AutoCloner

Multiple sequence alignment - TraesCS7D01G421300

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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	TraesCS7D01G421300	chr7D	100.000	3956	0	0	1	3956	540844438	540848393	0.000000e+00	7306.0
1	TraesCS7D01G421300	chr7D	87.211	563	38	15	98	654	430488249	430487715	9.400000e-171	610.0
2	TraesCS7D01G421300	chr7A	96.109	3315	105	6	662	3956	623448059	623451369	0.000000e+00	5385.0
3	TraesCS7D01G421300	chr7A	92.480	492	17	11	1	488	37851962	37852437	0.000000e+00	686.0
4	TraesCS7D01G421300	chr7A	79.412	102	9	5	492	589	37852391	37852484	1.190000e-05	62.1
5	TraesCS7D01G421300	chr7B	96.347	2710	74	3	1259	3955	584304825	584307522	0.000000e+00	4433.0
6	TraesCS7D01G421300	chr7B	87.260	573	38	17	94	654	447999276	447998727	4.340000e-174	621.0
7	TraesCS7D01G421300	chr6D	91.383	499	17	12	1	497	122520939	122520465	0.000000e+00	660.0
8	TraesCS7D01G421300	chr6D	96.104	77	3	0	578	654	122520414	122520338	4.150000e-25	126.0
9	TraesCS7D01G421300	chr6D	82.558	86	11	2	504	589	122520506	122520425	5.480000e-09	73.1
10	TraesCS7D01G421300	chr2A	86.414	633	43	19	22	647	196503417	196504013	0.000000e+00	652.0
11	TraesCS7D01G421300	chr2A	90.141	71	3	4	11	78	58397180	58397111	5.440000e-14	89.8
12	TraesCS7D01G421300	chr1B	86.641	262	24	9	11	263	100638660	100638401	3.010000e-71	279.0
13	TraesCS7D01G421300	chr1B	100.000	29	0	0	393	421	74247972	74248000	2.000000e-03	54.7
14	TraesCS7D01G421300	chr3B	85.393	267	20	17	11	263	582996645	582996384	3.920000e-65	259.0
15	TraesCS7D01G421300	chr2B	83.270	263	29	10	11	263	776403990	776403733	1.110000e-55	228.0
16	TraesCS7D01G421300	chr4B	82.022	267	27	13	393	654	538950215	538950465	1.440000e-49	207.0
17	TraesCS7D01G421300	chr5A	83.974	156	16	9	43	191	454444119	454444272	1.480000e-29	141.0
18	TraesCS7D01G421300	chr5A	89.024	82	5	4	1	78	605140167	605140248	9.050000e-17	99.0

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	TraesCS7D01G421300	chr7D	540844438	540848393	3955	False	7306.000000	7306	100.000	1	3956	1	chr7D.!!$F1	3955
1	TraesCS7D01G421300	chr7D	430487715	430488249	534	True	610.000000	610	87.211	98	654	1	chr7D.!!$R1	556
2	TraesCS7D01G421300	chr7A	623448059	623451369	3310	False	5385.000000	5385	96.109	662	3956	1	chr7A.!!$F1	3294
3	TraesCS7D01G421300	chr7A	37851962	37852484	522	False	374.050000	686	85.946	1	589	2	chr7A.!!$F2	588
4	TraesCS7D01G421300	chr7B	584304825	584307522	2697	False	4433.000000	4433	96.347	1259	3955	1	chr7B.!!$F1	2696
5	TraesCS7D01G421300	chr7B	447998727	447999276	549	True	621.000000	621	87.260	94	654	1	chr7B.!!$R1	560
6	TraesCS7D01G421300	chr6D	122520338	122520939	601	True	286.366667	660	90.015	1	654	3	chr6D.!!$R1	653
7	TraesCS7D01G421300	chr2A	196503417	196504013	596	False	652.000000	652	86.414	22	647	1	chr2A.!!$F1	625

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	Hairpin	End Stability	Orientation
660	700	0.462047	CATAGTCAGTCCCGGCCAAC	60.462	60.000	2.24	0.0	3.77	F
1752	1798	0.035056	GGACAGCCATGCTAACTGGT	60.035	55.000	7.78	36.4	4.00	F
1905	1951	1.615384	GCTGCTTGGGTTCAGGAGATT	60.615	52.381	0.00	0.0	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1983	2029	0.235665	AAACACTGCGTGCTTCATCG	59.764	50.0	8.31	36.98	3.84	R
2553	2599	0.795085	CTCTGCCTTCAAACGAGCTG	59.205	55.0	0.00	0.00	4.24	R
3114	3160	1.321474	CCAAGCCAAAACTGCTCTCA	58.679	50.0	0.00	38.34	3.27	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
488	501	1.733912	CTTGTGTACGTGAGCATGCAT	59.266	47.619	21.98	4.75	0.00	3.96
489	502	1.077915	TGTGTACGTGAGCATGCATG	58.922	50.000	22.70	22.70	0.00	4.06
526	539	2.124693	CGGTGGTGGGCTTGTGTTT	61.125	57.895	0.00	0.00	0.00	2.83
552	569	1.980951	ATGCATGCCGCTTGTGTACG	61.981	55.000	16.68	0.00	43.06	3.67
553	570	2.677003	GCATGCCGCTTGTGTACGT	61.677	57.895	6.36	0.00	37.77	3.57
554	571	1.132436	CATGCCGCTTGTGTACGTG	59.868	57.895	0.00	0.00	0.00	4.49
555	572	1.005512	ATGCCGCTTGTGTACGTGA	60.006	52.632	0.00	0.00	0.00	4.35
556	573	1.289109	ATGCCGCTTGTGTACGTGAC	61.289	55.000	0.00	0.00	0.00	3.67
591	608	3.202829	GGTAACAAAGTGACTGACCCA	57.797	47.619	0.00	0.00	0.00	4.51
654	694	4.082408	TCAACTTACACATAGTCAGTCCCG	60.082	45.833	0.00	0.00	33.66	5.14
655	695	2.758979	ACTTACACATAGTCAGTCCCGG	59.241	50.000	0.00	0.00	28.64	5.73
656	696	1.108776	TACACATAGTCAGTCCCGGC	58.891	55.000	0.00	0.00	0.00	6.13
657	697	1.144057	CACATAGTCAGTCCCGGCC	59.856	63.158	0.00	0.00	0.00	6.13
658	698	1.305802	ACATAGTCAGTCCCGGCCA	60.306	57.895	2.24	0.00	0.00	5.36
659	699	0.907704	ACATAGTCAGTCCCGGCCAA	60.908	55.000	2.24	0.00	0.00	4.52
660	700	0.462047	CATAGTCAGTCCCGGCCAAC	60.462	60.000	2.24	0.00	0.00	3.77
665	705	0.821711	TCAGTCCCGGCCAACTTTTG	60.822	55.000	2.24	0.00	0.00	2.44
677	717	4.161001	GGCCAACTTTTGATGAGATTGGAT	59.839	41.667	0.00	0.00	39.15	3.41
698	738	0.673985	GGGCTCCAAAGAAACACACC	59.326	55.000	0.00	0.00	0.00	4.16
699	739	1.398692	GGCTCCAAAGAAACACACCA	58.601	50.000	0.00	0.00	0.00	4.17
711	751	3.775661	AACACACCAAAAGAAAGACCG	57.224	42.857	0.00	0.00	0.00	4.79
715	755	1.263217	CACCAAAAGAAAGACCGGACG	59.737	52.381	9.46	0.00	0.00	4.79
719	759	2.165319	AAAGAAAGACCGGACGAAGG	57.835	50.000	9.46	0.00	0.00	3.46
735	775	0.971386	AAGGCAGCCCAATTTGTCTG	59.029	50.000	8.22	10.02	28.05	3.51
739	779	1.336240	GCAGCCCAATTTGTCTGTGAC	60.336	52.381	13.78	0.00	0.00	3.67
769	809	3.753434	AGGCAGACCGCGAGTGAG	61.753	66.667	8.23	0.00	43.84	3.51
782	822	1.276622	GAGTGAGGAGGCCCAAAGTA	58.723	55.000	0.00	0.00	33.88	2.24
846	890	1.467342	GCTCCGGCGTTTCAATAGTTT	59.533	47.619	6.01	0.00	0.00	2.66
913	957	1.466025	AACTAGCCACCGTCGAACCA	61.466	55.000	0.00	0.00	0.00	3.67
973	1019	3.923864	AGAACACCGCTCGCCACA	61.924	61.111	0.00	0.00	0.00	4.17
1102	1148	4.548513	CCCTCCTCCCTCCTCCCG	62.549	77.778	0.00	0.00	0.00	5.14
1170	1216	4.020617	CACCTCCGCAGCCTCCAA	62.021	66.667	0.00	0.00	0.00	3.53
1403	1449	3.775654	CTCCCGCCTCCTCCACAC	61.776	72.222	0.00	0.00	0.00	3.82
1685	1731	0.532862	AAGAGCGGCGATATGGGTTG	60.533	55.000	12.98	0.00	0.00	3.77
1731	1777	1.074775	GGTGAAGGACATGGTGGCA	59.925	57.895	0.00	0.00	0.00	4.92
1752	1798	0.035056	GGACAGCCATGCTAACTGGT	60.035	55.000	7.78	0.00	36.40	4.00
1905	1951	1.615384	GCTGCTTGGGTTCAGGAGATT	60.615	52.381	0.00	0.00	0.00	2.40
1983	2029	1.668419	ATGCCAAGTGCGGACTAATC	58.332	50.000	10.98	2.66	45.60	1.75
2028	2074	2.309755	TGGGATGCAGGAGAAGAATGTT	59.690	45.455	0.00	0.00	0.00	2.71
2265	2311	6.515832	TGCAGATCACTATACTTGTATGGTG	58.484	40.000	22.76	22.76	39.39	4.17
2324	2370	4.472470	TCTGGATCTTGTGAGGTCAATGAT	59.528	41.667	0.00	0.00	34.53	2.45
2505	2551	4.827284	GGAAAGTGGGATGAAGTCTCAAAA	59.173	41.667	0.00	0.00	39.57	2.44
2525	2571	7.636326	TCAAAAGTTCGGAAACTAATGAGAAC	58.364	34.615	0.00	0.00	45.07	3.01
2553	2599	2.163211	GCTGAAAAAGGATCCTGCTGTC	59.837	50.000	17.02	11.00	0.00	3.51
2618	2664	3.507233	GCTGGTGACAATTCTCATCCAAA	59.493	43.478	6.52	0.00	42.06	3.28
2869	2915	2.760634	TATGCGACTTGCCTCAAGAA	57.239	45.000	12.89	0.00	43.42	2.52
2959	3005	1.541588	GTGGTGGATTCTGGTGAAAGC	59.458	52.381	0.00	0.00	35.63	3.51
2975	3021	5.175673	GGTGAAAGCAGAAAAGCAACAATAC	59.824	40.000	0.00	0.00	36.85	1.89
3146	3192	2.801483	TGGCTTGGCTAATTTGCTACA	58.199	42.857	11.61	0.00	0.00	2.74
3268	3327	5.840243	TGGATGATGCAGATAAACAAAGG	57.160	39.130	0.00	0.00	0.00	3.11
3431	3490	7.066781	GGGGGAGGACAAATAAGAAATGAATA	58.933	38.462	0.00	0.00	0.00	1.75
3535	3595	7.016361	AGAATTCCGCATACAAATTACTCAC	57.984	36.000	0.65	0.00	0.00	3.51
3536	3596	5.751243	ATTCCGCATACAAATTACTCACC	57.249	39.130	0.00	0.00	0.00	4.02
3537	3597	4.209307	TCCGCATACAAATTACTCACCA	57.791	40.909	0.00	0.00	0.00	4.17
3551	3611	7.914427	ATTACTCACCATGACTGAGGTATAA	57.086	36.000	19.06	11.78	39.69	0.98
3773	3833	1.203112	TGAACTGGGGGCAATGCTTAA	60.203	47.619	4.82	0.00	0.00	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	7.656948	TGAAACCCTTTATGCAGAAAGAAAATG	59.343	33.333	30.36	15.54	38.48	2.32
378	389	6.604171	TGCTGGGTGATTCATGATTATACTT	58.396	36.000	0.00	0.00	0.00	2.24
438	450	1.170919	GGACCTAGGCTGCATGCATG	61.171	60.000	22.97	22.70	45.15	4.06
439	451	1.150081	GGACCTAGGCTGCATGCAT	59.850	57.895	22.97	9.42	45.15	3.96
440	452	2.591753	GGACCTAGGCTGCATGCA	59.408	61.111	21.29	21.29	45.15	3.96
441	453	2.203266	GGGACCTAGGCTGCATGC	60.203	66.667	11.82	11.82	41.94	4.06
442	454	2.109799	CGGGACCTAGGCTGCATG	59.890	66.667	9.30	0.00	0.00	4.06
443	455	3.164269	CCGGGACCTAGGCTGCAT	61.164	66.667	9.30	0.00	0.00	3.96
489	502	4.120331	GACCCTGGTTGCATGCGC	62.120	66.667	14.09	0.00	39.24	6.09
498	511	2.923035	CACCACCGAGACCCTGGT	60.923	66.667	0.00	0.00	38.95	4.00
552	569	2.874780	CCGCGCTCACGTAGTCAC	60.875	66.667	5.56	0.00	41.61	3.67
553	570	3.359523	ACCGCGCTCACGTAGTCA	61.360	61.111	5.56	0.00	41.61	3.41
554	571	2.874780	CACCGCGCTCACGTAGTC	60.875	66.667	5.56	0.00	41.61	2.59
556	573	2.531927	TTACCACCGCGCTCACGTAG	62.532	60.000	5.56	0.00	42.83	3.51
591	608	3.555547	GCAAGTCGCCTGAACAAATTTTT	59.444	39.130	0.00	0.00	32.94	1.94
654	694	3.511146	TCCAATCTCATCAAAAGTTGGCC	59.489	43.478	0.00	0.00	36.82	5.36
655	695	4.789012	TCCAATCTCATCAAAAGTTGGC	57.211	40.909	0.00	0.00	36.82	4.52
656	696	6.103997	CCAATCCAATCTCATCAAAAGTTGG	58.896	40.000	0.00	0.00	37.91	3.77
657	697	6.103997	CCCAATCCAATCTCATCAAAAGTTG	58.896	40.000	0.00	0.00	0.00	3.16
658	698	5.337813	GCCCAATCCAATCTCATCAAAAGTT	60.338	40.000	0.00	0.00	0.00	2.66
659	699	4.161001	GCCCAATCCAATCTCATCAAAAGT	59.839	41.667	0.00	0.00	0.00	2.66
660	700	4.404715	AGCCCAATCCAATCTCATCAAAAG	59.595	41.667	0.00	0.00	0.00	2.27
665	705	2.158564	TGGAGCCCAATCCAATCTCATC	60.159	50.000	0.00	0.00	46.45	2.92
677	717	1.754226	GTGTGTTTCTTTGGAGCCCAA	59.246	47.619	2.84	2.84	42.29	4.12
688	728	4.142469	CGGTCTTTCTTTTGGTGTGTTTCT	60.142	41.667	0.00	0.00	0.00	2.52
698	738	2.223377	CCTTCGTCCGGTCTTTCTTTTG	59.777	50.000	0.00	0.00	0.00	2.44
699	739	2.490991	CCTTCGTCCGGTCTTTCTTTT	58.509	47.619	0.00	0.00	0.00	2.27
711	751	1.250840	AAATTGGGCTGCCTTCGTCC	61.251	55.000	19.68	0.54	0.00	4.79
715	755	1.067354	CAGACAAATTGGGCTGCCTTC	60.067	52.381	19.68	2.99	0.00	3.46
719	759	0.961019	TCACAGACAAATTGGGCTGC	59.039	50.000	16.20	0.00	30.38	5.25
735	775	1.543429	GCCTGTATATGGGCTGGTCAC	60.543	57.143	10.48	0.00	44.48	3.67
769	809	0.034380	GAAGGGTACTTTGGGCCTCC	60.034	60.000	4.53	0.00	36.97	4.30
782	822	1.988406	GGCTACACCGGAGAAGGGT	60.988	63.158	9.46	0.00	38.65	4.34
1107	1153	3.591835	GCGAGGAGGAGCGAGGAG	61.592	72.222	0.00	0.00	0.00	3.69
1272	1318	4.570663	ACGGAGAGCGCGTATGGC	62.571	66.667	8.43	0.00	38.69	4.40
1275	1321	1.096386	AGAAGACGGAGAGCGCGTAT	61.096	55.000	8.43	0.00	0.00	3.06
1685	1731	3.423154	CAAACACCTCCTCGGCGC	61.423	66.667	0.00	0.00	35.61	6.53
1689	1735	2.664851	TGCGCAAACACCTCCTCG	60.665	61.111	8.16	0.00	0.00	4.63
1752	1798	2.159448	CGGCATGGAATTTTGAGCGTAA	60.159	45.455	0.00	0.00	0.00	3.18
1890	1936	1.704628	TCTGCAATCTCCTGAACCCAA	59.295	47.619	0.00	0.00	0.00	4.12
1905	1951	1.615116	CCAAAGCCATTCCTCTCTGCA	60.615	52.381	0.00	0.00	0.00	4.41
1983	2029	0.235665	AAACACTGCGTGCTTCATCG	59.764	50.000	8.31	0.00	36.98	3.84
2028	2074	8.839343	CCAACAATCATTGAGCTATATGTGTAA	58.161	33.333	3.79	0.00	0.00	2.41
2265	2311	1.678970	AGCCCGACCAAGCAAATCC	60.679	57.895	0.00	0.00	0.00	3.01
2525	2571	2.514516	ATCCTTTTTCAGCCCCCGGG	62.515	60.000	15.80	15.80	38.57	5.73
2553	2599	0.795085	CTCTGCCTTCAAACGAGCTG	59.205	55.000	0.00	0.00	0.00	4.24
2618	2664	7.486407	AATGCCTTCTTTATTTCATTGGTCT	57.514	32.000	0.00	0.00	0.00	3.85
2869	2915	5.306419	TGACTATAATCTCAGCCTGCTCAAT	59.694	40.000	0.00	0.00	0.00	2.57
2959	3005	7.754069	TTGTTGAAGTATTGTTGCTTTTCTG	57.246	32.000	0.00	0.00	0.00	3.02
2975	3021	5.865552	CCTGTTCTGCCATATTTTGTTGAAG	59.134	40.000	0.00	0.00	0.00	3.02
3114	3160	1.321474	CCAAGCCAAAACTGCTCTCA	58.679	50.000	0.00	0.00	38.34	3.27
3146	3192	7.629222	GCTTAGGTCTGCATCATGTAACAAATT	60.629	37.037	0.00	0.00	0.00	1.82
3268	3327	3.059166	AGTGTTTCGCCATTTGCATTTC	58.941	40.909	0.00	0.00	41.33	2.17
3302	3361	6.714810	TGCTCTAAAAGGAATTCTTGCTAACA	59.285	34.615	5.23	0.00	35.55	2.41
3431	3490	4.162040	AGATAGCAAAGTATTGGCAGCT	57.838	40.909	0.78	0.78	37.02	4.24
3535	3595	6.183361	TGGTCTGAATTATACCTCAGTCATGG	60.183	42.308	9.17	0.00	40.06	3.66
3536	3596	6.820335	TGGTCTGAATTATACCTCAGTCATG	58.180	40.000	9.17	0.00	40.06	3.07
3537	3597	7.437713	TTGGTCTGAATTATACCTCAGTCAT	57.562	36.000	9.17	0.00	40.06	3.06
3568	3628	1.751927	CTCCTTGACATGCTGGCCC	60.752	63.158	0.00	0.00	0.00	5.80
3773	3833	4.406972	TGGAAGGTGATCTCGATCTCAAAT	59.593	41.667	8.25	0.00	38.60	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.