AutoCloner

Multiple sequence alignment - TraesCS6B01G108300

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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	TraesCS6B01G108300	chr6B	100.000	2303	0	0	1	2303	88780384	88782686	0.000000e+00	4253
1	TraesCS6B01G108300	chr6B	96.976	926	26	2	1379	2303	88815889	88816813	0.000000e+00	1554
2	TraesCS6B01G108300	chr6B	85.753	744	55	21	672	1378	88735818	88736547	0.000000e+00	739
3	TraesCS6B01G108300	chr7A	96.760	926	29	1	1379	2303	690489796	690490721	0.000000e+00	1543
4	TraesCS6B01G108300	chr7A	85.835	473	50	9	920	1378	679004356	679003887	9.560000e-134	486
5	TraesCS6B01G108300	chr2A	96.567	932	25	3	1379	2303	664580571	664581502	0.000000e+00	1537
6	TraesCS6B01G108300	chr2A	96.548	927	31	1	1378	2303	628128517	628127591	0.000000e+00	1533
7	TraesCS6B01G108300	chr2A	96.320	924	32	2	1381	2303	628116316	628115394	0.000000e+00	1517
8	TraesCS6B01G108300	chr1B	95.587	929	38	3	1377	2303	543295440	543296367	0.000000e+00	1485
9	TraesCS6B01G108300	chr2B	95.494	932	34	4	1379	2303	428902587	428901657	0.000000e+00	1482
10	TraesCS6B01G108300	chr2B	78.399	537	67	23	1	513	568038187	568038698	1.030000e-78	303
11	TraesCS6B01G108300	chr3A	95.464	926	41	1	1379	2303	275936371	275937296	0.000000e+00	1476
12	TraesCS6B01G108300	chr3A	95.464	926	41	1	1379	2303	374503694	374502769	0.000000e+00	1476
13	TraesCS6B01G108300	chr3A	79.968	634	73	27	1	596	391883427	391884044	3.540000e-113	418
14	TraesCS6B01G108300	chr6A	85.945	804	61	18	598	1376	49196430	49197206	0.000000e+00	811
15	TraesCS6B01G108300	chr6A	89.721	574	41	9	821	1378	49550738	49551309	0.000000e+00	717
16	TraesCS6B01G108300	chr6A	88.484	521	41	10	872	1378	49201975	49202490	1.510000e-171	612
17	TraesCS6B01G108300	chr6A	85.965	570	40	15	821	1378	49499645	49500186	7.140000e-160	573
18	TraesCS6B01G108300	chr6A	87.069	232	23	3	367	597	144516601	144516826	2.940000e-64	255
19	TraesCS6B01G108300	chr6D	85.482	737	67	18	662	1378	38119573	38120289	0.000000e+00	732
20	TraesCS6B01G108300	chr6D	89.369	555	48	5	829	1378	37933935	37934483	0.000000e+00	688
21	TraesCS6B01G108300	chr6D	88.348	575	48	11	821	1378	37927680	37928252	0.000000e+00	673
22	TraesCS6B01G108300	chr6D	89.809	157	14	2	670	825	37927496	37927651	1.400000e-47	200
23	TraesCS6B01G108300	chr6D	87.500	168	20	1	659	825	37933732	37933899	2.330000e-45	193
24	TraesCS6B01G108300	chr7D	82.030	601	79	10	719	1295	587150433	587149838	3.440000e-133	484
25	TraesCS6B01G108300	chr5B	83.063	555	73	13	821	1374	511835353	511835887	3.440000e-133	484
26	TraesCS6B01G108300	chr4B	81.997	611	73	22	9	596	605797862	605797266	3.440000e-133	484
27	TraesCS6B01G108300	chrUn	81.833	611	71	15	1	597	41407079	41406495	5.760000e-131	477
28	TraesCS6B01G108300	chr3B	81.150	626	60	24	1	599	240791067	240791661	1.250000e-122	449
29	TraesCS6B01G108300	chr3B	78.933	375	59	16	240	596	734543835	734543463	1.060000e-58	237
30	TraesCS6B01G108300	chr7B	80.071	562	87	20	50	596	708506650	708506099	5.960000e-106	394
31	TraesCS6B01G108300	chr7B	86.813	182	21	3	100	278	501939510	501939691	1.400000e-47	200
32	TraesCS6B01G108300	chr1A	77.282	515	78	29	92	596	540889777	540890262	1.360000e-67	267

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	TraesCS6B01G108300	chr6B	88780384	88782686	2302	False	4253.0	4253	100.0000	1	2303	1	chr6B.!!$F2	2302
1	TraesCS6B01G108300	chr6B	88815889	88816813	924	False	1554.0	1554	96.9760	1379	2303	1	chr6B.!!$F3	924
2	TraesCS6B01G108300	chr6B	88735818	88736547	729	False	739.0	739	85.7530	672	1378	1	chr6B.!!$F1	706
3	TraesCS6B01G108300	chr7A	690489796	690490721	925	False	1543.0	1543	96.7600	1379	2303	1	chr7A.!!$F1	924
4	TraesCS6B01G108300	chr2A	664580571	664581502	931	False	1537.0	1537	96.5670	1379	2303	1	chr2A.!!$F1	924
5	TraesCS6B01G108300	chr2A	628127591	628128517	926	True	1533.0	1533	96.5480	1378	2303	1	chr2A.!!$R2	925
6	TraesCS6B01G108300	chr2A	628115394	628116316	922	True	1517.0	1517	96.3200	1381	2303	1	chr2A.!!$R1	922
7	TraesCS6B01G108300	chr1B	543295440	543296367	927	False	1485.0	1485	95.5870	1377	2303	1	chr1B.!!$F1	926
8	TraesCS6B01G108300	chr2B	428901657	428902587	930	True	1482.0	1482	95.4940	1379	2303	1	chr2B.!!$R1	924
9	TraesCS6B01G108300	chr2B	568038187	568038698	511	False	303.0	303	78.3990	1	513	1	chr2B.!!$F1	512
10	TraesCS6B01G108300	chr3A	275936371	275937296	925	False	1476.0	1476	95.4640	1379	2303	1	chr3A.!!$F1	924
11	TraesCS6B01G108300	chr3A	374502769	374503694	925	True	1476.0	1476	95.4640	1379	2303	1	chr3A.!!$R1	924
12	TraesCS6B01G108300	chr3A	391883427	391884044	617	False	418.0	418	79.9680	1	596	1	chr3A.!!$F2	595
13	TraesCS6B01G108300	chr6A	49196430	49197206	776	False	811.0	811	85.9450	598	1376	1	chr6A.!!$F1	778
14	TraesCS6B01G108300	chr6A	49550738	49551309	571	False	717.0	717	89.7210	821	1378	1	chr6A.!!$F4	557
15	TraesCS6B01G108300	chr6A	49201975	49202490	515	False	612.0	612	88.4840	872	1378	1	chr6A.!!$F2	506
16	TraesCS6B01G108300	chr6A	49499645	49500186	541	False	573.0	573	85.9650	821	1378	1	chr6A.!!$F3	557
17	TraesCS6B01G108300	chr6D	38119573	38120289	716	False	732.0	732	85.4820	662	1378	1	chr6D.!!$F1	716
18	TraesCS6B01G108300	chr6D	37933732	37934483	751	False	440.5	688	88.4345	659	1378	2	chr6D.!!$F3	719
19	TraesCS6B01G108300	chr6D	37927496	37928252	756	False	436.5	673	89.0785	670	1378	2	chr6D.!!$F2	708
20	TraesCS6B01G108300	chr7D	587149838	587150433	595	True	484.0	484	82.0300	719	1295	1	chr7D.!!$R1	576
21	TraesCS6B01G108300	chr5B	511835353	511835887	534	False	484.0	484	83.0630	821	1374	1	chr5B.!!$F1	553
22	TraesCS6B01G108300	chr4B	605797266	605797862	596	True	484.0	484	81.9970	9	596	1	chr4B.!!$R1	587
23	TraesCS6B01G108300	chrUn	41406495	41407079	584	True	477.0	477	81.8330	1	597	1	chrUn.!!$R1	596
24	TraesCS6B01G108300	chr3B	240791067	240791661	594	False	449.0	449	81.1500	1	599	1	chr3B.!!$F1	598
25	TraesCS6B01G108300	chr7B	708506099	708506650	551	True	394.0	394	80.0710	50	596	1	chr7B.!!$R1	546

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
612	678	0.390603	TCCGGAACATCACGCGAATT	60.391	50.0	15.93	0.0	0.0	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1873	2125	0.108377	CAGCGGTGCACAGTGGTATA	60.108	55.0	20.43	0.0	0.0	1.47	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
134	163	6.198216	AGGAACATTTTTCGAAATTGTGAACG	59.802	34.615	20.98	5.94	0.00	3.95
365	429	9.981114	AACTGGTTTTAAGTTTATCATTTCCTG	57.019	29.630	0.00	0.00	34.16	3.86
379	443	9.823647	TTATCATTTCCTGTAGCTTCTTTAGAG	57.176	33.333	0.00	0.00	0.00	2.43
382	446	7.604164	TCATTTCCTGTAGCTTCTTTAGAGTTG	59.396	37.037	0.00	0.00	0.00	3.16
410	474	5.070001	TGTTTTTCTTACACATCCAGGAGG	58.930	41.667	0.00	0.00	0.00	4.30
412	476	4.993705	TTTCTTACACATCCAGGAGGTT	57.006	40.909	3.27	0.00	35.89	3.50
442	506	3.478724	TACCGCGGCGTGCTCATAG	62.479	63.158	28.58	5.54	43.27	2.23
467	532	2.277756	GTCGTCGGTTCGATCCCG	60.278	66.667	15.75	15.75	46.83	5.14
521	587	2.151202	GAAGCGAACCCACTCAAATGA	58.849	47.619	0.00	0.00	0.00	2.57
575	641	2.027625	GCGACTACTTGCCGCAGTT	61.028	57.895	0.00	0.00	46.67	3.16
579	645	0.608640	ACTACTTGCCGCAGTTAGCT	59.391	50.000	9.28	0.00	42.61	3.32
612	678	0.390603	TCCGGAACATCACGCGAATT	60.391	50.000	15.93	0.00	0.00	2.17
653	719	1.451387	GTAGGATTGGCCCGTGTGG	60.451	63.158	0.00	0.00	37.37	4.17
654	720	1.613928	TAGGATTGGCCCGTGTGGA	60.614	57.895	0.00	0.00	37.49	4.02
711	778	2.978010	CGCCAAAGTTCCCAGCGT	60.978	61.111	0.00	0.00	41.78	5.07
718	795	2.032681	GTTCCCAGCGTGCTCCTT	59.967	61.111	0.00	0.00	0.00	3.36
729	822	4.388499	GCTCCTTCCCGCCACGAA	62.388	66.667	0.00	0.00	0.00	3.85
730	823	2.584608	CTCCTTCCCGCCACGAAT	59.415	61.111	0.00	0.00	0.00	3.34
731	824	1.521681	CTCCTTCCCGCCACGAATC	60.522	63.158	0.00	0.00	0.00	2.52
732	825	2.513897	CCTTCCCGCCACGAATCC	60.514	66.667	0.00	0.00	0.00	3.01
733	826	2.513897	CTTCCCGCCACGAATCCC	60.514	66.667	0.00	0.00	0.00	3.85
734	827	4.460683	TTCCCGCCACGAATCCCG	62.461	66.667	0.00	0.00	45.44	5.14
736	829	4.235762	CCCGCCACGAATCCCGAT	62.236	66.667	0.00	0.00	41.76	4.18
737	830	2.203015	CCGCCACGAATCCCGATT	60.203	61.111	0.00	0.00	41.76	3.34
738	831	1.817941	CCGCCACGAATCCCGATTT	60.818	57.895	0.00	0.00	41.76	2.17
739	832	1.641677	CGCCACGAATCCCGATTTC	59.358	57.895	0.00	0.00	41.76	2.17
740	833	1.641677	GCCACGAATCCCGATTTCG	59.358	57.895	11.17	11.17	41.76	3.46
767	876	6.138391	CCAAACATTTCGCGAAAATTTTCAAC	59.862	34.615	35.06	17.76	35.32	3.18
778	887	2.265073	ATTTTCAACATCCGCCGGCG	62.265	55.000	41.00	41.00	39.44	6.46
869	1049	2.837291	CCCTCTCGCTCCCTCCTG	60.837	72.222	0.00	0.00	0.00	3.86
918	1098	1.139498	TCCCAGTCCAATCCCAAGCA	61.139	55.000	0.00	0.00	0.00	3.91
1139	1333	1.078918	TGCCGCTCAAGGACATCAG	60.079	57.895	0.00	0.00	0.00	2.90
1140	1334	1.078848	GCCGCTCAAGGACATCAGT	60.079	57.895	0.00	0.00	0.00	3.41
1206	1403	2.828128	GCTCCAGCAGCCGCATTAC	61.828	63.158	0.00	0.00	43.17	1.89
1240	1455	1.301716	GAGCTGGCCGTGAAGAACA	60.302	57.895	0.00	0.00	0.00	3.18
1410	1648	3.096852	ACTGATCCACGAACACCTATGA	58.903	45.455	0.00	0.00	0.00	2.15
1598	1842	1.968493	AGAGCGTAGTGTTTTCTGGGA	59.032	47.619	0.00	0.00	0.00	4.37
1669	1921	4.201657	GGGCCTCCTTTTATACGCTAAAA	58.798	43.478	0.84	4.15	0.00	1.52
1825	2077	3.507622	GCCTAAACAGTGCAGAAAAGGAT	59.492	43.478	0.00	0.00	0.00	3.24
1873	2125	0.737715	GGCGATCTTGTCAGCTTCGT	60.738	55.000	3.90	0.00	31.54	3.85
1876	2128	3.550233	GGCGATCTTGTCAGCTTCGTATA	60.550	47.826	3.90	0.00	31.54	1.47

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
355	419	7.856415	ACTCTAAAGAAGCTACAGGAAATGAT	58.144	34.615	0.00	0.00	0.00	2.45
358	422	6.881602	CCAACTCTAAAGAAGCTACAGGAAAT	59.118	38.462	0.00	0.00	0.00	2.17
361	425	4.322801	GCCAACTCTAAAGAAGCTACAGGA	60.323	45.833	0.00	0.00	0.00	3.86
365	429	5.412904	ACAATGCCAACTCTAAAGAAGCTAC	59.587	40.000	0.00	0.00	0.00	3.58
377	441	6.039616	TGTGTAAGAAAAACAATGCCAACTC	58.960	36.000	0.00	0.00	0.00	3.01
379	443	6.073819	GGATGTGTAAGAAAAACAATGCCAAC	60.074	38.462	0.00	0.00	0.00	3.77
382	446	5.537188	TGGATGTGTAAGAAAAACAATGCC	58.463	37.500	0.00	0.00	0.00	4.40
436	500	2.032302	CCGACGACCTCTTGTCTATGAG	59.968	54.545	0.00	0.00	42.13	2.90
437	501	2.014857	CCGACGACCTCTTGTCTATGA	58.985	52.381	0.00	0.00	42.13	2.15
442	506	0.728466	CGAACCGACGACCTCTTGTC	60.728	60.000	0.00	0.00	40.81	3.18
509	575	2.409870	GCCGGCTCATTTGAGTGGG	61.410	63.158	22.15	14.71	43.85	4.61
575	641	3.882888	CCGGAATTTCCTATTTGCAGCTA	59.117	43.478	13.45	0.00	33.30	3.32
579	645	4.082845	TGTTCCGGAATTTCCTATTTGCA	58.917	39.130	22.04	5.87	33.30	4.08
615	681	4.382320	TTCTGCCGGCCCACGTAC	62.382	66.667	26.77	0.00	42.24	3.67
629	695	0.541863	CGGGCCAATCCTACAGTTCT	59.458	55.000	4.39	0.00	34.39	3.01
630	696	0.252197	ACGGGCCAATCCTACAGTTC	59.748	55.000	4.39	0.00	34.39	3.01
704	771	4.785453	GGGAAGGAGCACGCTGGG	62.785	72.222	0.00	0.00	0.00	4.45
725	818	0.533491	TGGACGAAATCGGGATTCGT	59.467	50.000	18.73	18.73	44.95	3.85
726	819	1.647346	TTGGACGAAATCGGGATTCG	58.353	50.000	7.81	13.81	44.95	3.34
727	820	2.745281	TGTTTGGACGAAATCGGGATTC	59.255	45.455	7.81	0.00	44.95	2.52
728	821	2.785562	TGTTTGGACGAAATCGGGATT	58.214	42.857	7.81	0.00	44.95	3.01
729	822	2.483014	TGTTTGGACGAAATCGGGAT	57.517	45.000	7.81	0.00	44.95	3.85
730	823	2.483014	ATGTTTGGACGAAATCGGGA	57.517	45.000	7.81	0.00	44.95	5.14
731	824	3.498082	GAAATGTTTGGACGAAATCGGG	58.502	45.455	7.81	0.00	44.95	5.14
732	825	3.160545	CGAAATGTTTGGACGAAATCGG	58.839	45.455	7.81	0.00	44.95	4.18
733	826	2.588106	GCGAAATGTTTGGACGAAATCG	59.412	45.455	0.48	0.48	46.33	3.34
734	827	2.588106	CGCGAAATGTTTGGACGAAATC	59.412	45.455	0.00	0.00	0.00	2.17
735	828	2.224549	TCGCGAAATGTTTGGACGAAAT	59.775	40.909	6.20	0.00	0.00	2.17
736	829	1.598132	TCGCGAAATGTTTGGACGAAA	59.402	42.857	6.20	0.00	0.00	3.46
737	830	1.218763	TCGCGAAATGTTTGGACGAA	58.781	45.000	6.20	0.00	0.00	3.85
738	831	1.218763	TTCGCGAAATGTTTGGACGA	58.781	45.000	21.14	0.00	0.00	4.20
739	832	2.025544	TTTCGCGAAATGTTTGGACG	57.974	45.000	29.22	0.00	0.00	4.79
740	833	4.965042	AATTTTCGCGAAATGTTTGGAC	57.035	36.364	32.58	0.00	37.98	4.02
788	898	1.591183	CTGCCATTTTTGGTCGGGG	59.409	57.895	0.00	0.00	0.00	5.73
789	899	0.897863	TCCTGCCATTTTTGGTCGGG	60.898	55.000	7.55	7.55	34.76	5.14
869	1049	0.179468	TGGGTATTTGTAGCGGAGGC	59.821	55.000	0.00	0.00	40.37	4.70
908	1088	0.542702	CTGGGTTGGTGCTTGGGATT	60.543	55.000	0.00	0.00	0.00	3.01
918	1098	3.953775	CGAGGTGGCTGGGTTGGT	61.954	66.667	0.00	0.00	0.00	3.67
1130	1324	3.366396	ACGATGAGGTTACTGATGTCCT	58.634	45.455	0.00	0.00	0.00	3.85
1873	2125	0.108377	CAGCGGTGCACAGTGGTATA	60.108	55.000	20.43	0.00	0.00	1.47
1876	2128	4.935495	CCAGCGGTGCACAGTGGT	62.935	66.667	20.43	10.47	0.00	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.