AutoCloner

Multiple sequence alignment - TraesCS7B01G109100

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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	TraesCS7B01G109100	chr7B	100.000	2417	0	0	1	2417	125067301	125064885	0.000000e+00	4464.0
1	TraesCS7B01G109100	chr7B	93.883	703	34	9	1	698	474280407	474281105	0.000000e+00	1051.0
2	TraesCS7B01G109100	chr7B	95.719	584	21	3	110	692	704470881	704470301	0.000000e+00	937.0
3	TraesCS7B01G109100	chr7B	94.889	587	21	4	110	695	608306193	608305615	0.000000e+00	909.0
4	TraesCS7B01G109100	chr7A	93.136	1253	69	7	800	2050	163917149	163915912	0.000000e+00	1821.0
5	TraesCS7B01G109100	chr7A	100.000	34	0	0	742	775	163917187	163917154	2.010000e-06	63.9
6	TraesCS7B01G109100	chr7D	96.330	763	28	0	1655	2417	163011493	163010731	0.000000e+00	1254.0
7	TraesCS7B01G109100	chr7D	93.260	727	37	4	700	1422	163012584	163011866	0.000000e+00	1061.0
8	TraesCS7B01G109100	chr1B	94.767	707	19	4	4	695	395229063	395228360	0.000000e+00	1085.0
9	TraesCS7B01G109100	chr1B	77.793	752	139	15	1692	2417	664610621	664611370	2.850000e-119	438.0
10	TraesCS7B01G109100	chr5B	93.362	708	27	9	1	692	590532538	590533241	0.000000e+00	1029.0
11	TraesCS7B01G109100	chr5B	93.220	708	28	9	1	692	590543940	590544643	0.000000e+00	1024.0
12	TraesCS7B01G109100	chr5B	91.678	721	22	6	4	695	293464399	293463688	0.000000e+00	965.0
13	TraesCS7B01G109100	chr5B	95.571	587	22	4	110	695	576927989	576927406	0.000000e+00	937.0
14	TraesCS7B01G109100	chr2B	90.366	737	28	12	1	695	30631750	30632485	0.000000e+00	928.0
15	TraesCS7B01G109100	chr2B	94.521	584	29	3	110	692	762460316	762459735	0.000000e+00	898.0
16	TraesCS7B01G109100	chr2B	84.182	550	36	18	1	506	188466874	188467416	1.000000e-133	486.0
17	TraesCS7B01G109100	chr2B	77.690	762	153	14	1666	2417	758922646	758921892	1.320000e-122	449.0
18	TraesCS7B01G109100	chr2B	77.261	752	151	16	1679	2417	759175541	759176285	7.990000e-115	424.0
19	TraesCS7B01G109100	chr3B	90.403	719	34	9	4	692	742478751	742478038	0.000000e+00	913.0
20	TraesCS7B01G109100	chr3B	90.069	725	32	18	4	695	666781793	666781076	0.000000e+00	904.0
21	TraesCS7B01G109100	chr3B	89.566	738	33	13	1	697	817191456	817192190	0.000000e+00	896.0
22	TraesCS7B01G109100	chr4A	89.583	720	26	7	1	692	708628667	708629365	0.000000e+00	869.0
23	TraesCS7B01G109100	chr2A	80.326	737	129	15	1692	2417	24003220	24002489	5.880000e-151	544.0
24	TraesCS7B01G109100	chr2D	79.161	763	143	12	1666	2417	22162303	22161546	4.610000e-142	514.0
25	TraesCS7B01G109100	chr2D	77.720	763	151	16	1666	2417	619604791	619605545	1.320000e-122	449.0
26	TraesCS7B01G109100	chr3A	77.341	737	92	33	1	689	728318190	728318899	1.370000e-97	366.0

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	TraesCS7B01G109100	chr7B	125064885	125067301	2416	True	4464.00	4464	100.000	1	2417	1	chr7B.!!$R1	2416
1	TraesCS7B01G109100	chr7B	474280407	474281105	698	False	1051.00	1051	93.883	1	698	1	chr7B.!!$F1	697
2	TraesCS7B01G109100	chr7B	704470301	704470881	580	True	937.00	937	95.719	110	692	1	chr7B.!!$R3	582
3	TraesCS7B01G109100	chr7B	608305615	608306193	578	True	909.00	909	94.889	110	695	1	chr7B.!!$R2	585
4	TraesCS7B01G109100	chr7A	163915912	163917187	1275	True	942.45	1821	96.568	742	2050	2	chr7A.!!$R1	1308
5	TraesCS7B01G109100	chr7D	163010731	163012584	1853	True	1157.50	1254	94.795	700	2417	2	chr7D.!!$R1	1717
6	TraesCS7B01G109100	chr1B	395228360	395229063	703	True	1085.00	1085	94.767	4	695	1	chr1B.!!$R1	691
7	TraesCS7B01G109100	chr1B	664610621	664611370	749	False	438.00	438	77.793	1692	2417	1	chr1B.!!$F1	725
8	TraesCS7B01G109100	chr5B	590532538	590533241	703	False	1029.00	1029	93.362	1	692	1	chr5B.!!$F1	691
9	TraesCS7B01G109100	chr5B	590543940	590544643	703	False	1024.00	1024	93.220	1	692	1	chr5B.!!$F2	691
10	TraesCS7B01G109100	chr5B	293463688	293464399	711	True	965.00	965	91.678	4	695	1	chr5B.!!$R1	691
11	TraesCS7B01G109100	chr5B	576927406	576927989	583	True	937.00	937	95.571	110	695	1	chr5B.!!$R2	585
12	TraesCS7B01G109100	chr2B	30631750	30632485	735	False	928.00	928	90.366	1	695	1	chr2B.!!$F1	694
13	TraesCS7B01G109100	chr2B	762459735	762460316	581	True	898.00	898	94.521	110	692	1	chr2B.!!$R2	582
14	TraesCS7B01G109100	chr2B	188466874	188467416	542	False	486.00	486	84.182	1	506	1	chr2B.!!$F2	505
15	TraesCS7B01G109100	chr2B	758921892	758922646	754	True	449.00	449	77.690	1666	2417	1	chr2B.!!$R1	751
16	TraesCS7B01G109100	chr2B	759175541	759176285	744	False	424.00	424	77.261	1679	2417	1	chr2B.!!$F3	738
17	TraesCS7B01G109100	chr3B	742478038	742478751	713	True	913.00	913	90.403	4	692	1	chr3B.!!$R2	688
18	TraesCS7B01G109100	chr3B	666781076	666781793	717	True	904.00	904	90.069	4	695	1	chr3B.!!$R1	691
19	TraesCS7B01G109100	chr3B	817191456	817192190	734	False	896.00	896	89.566	1	697	1	chr3B.!!$F1	696
20	TraesCS7B01G109100	chr4A	708628667	708629365	698	False	869.00	869	89.583	1	692	1	chr4A.!!$F1	691
21	TraesCS7B01G109100	chr2A	24002489	24003220	731	True	544.00	544	80.326	1692	2417	1	chr2A.!!$R1	725
22	TraesCS7B01G109100	chr2D	22161546	22162303	757	True	514.00	514	79.161	1666	2417	1	chr2D.!!$R1	751
23	TraesCS7B01G109100	chr2D	619604791	619605545	754	False	449.00	449	77.720	1666	2417	1	chr2D.!!$F1	751
24	TraesCS7B01G109100	chr3A	728318190	728318899	709	False	366.00	366	77.341	1	689	1	chr3A.!!$F1	688

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
945	1177	0.389817	CAACCGTGCGATCCTCAAGA	60.39	55.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2701	1.961277	CGTGCCTTTTCTGGACGCT	60.961	57.895	0.0	0.0	0.0	5.07	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
149	231	2.434359	GGTGAAGGCGGAGTTCGG	60.434	66.667	0.00	0.00	39.69	4.30
449	561	6.170506	TCAGCGCCTTTCTTTTTAGATTAGA	58.829	36.000	2.29	0.00	0.00	2.10
659	887	1.217882	CCAGACGACGCTTTTTGACT	58.782	50.000	0.00	0.00	0.00	3.41
669	897	1.480498	GCTTTTTGACTCCCCCTGGAA	60.480	52.381	0.00	0.00	41.17	3.53
731	959	3.584406	CTGTTCCACAGGAGTACAGAG	57.416	52.381	10.86	0.00	40.87	3.35
807	1037	1.003112	AGTCGCTCTCTCTCCGTGT	60.003	57.895	0.00	0.00	0.00	4.49
816	1046	2.077627	CTCTCTCCGTGTCTCTCGAAA	58.922	52.381	0.00	0.00	0.00	3.46
849	1080	4.572571	ACGCCGCAAACCCTTCCA	62.573	61.111	0.00	0.00	0.00	3.53
857	1088	3.066760	CCGCAAACCCTTCCAGATTTATC	59.933	47.826	0.00	0.00	0.00	1.75
877	1108	1.449601	CCCCCATCGTTCCAGTTCG	60.450	63.158	0.00	0.00	0.00	3.95
893	1125	1.065851	GTTCGTTCGCCTTTTTCCCAA	59.934	47.619	0.00	0.00	0.00	4.12
944	1176	1.361668	CCAACCGTGCGATCCTCAAG	61.362	60.000	0.00	0.00	0.00	3.02
945	1177	0.389817	CAACCGTGCGATCCTCAAGA	60.390	55.000	0.00	0.00	0.00	3.02
946	1178	0.389948	AACCGTGCGATCCTCAAGAC	60.390	55.000	0.00	0.00	0.00	3.01
947	1179	1.519455	CCGTGCGATCCTCAAGACC	60.519	63.158	0.00	0.00	0.00	3.85
948	1180	1.513158	CGTGCGATCCTCAAGACCT	59.487	57.895	0.00	0.00	0.00	3.85
949	1181	0.526524	CGTGCGATCCTCAAGACCTC	60.527	60.000	0.00	0.00	0.00	3.85
950	1182	0.532573	GTGCGATCCTCAAGACCTCA	59.467	55.000	0.00	0.00	0.00	3.86
951	1183	1.066858	GTGCGATCCTCAAGACCTCAA	60.067	52.381	0.00	0.00	0.00	3.02
960	1192	1.143305	CAAGACCTCAACTGCAGTCG	58.857	55.000	21.95	9.74	34.41	4.18
996	1228	1.040339	AGCTAGCTCTCCCGTTCCAG	61.040	60.000	12.68	0.00	0.00	3.86
1059	1291	2.836360	CTCTACGCCCGCCCCTTA	60.836	66.667	0.00	0.00	0.00	2.69
1114	1346	2.675423	CGACCTCCCACGTCCTCA	60.675	66.667	0.00	0.00	0.00	3.86
1212	1444	0.960861	CGGCCAAGGAGAAGGGAAAC	60.961	60.000	2.24	0.00	0.00	2.78
1229	1461	2.168666	AACGAGGGAAACGAGGAGGC	62.169	60.000	0.00	0.00	34.70	4.70
1427	1659	4.783621	GCTGTGAGGCCGCCATGA	62.784	66.667	13.15	0.00	0.00	3.07
1428	1660	2.046023	CTGTGAGGCCGCCATGAA	60.046	61.111	13.15	0.00	0.00	2.57
1429	1661	2.359850	TGTGAGGCCGCCATGAAC	60.360	61.111	13.15	4.59	0.00	3.18
1430	1662	3.134127	GTGAGGCCGCCATGAACC	61.134	66.667	13.15	0.00	0.00	3.62
1463	1695	2.489329	GGAGTACTGTTACTGCGGTGTA	59.511	50.000	8.92	0.00	38.77	2.90
1464	1696	3.129988	GGAGTACTGTTACTGCGGTGTAT	59.870	47.826	8.92	0.00	38.77	2.29
1466	1698	1.722011	ACTGTTACTGCGGTGTATGC	58.278	50.000	8.92	0.00	0.00	3.14
1467	1699	1.275291	ACTGTTACTGCGGTGTATGCT	59.725	47.619	8.92	0.00	0.00	3.79
1471	1703	1.720805	TACTGCGGTGTATGCTTGTG	58.279	50.000	8.92	0.00	0.00	3.33
1516	1748	6.543465	TCACTTGTGAAGTTGTGATCTGAATT	59.457	34.615	0.44	0.00	40.46	2.17
1517	1749	7.714813	TCACTTGTGAAGTTGTGATCTGAATTA	59.285	33.333	0.44	0.00	40.46	1.40
1593	1880	7.545265	TGCTTATGATAAACTGAAACATTTGGC	59.455	33.333	0.00	0.00	0.00	4.52
1595	1882	8.984891	TTATGATAAACTGAAACATTTGGCTG	57.015	30.769	0.00	0.00	0.00	4.85
1618	1905	8.403236	GCTGGTAATAAAGTTACGGAAATGATT	58.597	33.333	0.00	0.00	0.00	2.57
1677	2059	3.701664	TCTCTGAGCTCACTGGAATGTA	58.298	45.455	13.74	0.00	0.00	2.29
1835	2220	1.004918	CCGTCCTGTTCACCTCCAC	60.005	63.158	0.00	0.00	0.00	4.02
1947	2332	1.853319	CGCGAGCTTTCTCACGTTT	59.147	52.632	0.00	0.00	39.34	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
449	561	8.721019	AAATTCGCCATTTTCATGACATTAAT	57.279	26.923	0.00	0.00	30.09	1.40
659	887	3.264845	GTTGGCCTTCCAGGGGGA	61.265	66.667	3.32	0.00	44.53	4.81
697	925	1.202818	GGAACAGTTCCTTCAGCTGGT	60.203	52.381	23.40	0.00	46.57	4.00
698	926	1.528129	GGAACAGTTCCTTCAGCTGG	58.472	55.000	23.40	0.00	46.57	4.85
721	949	7.661968	TGTATGCTTTGATATCTCTGTACTCC	58.338	38.462	3.98	0.00	0.00	3.85
731	959	9.149225	CTTCTGGAGTATGTATGCTTTGATATC	57.851	37.037	0.00	0.00	0.00	1.63
807	1037	2.476352	CGTCAGAGCGATTTTCGAGAGA	60.476	50.000	0.32	0.00	43.74	3.10
816	1046	1.226046	CGTCGACGTCAGAGCGATT	60.226	57.895	29.08	0.00	36.37	3.34
849	1080	1.056660	ACGATGGGGGCGATAAATCT	58.943	50.000	0.00	0.00	0.00	2.40
857	1088	3.622060	AACTGGAACGATGGGGGCG	62.622	63.158	0.00	0.00	0.00	6.13
877	1108	1.334689	CGAGTTGGGAAAAAGGCGAAC	60.335	52.381	0.00	0.00	0.00	3.95
918	1150	1.933115	ATCGCACGGTTGGGAATTGC	61.933	55.000	0.00	0.00	46.84	3.56
944	1176	3.555428	GCGACTGCAGTTGAGGTC	58.445	61.111	33.87	14.88	42.15	3.85
960	1192	3.873026	CTCGGATGGGATCGGCTGC	62.873	68.421	0.00	0.00	0.00	5.25
996	1228	0.250513	AGAAGAGGTCCGCCATTGAC	59.749	55.000	0.00	0.00	37.19	3.18
1140	1372	1.524863	CCTGGACCTTGACGTCGTCT	61.525	60.000	24.75	5.74	33.30	4.18
1212	1444	2.184579	GCCTCCTCGTTTCCCTCG	59.815	66.667	0.00	0.00	0.00	4.63
1337	1569	4.702081	GCACGACGACGGTGAGCT	62.702	66.667	12.58	0.00	44.46	4.09
1429	1661	1.679977	TACTCCTGAACCCGGTCGG	60.680	63.158	0.00	1.86	37.81	4.79
1430	1662	0.964358	AGTACTCCTGAACCCGGTCG	60.964	60.000	0.00	0.00	0.00	4.79
1434	1666	2.824341	AGTAACAGTACTCCTGAACCCG	59.176	50.000	0.00	0.00	44.49	5.28
1445	1677	2.601763	GCATACACCGCAGTAACAGTAC	59.398	50.000	0.00	0.00	0.00	2.73
1459	1691	2.285834	GCTCGCATACACAAGCATACAC	60.286	50.000	0.00	0.00	34.86	2.90
1463	1695	1.012086	CAGCTCGCATACACAAGCAT	58.988	50.000	0.00	0.00	37.22	3.79
1464	1696	0.320683	ACAGCTCGCATACACAAGCA	60.321	50.000	0.00	0.00	37.22	3.91
1466	1698	1.127397	CACACAGCTCGCATACACAAG	59.873	52.381	0.00	0.00	0.00	3.16
1467	1699	1.147473	CACACAGCTCGCATACACAA	58.853	50.000	0.00	0.00	0.00	3.33
1471	1703	1.626654	AACGCACACAGCTCGCATAC	61.627	55.000	0.00	0.00	42.61	2.39
1618	1905	2.850060	GTGTCGCGACGAGATCAATTTA	59.150	45.455	31.88	9.04	36.23	1.40
1970	2355	2.488545	GTGCTCTTCTTGAGGTACGAGA	59.511	50.000	0.00	0.00	42.87	4.04
2286	2701	1.961277	CGTGCCTTTTCTGGACGCT	60.961	57.895	0.00	0.00	0.00	5.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.