.040692	GACACGTGCGAGTGAGTGTA	60.041	55.000	17.22	0.00	46.34	2.90
618	637	0.317603	ACACGTGCGAGTGAGTGTAC	60.318	55.000	17.22	0.00	44.79	2.90
631	650	4.098654	AGTGAGTGTACACATATCTGGCTC	59.901	45.833	27.06	12.97	42.45	4.70
638	657	9.179909	AGTGTACACATATCTGGCTCTATATAC	57.820	37.037	27.06	0.00	0.00	1.47
700	904	2.734079	GCCAAAAGACGTGAGAAGAGAG	59.266	50.000	0.00	0.00	0.00	3.20
723	937	3.613432	GCAAGATCTTTGCCCTTGTGAAG	60.613	47.826	4.86	0.00	39.41	3.02
745	959	3.655486	CACAACATACCACCGACACTAA	58.345	45.455	0.00	0.00	0.00	2.24
752	971	5.887598	ACATACCACCGACACTAATAGTACA	59.112	40.000	0.00	0.00	0.00	2.90
812	1032	4.826733	ACACATGACCACTTATGAAGCAAA	59.173	37.500	0.00	0.00	0.00	3.68
813	1033	5.301551	ACACATGACCACTTATGAAGCAAAA	59.698	36.000	0.00	0.00	0.00	2.44
815	1035	7.176515	ACACATGACCACTTATGAAGCAAAATA	59.823	33.333	0.00	0.00	0.00	1.40
816	1036	8.028354	CACATGACCACTTATGAAGCAAAATAA	58.972	33.333	0.00	0.00	0.00	1.40
1007	1271	4.472833	ACACTTCTTCTCCAATATGGCTCT	59.527	41.667	0.00	0.00	37.47	4.09
1024	1297	2.623502	GCTCTAGGTTCACCTACCCTCA	60.624	54.545	1.18	0.00	46.48	3.86
1076	1349	1.701292	TGCCATGATGATCCTTCCGAT	59.299	47.619	0.00	0.00	0.00	4.18
1126	1399	2.496899	AGAACTAGTAACGACCCCGA	57.503	50.000	0.00	0.00	39.50	5.14
1230	5776	0.884704	CCAAGTGCCGCAAGTACTGT	60.885	55.000	0.00	0.00	33.84	3.55
1713	10554	9.893634	TTTGTTTTCCGTTTCAGAGGATATATA	57.106	29.630	0.00	0.00	36.28	0.86
1830	10693	3.753272	ACAAATGCTGCCACTTACTACTG	59.247	43.478	0.00	0.00	0.00	2.74
1839	10702	3.508762	CCACTTACTACTGGCACTAACG	58.491	50.000	0.00	0.00	0.00	3.18
1840	10703	3.057033	CCACTTACTACTGGCACTAACGT	60.057	47.826	0.00	0.00	0.00	3.99
1841	10704	4.553323	CACTTACTACTGGCACTAACGTT	58.447	43.478	5.88	5.88	0.00	3.99
1842	10705	5.335897	CCACTTACTACTGGCACTAACGTTA	60.336	44.000	7.94	7.94	0.00	3.18
1843	10706	5.570589	CACTTACTACTGGCACTAACGTTAC	59.429	44.000	3.29	0.00	0.00	2.50
1844	10707	3.582714	ACTACTGGCACTAACGTTACC	57.417	47.619	3.29	5.21	0.00	2.85
1845	10708	2.892852	ACTACTGGCACTAACGTTACCA	59.107	45.455	13.66	13.66	0.00	3.25
1846	10709	2.159327	ACTGGCACTAACGTTACCAC	57.841	50.000	11.08	1.12	0.00	4.16
1847	10710	1.270465	ACTGGCACTAACGTTACCACC	60.270	52.381	11.08	9.58	0.00	4.61
1848	10711	0.757512	TGGCACTAACGTTACCACCA	59.242	50.000	11.08	11.69	0.00	4.17
1849	10712	1.270412	TGGCACTAACGTTACCACCAG	60.270	52.381	11.08	2.44	0.00	4.00
1850	10713	0.794473	GCACTAACGTTACCACCAGC	59.206	55.000	3.29	0.00	0.00	4.85
1851	10714	1.874739	GCACTAACGTTACCACCAGCA	60.875	52.381	3.29	0.00	0.00	4.41
1852	10715	1.796459	CACTAACGTTACCACCAGCAC	59.204	52.381	3.29	0.00	0.00	4.40
1853	10716	1.270465	ACTAACGTTACCACCAGCACC	60.270	52.381	3.29	0.00	0.00	5.01
1854	10717	0.757512	TAACGTTACCACCAGCACCA	59.242	50.000	3.29	0.00	0.00	4.17
1855	10718	0.534203	AACGTTACCACCAGCACCAG	60.534	55.000	0.00	0.00	0.00	4.00
1856	10719	2.325082	CGTTACCACCAGCACCAGC	61.325	63.158	0.00	0.00	42.56	4.85
1857	10720	1.228124	GTTACCACCAGCACCAGCA	60.228	57.895	0.00	0.00	45.49	4.41
1914	10777	3.118592	GGTCCTTCAAGATCTACCACCAG	60.119	52.174	0.00	0.00	0.00	4.00
1939	10802	3.369157	CCACCACCACTACTAGCTAAACC	60.369	52.174	0.00	0.00	0.00	3.27
1941	10804	4.020485	CACCACCACTACTAGCTAAACCTT	60.020	45.833	0.00	0.00	0.00	3.50
2207	11085	6.215845	AGTTGTGCTTCGCAAAGAAATTAAT	58.784	32.000	0.00	0.00	41.47	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	36	3.146066	TGCAGGACAATCACTACAAACC	58.854	45.455	0.00	0.00	0.00	3.27
36	38	4.397420	ACATGCAGGACAATCACTACAAA	58.603	39.130	4.84	0.00	0.00	2.83
64	66	3.027412	TGACAGGCTACAGAGGAGATTC	58.973	50.000	0.00	0.00	0.00	2.52
85	87	1.401931	GCACATCGCTGACAATTGCTT	60.402	47.619	5.05	0.00	37.77	3.91
157	167	9.489084	TGATGCTAAATGGTGAATGTAGTATAC	57.511	33.333	0.00	0.00	43.42	1.47
224	234	6.166279	TGACTAAACCATGCTCACTCTTTAG	58.834	40.000	0.00	0.00	0.00	1.85
230	240	5.683876	AGTATGACTAAACCATGCTCACT	57.316	39.130	0.00	0.00	32.75	3.41
232	242	5.185454	CCAAGTATGACTAAACCATGCTCA	58.815	41.667	0.00	0.00	36.25	4.26
236	246	7.687941	AAAGACCAAGTATGACTAAACCATG	57.312	36.000	0.00	0.00	0.00	3.66
330	340	1.645710	GGAGAAACCAGTCCTCCTCA	58.354	55.000	10.33	0.00	42.36	3.86
355	368	6.818142	ACATCAATGACAACTACATCGATTCA	59.182	34.615	0.00	0.00	0.00	2.57
364	377	6.017934	ACACTGACAACATCAATGACAACTAC	60.018	38.462	0.00	0.00	36.64	2.73
369	382	5.356470	TCAAACACTGACAACATCAATGACA	59.644	36.000	0.00	0.00	36.64	3.58
440	456	3.081061	CAAGGGACATTTGATCCACGAA	58.919	45.455	0.00	0.00	38.06	3.85
467	484	9.421399	TCTCATATCCACAGTAGAAAGATAACA	57.579	33.333	0.00	0.00	0.00	2.41
549	566	1.340889	GACAACACATGTGCCACCAAT	59.659	47.619	25.68	0.98	44.12	3.16
550	567	0.743688	GACAACACATGTGCCACCAA	59.256	50.000	25.68	0.00	44.12	3.67
567	584	2.872001	CGCTGCAGACGACGAGAC	60.872	66.667	20.43	0.00	0.00	3.36
568	585	4.760840	GCGCTGCAGACGACGAGA	62.761	66.667	27.07	0.00	0.00	4.04
575	592	3.720193	CACTGGTGCGCTGCAGAC	61.720	66.667	20.43	9.26	40.08	3.51
586	603	0.742990	CACGTGTCACAACCACTGGT	60.743	55.000	7.58	0.00	37.65	4.00
605	622	4.038361	CAGATATGTGTACACTCACTCGC	58.962	47.826	25.60	9.46	38.90	5.03
617	636	8.422577	TTGTGTATATAGAGCCAGATATGTGT	57.577	34.615	0.00	0.00	0.00	3.72
618	637	9.310716	CATTGTGTATATAGAGCCAGATATGTG	57.689	37.037	0.00	0.00	0.00	3.21
631	650	4.142534	GGCCATGCTGCATTGTGTATATAG	60.143	45.833	13.38	0.00	0.00	1.31
638	657	1.447140	GTGGCCATGCTGCATTGTG	60.447	57.895	13.38	3.34	0.00	3.33
723	937	0.515564	GTGTCGGTGGTATGTTGTGC	59.484	55.000	0.00	0.00	0.00	4.57
731	945	6.832520	TTTGTACTATTAGTGTCGGTGGTA	57.167	37.500	6.60	0.00	0.00	3.25
861	1116	1.563435	CTGCGTTCACCTGTCAGCTG	61.563	60.000	7.63	7.63	0.00	4.24
1007	1271	2.653366	AGAGTGAGGGTAGGTGAACCTA	59.347	50.000	5.05	5.05	46.48	3.08
1024	1297	2.032681	GGTGGCCGCTTTGAGAGT	59.967	61.111	17.49	0.00	0.00	3.24
1096	1369	4.648651	GTTACTAGTTCTTCTTGGCCCAA	58.351	43.478	0.00	0.00	0.00	4.12
1126	1399	4.457496	CGGCTCCGATGCTGGTGT	62.457	66.667	1.35	0.00	42.83	4.16
1230	5776	2.034532	TCGTAGCTGGGGACGTCA	59.965	61.111	18.91	0.00	40.00	4.35
1650	10486	2.805671	CAAATAACACACGACAGGAGCA	59.194	45.455	0.00	0.00	0.00	4.26
1713	10554	9.293404	CATCTATGTTCAGGTCATTAATCCAAT	57.707	33.333	0.00	0.00	0.00	3.16
1714	10555	7.720957	CCATCTATGTTCAGGTCATTAATCCAA	59.279	37.037	0.00	0.00	0.00	3.53
1830	10693	1.435577	CTGGTGGTAACGTTAGTGCC	58.564	55.000	8.60	11.04	42.51	5.01
1837	10700	1.070786	CTGGTGCTGGTGGTAACGT	59.929	57.895	0.00	0.00	42.51	3.99
1839	10702	1.228124	TGCTGGTGCTGGTGGTAAC	60.228	57.895	0.00	0.00	40.48	2.50
1840	10703	1.228124	GTGCTGGTGCTGGTGGTAA	60.228	57.895	0.00	0.00	40.48	2.85
1841	10704	2.429930	GTGCTGGTGCTGGTGGTA	59.570	61.111	0.00	0.00	40.48	3.25
1842	10705	4.586235	GGTGCTGGTGCTGGTGGT	62.586	66.667	0.00	0.00	40.48	4.16
1843	10706	4.584518	TGGTGCTGGTGCTGGTGG	62.585	66.667	0.00	0.00	40.48	4.61
1844	10707	3.289834	GTGGTGCTGGTGCTGGTG	61.290	66.667	0.00	0.00	40.48	4.17
1845	10708	4.586235	GGTGGTGCTGGTGCTGGT	62.586	66.667	0.00	0.00	40.48	4.00
1846	10709	4.584518	TGGTGGTGCTGGTGCTGG	62.585	66.667	0.00	0.00	40.48	4.85
1847	10710	3.289834	GTGGTGGTGCTGGTGCTG	61.290	66.667	0.00	0.00	40.48	4.41
1848	10711	4.586235	GGTGGTGGTGCTGGTGCT	62.586	66.667	0.00	0.00	40.48	4.40
1849	10712	4.892965	TGGTGGTGGTGCTGGTGC	62.893	66.667	0.00	0.00	40.20	5.01
1850	10713	2.906897	GTGGTGGTGGTGCTGGTG	60.907	66.667	0.00	0.00	0.00	4.17
1851	10714	4.204028	GGTGGTGGTGGTGCTGGT	62.204	66.667	0.00	0.00	0.00	4.00
1852	10715	4.202574	TGGTGGTGGTGGTGCTGG	62.203	66.667	0.00	0.00	0.00	4.85
1853	10716	2.050836	TAGTGGTGGTGGTGGTGCTG	62.051	60.000	0.00	0.00	0.00	4.41
1854	10717	1.768482	TAGTGGTGGTGGTGGTGCT	60.768	57.895	0.00	0.00	0.00	4.40
1855	10718	1.599797	GTAGTGGTGGTGGTGGTGC	60.600	63.158	0.00	0.00	0.00	5.01
1856	10719	1.072505	GGTAGTGGTGGTGGTGGTG	59.927	63.158	0.00	0.00	0.00	4.17
1857	10720	0.191563	TAGGTAGTGGTGGTGGTGGT	59.808	55.000	0.00	0.00	0.00	4.16
1914	10777	0.391263	GCTAGTAGTGGTGGTGGTGC	60.391	60.000	0.00	0.00	0.00	5.01
2207	11085	6.154192	TGCCTTGCTTCCATACAATTGAAATA	59.846	34.615	13.59	0.00	0.00	1.40
2262	11140	4.712829	TGCTACCTACAACTTGCCATACTA	59.287	41.667	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.