AutoCloner

Multiple sequence alignment - TraesCS1A01G254900

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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	TraesCS1A01G254900	chr1A	100.000	2222	0	0	1	2222	446243779	446246000	0.000000e+00	4104
1	TraesCS1A01G254900	chr1A	93.920	1102	59	3	1	1094	20992215	20991114	0.000000e+00	1657
2	TraesCS1A01G254900	chr3A	95.097	1550	64	4	1	1540	11605927	11604380	0.000000e+00	2431
3	TraesCS1A01G254900	chr3A	94.968	1550	66	3	1	1542	684743934	684745479	0.000000e+00	2420
4	TraesCS1A01G254900	chr3A	94.903	1550	67	4	1	1540	11599039	11597492	0.000000e+00	2414
5	TraesCS1A01G254900	chr3A	94.903	1550	66	3	1	1542	459623252	459621708	0.000000e+00	2412
6	TraesCS1A01G254900	chr4B	95.032	1550	65	3	1	1542	604142978	604144523	0.000000e+00	2425
7	TraesCS1A01G254900	chr4B	94.964	1549	65	3	1	1541	85985490	85987033	0.000000e+00	2416
8	TraesCS1A01G254900	chr2B	94.835	1549	68	3	1	1541	721723148	721724692	0.000000e+00	2407
9	TraesCS1A01G254900	chr6A	94.645	1550	71	3	1	1542	531392495	531390950	0.000000e+00	2392
10	TraesCS1A01G254900	chr2A	94.505	1547	75	5	1	1542	48258083	48259624	0.000000e+00	2377
11	TraesCS1A01G254900	chr2A	94.194	1550	74	4	1	1542	765851487	765849946	0.000000e+00	2350
12	TraesCS1A01G254900	chr2A	93.351	1549	91	3	1	1541	619740921	619739377	0.000000e+00	2279
13	TraesCS1A01G254900	chr7A	93.871	1550	84	3	1	1542	668556304	668554758	0.000000e+00	2326
14	TraesCS1A01G254900	chr7A	92.157	306	22	1	1540	1845	118713790	118714093	4.380000e-117	431
15	TraesCS1A01G254900	chr5B	95.520	1183	41	4	368	1541	492816575	492815396	0.000000e+00	1881
16	TraesCS1A01G254900	chr5A	94.472	1212	56	2	1	1201	1240755	1241966	0.000000e+00	1857
17	TraesCS1A01G254900	chr2D	89.520	687	60	5	1540	2222	116835492	116836170	0.000000e+00	859
18	TraesCS1A01G254900	chr3D	91.643	359	28	1	1540	1898	512482063	512482419	1.530000e-136	496
19	TraesCS1A01G254900	chr3D	91.525	295	23	1	1928	2222	512487851	512488143	2.660000e-109	405

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	TraesCS1A01G254900	chr1A	446243779	446246000	2221	False	4104	4104	100.000	1	2222	1	chr1A.!!$F1	2221
1	TraesCS1A01G254900	chr1A	20991114	20992215	1101	True	1657	1657	93.920	1	1094	1	chr1A.!!$R1	1093
2	TraesCS1A01G254900	chr3A	11604380	11605927	1547	True	2431	2431	95.097	1	1540	1	chr3A.!!$R2	1539
3	TraesCS1A01G254900	chr3A	684743934	684745479	1545	False	2420	2420	94.968	1	1542	1	chr3A.!!$F1	1541
4	TraesCS1A01G254900	chr3A	11597492	11599039	1547	True	2414	2414	94.903	1	1540	1	chr3A.!!$R1	1539
5	TraesCS1A01G254900	chr3A	459621708	459623252	1544	True	2412	2412	94.903	1	1542	1	chr3A.!!$R3	1541
6	TraesCS1A01G254900	chr4B	604142978	604144523	1545	False	2425	2425	95.032	1	1542	1	chr4B.!!$F2	1541
7	TraesCS1A01G254900	chr4B	85985490	85987033	1543	False	2416	2416	94.964	1	1541	1	chr4B.!!$F1	1540
8	TraesCS1A01G254900	chr2B	721723148	721724692	1544	False	2407	2407	94.835	1	1541	1	chr2B.!!$F1	1540
9	TraesCS1A01G254900	chr6A	531390950	531392495	1545	True	2392	2392	94.645	1	1542	1	chr6A.!!$R1	1541
10	TraesCS1A01G254900	chr2A	48258083	48259624	1541	False	2377	2377	94.505	1	1542	1	chr2A.!!$F1	1541
11	TraesCS1A01G254900	chr2A	765849946	765851487	1541	True	2350	2350	94.194	1	1542	1	chr2A.!!$R2	1541
12	TraesCS1A01G254900	chr2A	619739377	619740921	1544	True	2279	2279	93.351	1	1541	1	chr2A.!!$R1	1540
13	TraesCS1A01G254900	chr7A	668554758	668556304	1546	True	2326	2326	93.871	1	1542	1	chr7A.!!$R1	1541
14	TraesCS1A01G254900	chr5B	492815396	492816575	1179	True	1881	1881	95.520	368	1541	1	chr5B.!!$R1	1173
15	TraesCS1A01G254900	chr5A	1240755	1241966	1211	False	1857	1857	94.472	1	1201	1	chr5A.!!$F1	1200
16	TraesCS1A01G254900	chr2D	116835492	116836170	678	False	859	859	89.520	1540	2222	1	chr2D.!!$F1	682

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
678	684	2.190981	GCGTTACCTCTTGATACGGTG	58.809	52.381	0.0	0.0	33.17	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1857	1875	0.178068	ATTCTGATGGGGACGGTTCG	59.822	55.0	0.0	0.0	0.0	3.95	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
121	122	9.889128	AAATATATGTGCCAAAATAGCAAAAGT	57.111	25.926	0.00	0.00	43.02	2.66
218	224	4.081087	ACGGCAGTTGTATTAGGACAGATT	60.081	41.667	0.00	0.00	0.00	2.40
223	229	7.769044	GGCAGTTGTATTAGGACAGATTCTTTA	59.231	37.037	0.00	0.00	0.00	1.85
316	322	9.302345	CTCTTTATTGAAACGCAGTAGAGATTA	57.698	33.333	0.00	0.00	45.00	1.75
678	684	2.190981	GCGTTACCTCTTGATACGGTG	58.809	52.381	0.00	0.00	33.17	4.94
789	803	4.399219	TGAGTATCCCTCTTGATCCTACG	58.601	47.826	0.00	0.00	41.11	3.51
1050	1065	2.885861	GTGGATGGAGTCGTCGCT	59.114	61.111	0.00	0.00	0.00	4.93
1055	1070	0.733729	GATGGAGTCGTCGCTGTAGT	59.266	55.000	0.00	0.00	0.00	2.73
1069	1084	1.079819	GTAGTGGCAGAAGAGCGCA	60.080	57.895	11.47	0.00	34.64	6.09
1156	1171	2.677228	CTTCCCCCATCGTGGCTT	59.323	61.111	0.00	0.00	35.79	4.35
1175	1190	3.945434	CGTGCATGATGGCGGCTC	61.945	66.667	11.43	6.00	36.28	4.70
1351	1369	3.118408	TGCTTAGGCGTGGAGTTTCATAT	60.118	43.478	0.00	0.00	42.25	1.78
1352	1370	3.877508	GCTTAGGCGTGGAGTTTCATATT	59.122	43.478	0.00	0.00	0.00	1.28
1385	1403	2.756760	GGTGGAGTACGGTCAGTCAATA	59.243	50.000	0.00	0.00	0.00	1.90
1462	1480	3.985019	TTTTAGTGGGCCTAATCGTGA	57.015	42.857	4.53	0.00	35.59	4.35
1473	1491	3.181469	GCCTAATCGTGAGGTGGTATTGA	60.181	47.826	2.75	0.00	36.37	2.57
1553	1571	6.987386	AGTAGTATAGATGACTTGGATGCAC	58.013	40.000	0.00	0.00	0.00	4.57
1558	1576	1.806542	GATGACTTGGATGCACAACGT	59.193	47.619	0.00	0.00	0.00	3.99
1562	1580	3.002862	TGACTTGGATGCACAACGTTAAC	59.997	43.478	0.00	0.00	0.00	2.01
1565	1583	4.097286	ACTTGGATGCACAACGTTAACTTT	59.903	37.500	0.00	0.00	0.00	2.66
1570	1588	6.205853	TGGATGCACAACGTTAACTTTAGATT	59.794	34.615	0.00	0.00	0.00	2.40
1634	1652	9.520515	AACATCATCAACAAATAGTAGAACCTT	57.479	29.630	0.00	0.00	0.00	3.50
1679	1697	9.545105	AATGAATACAATTCAAAGACTGCAAAA	57.455	25.926	6.43	0.00	31.55	2.44
1705	1723	9.907229	ATAAAGATCCTAGGGTAACAAAGAAAG	57.093	33.333	9.46	0.00	39.74	2.62
1721	1739	6.207614	ACAAAGAAAGAATTAAGGAGGAGCAC	59.792	38.462	0.00	0.00	0.00	4.40
1722	1740	5.505181	AGAAAGAATTAAGGAGGAGCACA	57.495	39.130	0.00	0.00	0.00	4.57
1725	1743	6.376581	AGAAAGAATTAAGGAGGAGCACAATG	59.623	38.462	0.00	0.00	0.00	2.82
1727	1745	5.189180	AGAATTAAGGAGGAGCACAATGAC	58.811	41.667	0.00	0.00	0.00	3.06
1729	1747	2.957402	AAGGAGGAGCACAATGACAA	57.043	45.000	0.00	0.00	0.00	3.18
1731	1749	1.421268	AGGAGGAGCACAATGACAACA	59.579	47.619	0.00	0.00	0.00	3.33
1732	1750	2.040813	AGGAGGAGCACAATGACAACAT	59.959	45.455	0.00	0.00	38.50	2.71
1763	1781	2.942710	TCGAAAGTTGTCGATCAGGTC	58.057	47.619	0.00	0.00	44.76	3.85
1795	1813	1.759445	AGAGAAGTATGTCGCCAGCAT	59.241	47.619	0.00	0.00	0.00	3.79
1799	1817	3.133003	AGAAGTATGTCGCCAGCATAACT	59.867	43.478	0.00	0.00	31.54	2.24
1801	1819	1.787155	GTATGTCGCCAGCATAACTCG	59.213	52.381	0.00	0.00	31.54	4.18
1812	1830	3.123621	CAGCATAACTCGGAATTATCGCC	59.876	47.826	8.77	0.00	0.00	5.54
1857	1875	0.517316	CTAGTGGCGGTTTCTTGCAC	59.483	55.000	0.00	0.00	0.00	4.57
1859	1877	2.203084	TGGCGGTTTCTTGCACGA	60.203	55.556	0.00	0.00	0.00	4.35
1864	1882	1.768112	CGGTTTCTTGCACGAACCGT	61.768	55.000	26.88	0.00	42.36	4.83
1873	1891	1.447838	CACGAACCGTCCCCATCAG	60.448	63.158	0.00	0.00	38.32	2.90
1874	1892	1.608336	ACGAACCGTCCCCATCAGA	60.608	57.895	0.00	0.00	33.69	3.27
1875	1893	1.189524	ACGAACCGTCCCCATCAGAA	61.190	55.000	0.00	0.00	33.69	3.02
1881	1899	2.037251	ACCGTCCCCATCAGAATATTCG	59.963	50.000	9.78	5.54	0.00	3.34
1882	1900	2.299013	CCGTCCCCATCAGAATATTCGA	59.701	50.000	9.78	10.39	0.00	3.71
1888	1906	4.864806	CCCCATCAGAATATTCGACATACG	59.135	45.833	9.78	0.00	44.09	3.06
1903	1921	2.271800	CATACGTGCTCTTCCTCAACC	58.728	52.381	0.00	0.00	0.00	3.77
1919	1937	4.137543	CTCAACCTTTTCTACTGGCTTGT	58.862	43.478	0.00	0.00	0.00	3.16
1920	1938	4.134563	TCAACCTTTTCTACTGGCTTGTC	58.865	43.478	0.00	0.00	0.00	3.18
1921	1939	3.141767	ACCTTTTCTACTGGCTTGTCC	57.858	47.619	0.00	0.00	0.00	4.02
1922	1940	2.441750	ACCTTTTCTACTGGCTTGTCCA	59.558	45.455	0.00	0.00	44.18	4.02
1926	1944	0.253044	TCTACTGGCTTGTCCATGCC	59.747	55.000	15.27	15.27	45.50	4.40
1959	1977	2.962421	GGCTAGCTCAGTTCAGTAGGAT	59.038	50.000	15.72	0.00	0.00	3.24
1976	1994	8.556589	TCAGTAGGATCCAAATCTTAATTTCCA	58.443	33.333	15.82	0.00	32.69	3.53
2011	2033	5.509272	CGATCACAAATAATGTTCTGTGCAC	59.491	40.000	10.75	10.75	41.46	4.57
2016	2038	5.243507	ACAAATAATGTTCTGTGCACATCCA	59.756	36.000	22.00	16.86	40.06	3.41
2058	2080	5.810587	GCACATCCGTAGAAATCTTCAGTTA	59.189	40.000	0.00	0.00	0.00	2.24
2065	2087	7.544566	TCCGTAGAAATCTTCAGTTACACAATC	59.455	37.037	0.00	0.00	0.00	2.67
2066	2088	7.545965	CCGTAGAAATCTTCAGTTACACAATCT	59.454	37.037	0.00	0.00	0.00	2.40
2111	2133	8.061920	TCAATCCCACAATACCATTTATTACCA	58.938	33.333	0.00	0.00	0.00	3.25
2112	2134	8.700051	CAATCCCACAATACCATTTATTACCAA	58.300	33.333	0.00	0.00	0.00	3.67
2126	2148	9.033481	CATTTATTACCAAGCACAAATATGGTG	57.967	33.333	6.56	3.93	45.43	4.17
2127	2149	7.710676	TTATTACCAAGCACAAATATGGTGT	57.289	32.000	6.56	0.00	45.43	4.16
2128	2150	3.940209	ACCAAGCACAAATATGGTGTG	57.060	42.857	13.16	13.16	44.25	3.82
2164	2186	4.962362	TCTTCTATTAGTGCACATCCCTCA	59.038	41.667	21.04	0.00	0.00	3.86
2200	2222	9.421806	CATAATTTGCTTAATCAAAGACCACAA	57.578	29.630	10.01	0.00	39.06	3.33
2210	2232	0.251787	AAGACCACAAATCCAGCCCC	60.252	55.000	0.00	0.00	0.00	5.80

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	6.653020	TGATCCAACATATCTGCAGTAAACT	58.347	36.000	14.67	0.00	0.00	2.66
45	46	7.774625	TGAATGATCCAACATATCTGCAGTAAA	59.225	33.333	14.67	0.41	0.00	2.01
47	48	6.829849	TGAATGATCCAACATATCTGCAGTA	58.170	36.000	14.67	6.05	0.00	2.74
223	229	8.864087	GGCTGAATTCCAATAAATAGATCCTTT	58.136	33.333	2.27	0.00	0.00	3.11
243	249	6.349280	CCAATGAAGAAACTAATTCGGCTGAA	60.349	38.462	11.11	11.11	43.15	3.02
316	322	4.219944	TCTCGCTGTTCTGTAAAGGTATGT	59.780	41.667	0.00	0.00	0.00	2.29
567	573	3.451402	ACCTGGAATTAAGGTGGGTTC	57.549	47.619	10.77	0.00	46.51	3.62
678	684	4.654091	ACCACCATATGCATTAAACTGC	57.346	40.909	3.54	0.00	42.62	4.40
789	803	4.488126	TGCAGCAATCTTGTCTTACAAC	57.512	40.909	0.00	0.00	33.96	3.32
890	905	3.118038	TCGTGGGGCTTTAAGCAATCTAT	60.118	43.478	19.10	0.00	44.75	1.98
901	916	8.576442	CATATTAAATAAGAATCGTGGGGCTTT	58.424	33.333	0.00	0.00	0.00	3.51
1050	1065	1.079819	GCGCTCTTCTGCCACTACA	60.080	57.895	0.00	0.00	0.00	2.74
1055	1070	2.437180	CCATGCGCTCTTCTGCCA	60.437	61.111	9.73	0.00	0.00	4.92
1069	1084	1.673033	CGTCTTCTGTTTCGAGGCCAT	60.673	52.381	5.01	0.00	0.00	4.40
1107	1122	1.000607	TCGTCTTTCTCTGGGAACACG	60.001	52.381	12.59	12.59	39.72	4.49
1462	1480	4.755411	CGTACACAGATTCAATACCACCT	58.245	43.478	0.00	0.00	0.00	4.00
1473	1491	2.151202	CCCACAAAGCGTACACAGATT	58.849	47.619	0.00	0.00	0.00	2.40
1542	1560	3.211045	AGTTAACGTTGTGCATCCAAGT	58.789	40.909	11.99	0.00	0.00	3.16
1543	1561	3.896648	AGTTAACGTTGTGCATCCAAG	57.103	42.857	11.99	0.00	0.00	3.61
1544	1562	4.640789	AAAGTTAACGTTGTGCATCCAA	57.359	36.364	11.99	0.00	0.00	3.53
1613	1631	9.965824	ACAAAAAGGTTCTACTATTTGTTGATG	57.034	29.630	0.00	0.00	37.63	3.07
1665	1683	7.765695	AGGATCTTTATTTTGCAGTCTTTGA	57.234	32.000	0.00	0.00	0.00	2.69
1679	1697	9.907229	CTTTCTTTGTTACCCTAGGATCTTTAT	57.093	33.333	11.48	0.00	0.00	1.40
1705	1723	4.943705	TGTCATTGTGCTCCTCCTTAATTC	59.056	41.667	0.00	0.00	0.00	2.17
1721	1739	3.630769	AGAGCTGGCATATGTTGTCATTG	59.369	43.478	4.29	0.00	39.74	2.82
1722	1740	3.881688	GAGAGCTGGCATATGTTGTCATT	59.118	43.478	4.29	0.00	39.74	2.57
1725	1743	1.863454	CGAGAGCTGGCATATGTTGTC	59.137	52.381	4.29	0.00	0.00	3.18
1727	1745	2.229675	TCGAGAGCTGGCATATGTTG	57.770	50.000	4.29	0.00	0.00	3.33
1729	1747	2.169352	ACTTTCGAGAGCTGGCATATGT	59.831	45.455	2.28	0.00	0.00	2.29
1731	1749	3.201290	CAACTTTCGAGAGCTGGCATAT	58.799	45.455	2.28	0.00	0.00	1.78
1732	1750	2.028112	ACAACTTTCGAGAGCTGGCATA	60.028	45.455	10.69	0.00	0.00	3.14
1763	1781	7.149112	GCGACATACTTCTCTACATAACATTCG	60.149	40.741	0.00	0.00	0.00	3.34
1767	1785	5.358725	TGGCGACATACTTCTCTACATAACA	59.641	40.000	0.00	0.00	33.40	2.41
1795	1813	2.431419	TGTGGGCGATAATTCCGAGTTA	59.569	45.455	4.59	0.00	0.00	2.24
1799	1817	1.877637	CATGTGGGCGATAATTCCGA	58.122	50.000	4.59	0.00	0.00	4.55
1801	1819	0.598065	GGCATGTGGGCGATAATTCC	59.402	55.000	0.00	0.00	33.57	3.01
1845	1863	1.083015	CGGTTCGTGCAAGAAACCG	60.083	57.895	27.17	27.17	37.92	4.44
1857	1875	0.178068	ATTCTGATGGGGACGGTTCG	59.822	55.000	0.00	0.00	0.00	3.95
1859	1877	3.494398	CGAATATTCTGATGGGGACGGTT	60.494	47.826	13.45	0.00	0.00	4.44
1864	1882	5.336451	CGTATGTCGAATATTCTGATGGGGA	60.336	44.000	13.45	0.00	42.86	4.81
1873	1891	5.117287	GGAAGAGCACGTATGTCGAATATTC	59.883	44.000	5.30	5.30	42.86	1.75
1874	1892	4.982916	GGAAGAGCACGTATGTCGAATATT	59.017	41.667	0.00	0.00	42.86	1.28
1875	1893	4.278669	AGGAAGAGCACGTATGTCGAATAT	59.721	41.667	0.00	0.00	42.86	1.28
1881	1899	2.924290	GTTGAGGAAGAGCACGTATGTC	59.076	50.000	0.00	0.00	0.00	3.06
1882	1900	2.353803	GGTTGAGGAAGAGCACGTATGT	60.354	50.000	0.00	0.00	0.00	2.29
1888	1906	3.481453	AGAAAAGGTTGAGGAAGAGCAC	58.519	45.455	0.00	0.00	0.00	4.40
1932	1950	3.649277	AACTGAGCTAGCCGCACGG	62.649	63.158	12.13	4.30	42.61	4.94
1935	1953	1.216444	CTGAACTGAGCTAGCCGCA	59.784	57.895	12.13	9.44	42.61	5.69
1941	1959	4.251103	TGGATCCTACTGAACTGAGCTA	57.749	45.455	14.23	0.00	0.00	3.32
2042	2064	9.424319	TGAGATTGTGTAACTGAAGATTTCTAC	57.576	33.333	0.00	0.00	38.04	2.59
2058	2080	6.116126	GGCTCCTAATTAAGTGAGATTGTGT	58.884	40.000	9.40	0.00	0.00	3.72
2065	2087	7.040823	GGATTGATTGGCTCCTAATTAAGTGAG	60.041	40.741	0.00	3.20	0.00	3.51
2066	2088	6.772716	GGATTGATTGGCTCCTAATTAAGTGA	59.227	38.462	0.00	0.00	0.00	3.41
2121	2143	0.895100	GGGACATGCACACACACCAT	60.895	55.000	0.00	0.00	0.00	3.55
2126	2148	1.160137	GAAGAGGGACATGCACACAC	58.840	55.000	0.00	0.00	0.00	3.82
2127	2149	1.059098	AGAAGAGGGACATGCACACA	58.941	50.000	0.00	0.00	0.00	3.72
2128	2150	3.550437	ATAGAAGAGGGACATGCACAC	57.450	47.619	0.00	0.00	0.00	3.82
2194	2216	0.251787	GAAGGGGCTGGATTTGTGGT	60.252	55.000	0.00	0.00	0.00	4.16
2200	2222	3.774842	TTAAATGGAAGGGGCTGGATT	57.225	42.857	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.