AutoCloner

Multiple sequence alignment - TraesCS2A01G367400

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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	TraesCS2A01G367400	chr2A	100.000	3665	0	0	1	3665	611301829	611305493	0.000000e+00	6769.0
1	TraesCS2A01G367400	chr2A	83.346	2636	348	49	959	3561	733628863	733631440	0.000000e+00	2351.0
2	TraesCS2A01G367400	chr2B	93.819	3689	170	31	1	3665	548622999	548626653	0.000000e+00	5496.0
3	TraesCS2A01G367400	chr2D	94.469	3164	109	19	518	3665	469990143	469993256	0.000000e+00	4813.0
4	TraesCS2A01G367400	chr2D	87.652	494	36	14	1	482	469989574	469990054	5.350000e-153	551.0
5	TraesCS2A01G367400	chr2D	93.182	44	3	0	486	529	469990087	469990130	8.500000e-07	65.8
6	TraesCS2A01G367400	chr1A	86.396	2661	332	25	904	3554	8331856	8334496	0.000000e+00	2881.0
7	TraesCS2A01G367400	chr1A	85.431	2677	356	29	901	3564	8341950	8344605	0.000000e+00	2752.0
8	TraesCS2A01G367400	chr1A	84.533	1862	245	26	992	2840	9375656	9373825	0.000000e+00	1803.0
9	TraesCS2A01G367400	chr1D	85.551	2630	350	24	939	3562	6913108	6915713	0.000000e+00	2724.0
10	TraesCS2A01G367400	chr1D	84.338	2605	330	50	985	3563	407672559	407670007	0.000000e+00	2479.0
11	TraesCS2A01G367400	chr1B	84.906	2670	356	34	904	3559	8820012	8817376	0.000000e+00	2654.0
12	TraesCS2A01G367400	chr1B	84.615	2587	348	35	992	3560	10007493	10004939	0.000000e+00	2527.0
13	TraesCS2A01G367400	chr5A	83.730	2606	342	49	985	3562	12194231	12191680	0.000000e+00	2388.0
14	TraesCS2A01G367400	chr4A	96.875	32	1	0	60	91	222107078	222107109	2.000000e-03	54.7

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	TraesCS2A01G367400	chr2A	611301829	611305493	3664	False	6769.000000	6769	100.000000	1	3665	1	chr2A.!!$F1	3664
1	TraesCS2A01G367400	chr2A	733628863	733631440	2577	False	2351.000000	2351	83.346000	959	3561	1	chr2A.!!$F2	2602
2	TraesCS2A01G367400	chr2B	548622999	548626653	3654	False	5496.000000	5496	93.819000	1	3665	1	chr2B.!!$F1	3664
3	TraesCS2A01G367400	chr2D	469989574	469993256	3682	False	1809.933333	4813	91.767667	1	3665	3	chr2D.!!$F1	3664
4	TraesCS2A01G367400	chr1A	8331856	8334496	2640	False	2881.000000	2881	86.396000	904	3554	1	chr1A.!!$F1	2650
5	TraesCS2A01G367400	chr1A	8341950	8344605	2655	False	2752.000000	2752	85.431000	901	3564	1	chr1A.!!$F2	2663
6	TraesCS2A01G367400	chr1A	9373825	9375656	1831	True	1803.000000	1803	84.533000	992	2840	1	chr1A.!!$R1	1848
7	TraesCS2A01G367400	chr1D	6913108	6915713	2605	False	2724.000000	2724	85.551000	939	3562	1	chr1D.!!$F1	2623
8	TraesCS2A01G367400	chr1D	407670007	407672559	2552	True	2479.000000	2479	84.338000	985	3563	1	chr1D.!!$R1	2578
9	TraesCS2A01G367400	chr1B	8817376	8820012	2636	True	2654.000000	2654	84.906000	904	3559	1	chr1B.!!$R1	2655
10	TraesCS2A01G367400	chr1B	10004939	10007493	2554	True	2527.000000	2527	84.615000	992	3560	1	chr1B.!!$R2	2568
11	TraesCS2A01G367400	chr5A	12191680	12194231	2551	True	2388.000000	2388	83.730000	985	3562	1	chr5A.!!$R1	2577

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
30	31	0.458543	CCAGTAAGCGTGTGAGCGAT	60.459	55.0	0.00	0.00	43.00	4.58	F
660	729	0.474184	ACTTGACCTTGACCTGGTGG	59.526	55.0	2.82	1.32	38.03	4.61	F
664	733	0.606673	GACCTTGACCTGGTGGAAGC	60.607	60.0	2.82	0.00	38.03	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1107	1198	2.032528	TTGTCAGCGAAGGCCAGG	59.967	61.111	5.01	0.00	41.24	4.45	R
2631	2765	0.468029	AACCTCCACCACCAAGCTTG	60.468	55.000	19.93	19.93	0.00	4.01	R
2664	2798	2.414612	TGAGTCACTTAACACCCCCTT	58.585	47.619	0.00	0.00	0.00	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
30	31	0.458543	CCAGTAAGCGTGTGAGCGAT	60.459	55.000	0.00	0.00	43.00	4.58
51	52	3.575630	TCAAACGAGAGGAATTGACGAG	58.424	45.455	0.00	0.00	30.83	4.18
152	164	1.666209	CCAATACTGCCGCCCCTTTG	61.666	60.000	0.00	0.00	0.00	2.77
156	168	1.490416	TACTGCCGCCCCTTTGGTTA	61.490	55.000	0.00	0.00	36.04	2.85
158	170	0.970427	CTGCCGCCCCTTTGGTTAAT	60.970	55.000	0.00	0.00	36.04	1.40
161	173	1.404986	GCCGCCCCTTTGGTTAATTTC	60.405	52.381	0.00	0.00	36.04	2.17
162	174	2.176045	CCGCCCCTTTGGTTAATTTCT	58.824	47.619	0.00	0.00	36.04	2.52
163	175	2.094234	CCGCCCCTTTGGTTAATTTCTG	60.094	50.000	0.00	0.00	36.04	3.02
164	176	2.673893	CGCCCCTTTGGTTAATTTCTGC	60.674	50.000	0.00	0.00	36.04	4.26
165	177	2.567169	GCCCCTTTGGTTAATTTCTGCT	59.433	45.455	0.00	0.00	36.04	4.24
182	195	1.710809	TGCTTTTTCCCCCTAGCTCTT	59.289	47.619	0.00	0.00	34.77	2.85
323	336	6.567687	TGTGTTCATATCCGTTGAATTTGT	57.432	33.333	0.00	0.00	35.68	2.83
455	468	7.865889	GTGGTTAATTTGTGTTCCTTTTCTAGG	59.134	37.037	0.00	0.00	46.27	3.02
463	476	3.904339	TGTTCCTTTTCTAGGTGCTCTCT	59.096	43.478	0.00	0.00	45.03	3.10
464	477	4.348168	TGTTCCTTTTCTAGGTGCTCTCTT	59.652	41.667	0.00	0.00	45.03	2.85
529	572	9.132521	GGTCTTTTGTGTTGATATTCATTGAAG	57.867	33.333	5.21	0.00	0.00	3.02
534	577	8.523523	TTGTGTTGATATTCATTGAAGCAAAG	57.476	30.769	5.21	0.00	0.00	2.77
582	651	1.073763	TCTGTTGGTTAGCACATGCCT	59.926	47.619	0.00	0.00	43.38	4.75
655	724	4.042062	TCATGATTGACTTGACCTTGACCT	59.958	41.667	0.00	0.00	0.00	3.85
656	725	3.743521	TGATTGACTTGACCTTGACCTG	58.256	45.455	0.00	0.00	0.00	4.00
657	726	2.638480	TTGACTTGACCTTGACCTGG	57.362	50.000	0.00	0.00	0.00	4.45
658	727	1.507140	TGACTTGACCTTGACCTGGT	58.493	50.000	0.00	0.00	41.07	4.00
659	728	1.140852	TGACTTGACCTTGACCTGGTG	59.859	52.381	2.82	0.00	38.03	4.17
660	729	0.474184	ACTTGACCTTGACCTGGTGG	59.526	55.000	2.82	1.32	38.03	4.61
661	730	0.764890	CTTGACCTTGACCTGGTGGA	59.235	55.000	2.82	0.00	38.03	4.02
662	731	1.142870	CTTGACCTTGACCTGGTGGAA	59.857	52.381	2.82	0.00	38.03	3.53
663	732	0.764890	TGACCTTGACCTGGTGGAAG	59.235	55.000	2.82	6.14	38.03	3.46
664	733	0.606673	GACCTTGACCTGGTGGAAGC	60.607	60.000	2.82	0.00	38.03	3.86
665	734	1.303643	CCTTGACCTGGTGGAAGCC	60.304	63.158	2.82	0.00	37.04	4.35
666	735	1.763770	CTTGACCTGGTGGAAGCCT	59.236	57.895	2.82	0.00	37.04	4.58
667	736	0.607489	CTTGACCTGGTGGAAGCCTG	60.607	60.000	2.82	0.00	37.04	4.85
670	739	2.352805	CCTGGTGGAAGCCTGGTC	59.647	66.667	0.00	0.00	41.17	4.02
671	740	2.046892	CTGGTGGAAGCCTGGTCG	60.047	66.667	0.00	0.00	0.00	4.79
672	741	2.847234	TGGTGGAAGCCTGGTCGT	60.847	61.111	0.00	0.00	0.00	4.34
673	742	2.047179	GGTGGAAGCCTGGTCGTC	60.047	66.667	0.00	0.00	0.00	4.20
674	743	2.047179	GTGGAAGCCTGGTCGTCC	60.047	66.667	13.27	13.27	35.56	4.79
695	774	1.819632	GGTGGTTCTATGCAGCCCG	60.820	63.158	0.00	0.00	0.00	6.13
770	849	9.834628	GCACTTGCTTTTTATGTTAATACTGTA	57.165	29.630	0.00	0.00	38.21	2.74
844	923	3.865745	CGCTGTCCGTCTCTGAATAATTT	59.134	43.478	0.00	0.00	0.00	1.82
876	955	5.582665	GTGGATTGTAGTGAATTCTCTGGTC	59.417	44.000	18.11	10.77	0.00	4.02
880	959	5.808366	TGTAGTGAATTCTCTGGTCAGTT	57.192	39.130	18.11	0.00	0.00	3.16
884	963	3.614616	GTGAATTCTCTGGTCAGTTAGCG	59.385	47.826	7.05	0.00	0.00	4.26
899	978	0.946528	TAGCGGAACATGCATGCATC	59.053	50.000	30.07	22.57	33.90	3.91
901	980	1.731433	GCGGAACATGCATGCATCCT	61.731	55.000	32.74	19.43	35.87	3.24
1118	1209	2.650778	CCAAAACCTGGCCTTCGC	59.349	61.111	3.32	0.00	38.76	4.70
1267	1364	7.308830	GCATATGGTTCAATAAGATCCCAGTTC	60.309	40.741	4.56	0.00	35.58	3.01
1586	1704	2.039879	AGTTAGGCCGAAACAAGGTCAT	59.960	45.455	21.47	1.54	35.42	3.06
1782	1900	3.406764	ACTCAACTCACTGCTTGATTCC	58.593	45.455	0.00	0.00	32.17	3.01
1867	1988	9.151471	ACTACATGTACACTTCACATAATGAAC	57.849	33.333	0.08	0.00	42.62	3.18
1984	2105	1.811266	CCTGACGATCCCTGCAACG	60.811	63.158	0.00	0.00	0.00	4.10
2013	2134	1.880027	GCCTGTGGACCTTTTACAGTG	59.120	52.381	8.45	0.00	40.04	3.66
2226	2356	1.202290	CCACAAATCATAGCCGTTGCC	60.202	52.381	0.00	0.00	38.69	4.52
2546	2680	4.918810	AGTGGTGTGGTTTTCTTTCATC	57.081	40.909	0.00	0.00	0.00	2.92
2631	2765	5.919141	TCGTGCTACTAAAAACTTCTCTGAC	59.081	40.000	0.00	0.00	0.00	3.51
2664	2798	5.163077	TGGTGGAGGTTTTGGTTCTGTATAA	60.163	40.000	0.00	0.00	0.00	0.98
2666	2800	6.072119	GGTGGAGGTTTTGGTTCTGTATAAAG	60.072	42.308	0.00	0.00	0.00	1.85
3033	3171	4.331992	CAGAGAACATACTTGTGGATGCAG	59.668	45.833	0.00	0.00	35.83	4.41
3203	3342	0.179084	GCTTCGGCATGGTACTGCTA	60.179	55.000	7.01	0.00	41.95	3.49
3250	3389	3.118775	TCCTCACCGGAAATATCACACAG	60.119	47.826	9.46	0.00	39.40	3.66
3342	3487	4.527038	ACGAGGGAGATGTGAAGAGTTTAA	59.473	41.667	0.00	0.00	0.00	1.52
3629	3780	4.443034	GGAATAAAAGAAGGAGGCGAGCTA	60.443	45.833	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	0.458543	ATCGCTCACACGCTTACTGG	60.459	55.000	0.00	0.00	0.00	4.00
26	27	2.930040	TCAATTCCTCTCGTTTGATCGC	59.070	45.455	0.00	0.00	0.00	4.58
30	31	3.005472	ACTCGTCAATTCCTCTCGTTTGA	59.995	43.478	0.00	0.00	0.00	2.69
51	52	4.514401	CCAAGGTCCTGTTTGGTATAGAC	58.486	47.826	0.00	0.00	39.18	2.59
152	164	4.286032	AGGGGGAAAAAGCAGAAATTAACC	59.714	41.667	0.00	0.00	0.00	2.85
156	168	3.515502	GCTAGGGGGAAAAAGCAGAAATT	59.484	43.478	0.00	0.00	35.05	1.82
158	170	2.110011	AGCTAGGGGGAAAAAGCAGAAA	59.890	45.455	0.00	0.00	37.44	2.52
161	173	1.283321	AGAGCTAGGGGGAAAAAGCAG	59.717	52.381	0.00	0.00	37.44	4.24
162	174	1.372501	AGAGCTAGGGGGAAAAAGCA	58.627	50.000	0.00	0.00	37.44	3.91
163	175	2.493675	CAAAGAGCTAGGGGGAAAAAGC	59.506	50.000	0.00	0.00	35.16	3.51
164	176	3.767711	ACAAAGAGCTAGGGGGAAAAAG	58.232	45.455	0.00	0.00	0.00	2.27
165	177	3.895704	ACAAAGAGCTAGGGGGAAAAA	57.104	42.857	0.00	0.00	0.00	1.94
218	231	6.709018	AGTTGGCAACTTAAAACACATACT	57.291	33.333	26.54	0.00	39.04	2.12
273	286	0.443869	CATGCGTAAGTGTGACCAGC	59.556	55.000	0.00	0.00	41.68	4.85
362	375	7.497249	CCAACCCACAAAGATAAATGTTTTTGA	59.503	33.333	3.15	0.00	35.21	2.69
363	376	7.281999	ACCAACCCACAAAGATAAATGTTTTTG	59.718	33.333	0.00	0.00	36.77	2.44
399	412	4.583489	CGGTGGTAGTACTGTCAATATCCT	59.417	45.833	5.39	0.00	0.00	3.24
455	468	7.113544	GCAAACTTAAAACACATAAGAGAGCAC	59.886	37.037	0.67	0.00	35.00	4.40
463	476	6.689241	CACAGACGCAAACTTAAAACACATAA	59.311	34.615	0.00	0.00	0.00	1.90
464	477	6.195868	CACAGACGCAAACTTAAAACACATA	58.804	36.000	0.00	0.00	0.00	2.29
655	724	2.847234	ACGACCAGGCTTCCACCA	60.847	61.111	0.00	0.00	0.00	4.17
656	725	2.047179	GACGACCAGGCTTCCACC	60.047	66.667	0.00	0.00	0.00	4.61
657	726	2.047179	GGACGACCAGGCTTCCAC	60.047	66.667	0.00	0.00	35.97	4.02
658	727	2.525629	TGGACGACCAGGCTTCCA	60.526	61.111	1.37	0.68	41.77	3.53
667	736	0.899720	TAGAACCACCATGGACGACC	59.100	55.000	21.47	4.41	40.96	4.79
668	737	2.550978	CATAGAACCACCATGGACGAC	58.449	52.381	21.47	5.70	40.96	4.34
669	738	1.134521	GCATAGAACCACCATGGACGA	60.135	52.381	21.47	1.14	40.96	4.20
670	739	1.299541	GCATAGAACCACCATGGACG	58.700	55.000	21.47	10.12	40.96	4.79
671	740	2.292267	CTGCATAGAACCACCATGGAC	58.708	52.381	21.47	4.24	40.96	4.02
672	741	1.408683	GCTGCATAGAACCACCATGGA	60.409	52.381	21.47	0.00	40.96	3.41
673	742	1.027357	GCTGCATAGAACCACCATGG	58.973	55.000	11.19	11.19	45.02	3.66
674	743	1.027357	GGCTGCATAGAACCACCATG	58.973	55.000	0.50	0.00	0.00	3.66
768	847	7.011828	TGCAACTTGAACTCAAAGTTAGTAC	57.988	36.000	1.54	0.00	38.80	2.73
770	849	5.449177	GCTGCAACTTGAACTCAAAGTTAGT	60.449	40.000	0.00	0.00	38.80	2.24
771	850	4.972440	GCTGCAACTTGAACTCAAAGTTAG	59.028	41.667	0.00	0.00	38.80	2.34
772	851	4.202010	GGCTGCAACTTGAACTCAAAGTTA	60.202	41.667	0.50	0.00	38.80	2.24
773	852	3.429410	GGCTGCAACTTGAACTCAAAGTT	60.429	43.478	0.50	0.00	41.95	2.66
774	853	2.099756	GGCTGCAACTTGAACTCAAAGT	59.900	45.455	0.50	0.00	35.15	2.66
778	857	0.106769	TGGGCTGCAACTTGAACTCA	60.107	50.000	0.50	0.00	0.00	3.41
819	898	0.958876	TTCAGAGACGGACAGCGCTA	60.959	55.000	10.99	0.00	0.00	4.26
820	899	1.599606	ATTCAGAGACGGACAGCGCT	61.600	55.000	2.64	2.64	0.00	5.92
823	902	4.631813	ACAAATTATTCAGAGACGGACAGC	59.368	41.667	0.00	0.00	0.00	4.40
825	904	5.175859	GGACAAATTATTCAGAGACGGACA	58.824	41.667	0.00	0.00	0.00	4.02
826	905	5.175859	TGGACAAATTATTCAGAGACGGAC	58.824	41.667	0.00	0.00	0.00	4.79
828	907	6.149474	ACTTTGGACAAATTATTCAGAGACGG	59.851	38.462	0.00	0.00	0.00	4.79
829	908	7.017645	CACTTTGGACAAATTATTCAGAGACG	58.982	38.462	0.00	0.00	0.00	4.18
830	909	7.174946	TCCACTTTGGACAAATTATTCAGAGAC	59.825	37.037	0.00	0.00	42.67	3.36
831	910	7.230747	TCCACTTTGGACAAATTATTCAGAGA	58.769	34.615	0.00	0.00	42.67	3.10
832	911	7.452880	TCCACTTTGGACAAATTATTCAGAG	57.547	36.000	0.00	0.00	42.67	3.35
876	955	1.532505	GCATGCATGTTCCGCTAACTG	60.533	52.381	26.79	0.00	38.99	3.16
880	959	0.946528	GATGCATGCATGTTCCGCTA	59.053	50.000	36.73	3.35	36.70	4.26
884	963	3.382546	AGTTAAGGATGCATGCATGTTCC	59.617	43.478	36.73	30.28	36.70	3.62
899	978	4.870991	GCTGAGCCTAACAAGTAGTTAAGG	59.129	45.833	0.00	2.51	41.89	2.69
901	980	4.828829	GGCTGAGCCTAACAAGTAGTTAA	58.171	43.478	17.96	0.00	46.69	2.01
981	1072	3.380637	GCATGGAGAAGAATGTGAATGCT	59.619	43.478	0.00	0.00	36.96	3.79
1107	1198	2.032528	TTGTCAGCGAAGGCCAGG	59.967	61.111	5.01	0.00	41.24	4.45
1267	1364	2.632377	AGCAATCCATACGGTTGTGAG	58.368	47.619	0.00	0.00	0.00	3.51
1782	1900	2.503895	AGCCTTTGGTCAGAGGATTG	57.496	50.000	11.20	0.00	34.83	2.67
1867	1988	3.535561	AGACAAATACAGAAGGCGATGG	58.464	45.455	0.00	0.00	0.00	3.51
2226	2356	1.690283	CGCATTCGCTCTGAGTGGTG	61.690	60.000	17.44	16.28	35.03	4.17
2546	2680	5.819379	ACACTGCCTTGATTGTCATAGTATG	59.181	40.000	3.55	3.55	0.00	2.39
2631	2765	0.468029	AACCTCCACCACCAAGCTTG	60.468	55.000	19.93	19.93	0.00	4.01
2664	2798	2.414612	TGAGTCACTTAACACCCCCTT	58.585	47.619	0.00	0.00	0.00	3.95
2666	2800	2.943036	TTGAGTCACTTAACACCCCC	57.057	50.000	0.00	0.00	0.00	5.40
3033	3171	3.188460	TCTGCGACTTTAGGAACAAATGC	59.812	43.478	0.00	0.00	0.00	3.56
3236	3375	4.507710	TCTCAGTGCTGTGTGATATTTCC	58.492	43.478	0.00	0.00	0.00	3.13
3250	3389	1.964891	TTGCTGCTGCTCTCAGTGC	60.965	57.895	17.00	0.00	42.29	4.40
3342	3487	4.098349	GTCACCATGCAATTGTGTATCCAT	59.902	41.667	7.40	0.00	40.56	3.41
3629	3780	0.108615	CAGACGATTTGGAGACCGCT	60.109	55.000	0.00	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.