AutoCloner

Multiple sequence alignment - TraesCS7D01G344400

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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	TraesCS7D01G344400	chr7D	100.000	3236	0	0	1	3236	441983446	441980211	0.000000e+00	5976.0
1	TraesCS7D01G344400	chr7D	85.566	769	86	6	2444	3210	180829693	180828948	0.000000e+00	782.0
2	TraesCS7D01G344400	chr7B	93.803	3276	117	34	7	3236	458613695	458610460	0.000000e+00	4846.0
3	TraesCS7D01G344400	chr7A	92.063	1726	78	26	793	2505	492782150	492780471	0.000000e+00	2374.0
4	TraesCS7D01G344400	chr7A	86.387	764	93	7	2454	3210	191278410	191279169	0.000000e+00	824.0
5	TraesCS7D01G344400	chr7A	85.457	777	57	28	2	750	492782896	492782148	0.000000e+00	758.0
6	TraesCS7D01G344400	chr7A	80.556	468	43	28	30	452	492819667	492819203	1.870000e-82	316.0
7	TraesCS7D01G344400	chr3B	87.270	652	58	11	2440	3075	753796027	753795385	0.000000e+00	721.0
8	TraesCS7D01G344400	chr4D	83.313	809	95	18	2440	3209	356319976	356320783	0.000000e+00	710.0
9	TraesCS7D01G344400	chr2A	83.397	783	109	14	2444	3210	115142340	115143117	0.000000e+00	706.0
10	TraesCS7D01G344400	chrUn	84.268	731	81	20	2509	3210	22351766	22351041	0.000000e+00	682.0
11	TraesCS7D01G344400	chrUn	88.612	562	48	9	2521	3075	442311884	442312436	0.000000e+00	669.0
12	TraesCS7D01G344400	chrUn	100.000	28	0	0	3209	3236	21179097	21179124	6.000000e-03	52.8
13	TraesCS7D01G344400	chrUn	100.000	28	0	0	3209	3236	297628127	297628154	6.000000e-03	52.8
14	TraesCS7D01G344400	chr2D	82.416	745	111	12	2479	3210	113511396	113512133	1.640000e-177	632.0
15	TraesCS7D01G344400	chr5D	96.970	33	1	0	3204	3236	377139623	377139655	4.510000e-04	56.5
16	TraesCS7D01G344400	chr3A	96.970	33	0	1	3204	3236	690347441	690347410	2.000000e-03	54.7
17	TraesCS7D01G344400	chr6D	100.000	28	0	0	3209	3236	373642471	373642498	6.000000e-03	52.8
18	TraesCS7D01G344400	chr6D	100.000	28	0	0	3209	3236	420527785	420527812	6.000000e-03	52.8
19	TraesCS7D01G344400	chr2B	100.000	28	0	0	3209	3236	560169769	560169742	6.000000e-03	52.8
20	TraesCS7D01G344400	chr2B	96.875	32	0	1	3205	3236	597566109	597566079	6.000000e-03	52.8

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	TraesCS7D01G344400	chr7D	441980211	441983446	3235	True	5976	5976	100.000	1	3236	1	chr7D.!!$R2	3235
1	TraesCS7D01G344400	chr7D	180828948	180829693	745	True	782	782	85.566	2444	3210	1	chr7D.!!$R1	766
2	TraesCS7D01G344400	chr7B	458610460	458613695	3235	True	4846	4846	93.803	7	3236	1	chr7B.!!$R1	3229
3	TraesCS7D01G344400	chr7A	492780471	492782896	2425	True	1566	2374	88.760	2	2505	2	chr7A.!!$R2	2503
4	TraesCS7D01G344400	chr7A	191278410	191279169	759	False	824	824	86.387	2454	3210	1	chr7A.!!$F1	756
5	TraesCS7D01G344400	chr3B	753795385	753796027	642	True	721	721	87.270	2440	3075	1	chr3B.!!$R1	635
6	TraesCS7D01G344400	chr4D	356319976	356320783	807	False	710	710	83.313	2440	3209	1	chr4D.!!$F1	769
7	TraesCS7D01G344400	chr2A	115142340	115143117	777	False	706	706	83.397	2444	3210	1	chr2A.!!$F1	766
8	TraesCS7D01G344400	chrUn	22351041	22351766	725	True	682	682	84.268	2509	3210	1	chrUn.!!$R1	701
9	TraesCS7D01G344400	chrUn	442311884	442312436	552	False	669	669	88.612	2521	3075	1	chrUn.!!$F3	554
10	TraesCS7D01G344400	chr2D	113511396	113512133	737	False	632	632	82.416	2479	3210	1	chr2D.!!$F1	731

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	End Stability	Orientation
280	299	0.034337	TAGCAAACCACGGACACTCC	59.966	55.0	3.85	F
378	398	0.106708	AGTGAACGGATGTGTGCAGT	59.893	50.0	4.40	F
848	896	0.824109	CTCATCGCAACCCACCTCTA	59.176	55.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1470	1538	0.833287	GCTTCCTGGTGATGAGCCTA	59.167	55.0	0.00	3.93	R
1872	1949	1.012086	CATCAGGATCTGTGTTGCCG	58.988	55.0	32.61	5.69	R
2552	2639	0.467804	ATTTTTGTGCGTTTGGGGCT	59.532	45.0	0.00	5.19	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
22	23	2.278404	CCATCCCCGGGATTGCAA	59.722	61.111	26.32	0.00	39.79	4.08
102	103	7.010552	GTGAACATTCACGATATAGCAAACTCT	59.989	37.037	8.90	0.00	46.80	3.24
244	262	0.538516	AAACCCCTTGCATGCGTACA	60.539	50.000	14.09	0.00	0.00	2.90
246	264	0.748005	ACCCCTTGCATGCGTACATC	60.748	55.000	14.09	0.00	32.87	3.06
278	297	0.602905	GCTAGCAAACCACGGACACT	60.603	55.000	10.63	0.00	0.00	3.55
279	298	1.429463	CTAGCAAACCACGGACACTC	58.571	55.000	0.00	0.00	0.00	3.51
280	299	0.034337	TAGCAAACCACGGACACTCC	59.966	55.000	0.00	0.00	0.00	3.85
281	300	1.525077	GCAAACCACGGACACTCCA	60.525	57.895	0.00	0.00	35.91	3.86
282	301	1.782028	GCAAACCACGGACACTCCAC	61.782	60.000	0.00	0.00	35.91	4.02
283	302	1.227438	AAACCACGGACACTCCACG	60.227	57.895	0.00	0.00	35.91	4.94
284	303	2.653953	AAACCACGGACACTCCACGG	62.654	60.000	0.00	0.00	35.91	4.94
331	350	3.928727	AAACACACATCCTTGAGCATG	57.071	42.857	0.00	0.00	0.00	4.06
368	388	0.387929	AGAAAGCACGAGTGAACGGA	59.612	50.000	7.50	0.00	37.61	4.69
372	392	0.667487	AGCACGAGTGAACGGATGTG	60.667	55.000	7.50	0.00	37.61	3.21
378	398	0.106708	AGTGAACGGATGTGTGCAGT	59.893	50.000	0.00	0.00	0.00	4.40
410	430	6.509418	TCCAAAATGGAAAGCTGTATGTAC	57.491	37.500	0.00	0.00	45.00	2.90
411	431	5.123186	TCCAAAATGGAAAGCTGTATGTACG	59.877	40.000	0.00	0.00	45.00	3.67
412	432	4.616181	AAATGGAAAGCTGTATGTACGC	57.384	40.909	0.00	0.00	0.00	4.42
413	433	2.753055	TGGAAAGCTGTATGTACGCA	57.247	45.000	0.00	0.00	0.00	5.24
429	456	6.108097	TGTACGCAGCTATATATCTCTTCG	57.892	41.667	0.00	0.00	0.00	3.79
482	513	2.359169	CCTCGCACCCTGAAGGCTA	61.359	63.158	0.00	0.00	40.58	3.93
483	514	1.153549	CTCGCACCCTGAAGGCTAC	60.154	63.158	0.00	0.00	40.58	3.58
484	515	1.888436	CTCGCACCCTGAAGGCTACA	61.888	60.000	0.00	0.00	40.58	2.74
485	516	1.221840	CGCACCCTGAAGGCTACAT	59.778	57.895	0.00	0.00	40.58	2.29
551	595	2.596631	GCATGCATGGCCGGAGAT	60.597	61.111	27.34	0.00	0.00	2.75
556	600	3.113745	CATGGCCGGAGATGCAAC	58.886	61.111	5.05	0.00	0.00	4.17
563	607	2.670635	CGGAGATGCAACGGAAGAG	58.329	57.895	0.00	0.00	0.00	2.85
639	683	2.940890	ATTAGGGTGGCACGCATCCG	62.941	60.000	32.29	0.00	43.02	4.18
688	736	1.597937	CGTTTGTCTGCTTGGCTCAAC	60.598	52.381	0.00	0.00	0.00	3.18
730	778	3.069872	TGTTTCAGCAAAGCAATGGACAT	59.930	39.130	0.00	0.00	0.00	3.06
848	896	0.824109	CTCATCGCAACCCACCTCTA	59.176	55.000	0.00	0.00	0.00	2.43
857	905	0.984995	ACCCACCTCTAGCTTCCAAC	59.015	55.000	0.00	0.00	0.00	3.77
862	910	3.131400	CCACCTCTAGCTTCCAACTCTAC	59.869	52.174	0.00	0.00	0.00	2.59
863	911	4.020543	CACCTCTAGCTTCCAACTCTACT	58.979	47.826	0.00	0.00	0.00	2.57
907	971	7.425224	AAGGTAACACATCTATCTGCTTAGT	57.575	36.000	0.00	0.00	41.41	2.24
933	997	7.883391	TGGTTCTTCTTACAGATACTCCTAG	57.117	40.000	0.00	0.00	0.00	3.02
974	1038	3.897502	CGATGGTACGTGCGTGCG	61.898	66.667	7.55	0.00	37.94	5.34
976	1040	3.066645	GATGGTACGTGCGTGCGTG	62.067	63.158	14.68	0.00	45.33	5.34
1230	1295	2.667536	GGCATGATGATCGCCGCT	60.668	61.111	0.00	0.00	35.79	5.52
1371	1436	4.509737	GCCGCCTACACCGAGTCC	62.510	72.222	0.00	0.00	0.00	3.85
1456	1524	4.895854	CGACAACGGTTCCGGTAT	57.104	55.556	15.66	0.00	35.72	2.73
2371	2448	1.960763	TGCGTGTGACATGGACTGC	60.961	57.895	6.95	3.22	0.00	4.40
2374	2451	2.006552	GCGTGTGACATGGACTGCATA	61.007	52.381	6.95	0.00	0.00	3.14
2392	2469	5.616270	TGCATAGTTCGCCCTGAATTTATA	58.384	37.500	0.00	0.00	39.21	0.98
2393	2470	5.468746	TGCATAGTTCGCCCTGAATTTATAC	59.531	40.000	0.00	0.00	39.21	1.47
2519	2606	0.806241	GCGTTTTATTCGGCTTGGGA	59.194	50.000	0.00	0.00	0.00	4.37
2552	2639	4.697756	CCGCGCTCCCAGGTTTCA	62.698	66.667	5.56	0.00	0.00	2.69
2826	2970	2.356553	GTGCTCGGTGTTGGCGTA	60.357	61.111	0.00	0.00	0.00	4.42
2828	2972	2.813908	GCTCGGTGTTGGCGTAGG	60.814	66.667	0.00	0.00	0.00	3.18
2841	2985	2.438434	GTAGGCATGGGCGCAGTT	60.438	61.111	10.83	0.00	42.47	3.16
2883	3027	2.103143	AAGATGAGGTCGCGCTCG	59.897	61.111	5.56	0.00	0.00	5.03
2912	3057	0.532862	CACGTCTTCACCTGCTGGTT	60.533	55.000	13.36	0.00	46.05	3.67
2930	3075	0.530288	TTCATCGTCGCCATGTCTGA	59.470	50.000	0.00	0.00	0.00	3.27
3166	3312	2.494870	GCTTTCTTGTTGCCATCAGGAT	59.505	45.455	0.00	0.00	36.89	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.757124	AATCCCGGGGATGGCAGTC	61.757	63.158	28.86	0.00	42.27	3.51
60	61	9.296400	TGAATGTTCACAAGTTAACTAAAAAGC	57.704	29.630	8.92	0.00	31.01	3.51
102	103	9.567776	TCTCAAAAGTGACAAACCTATCATTTA	57.432	29.630	0.00	0.00	0.00	1.40
182	196	6.341316	TCAGTTTCTATCTCATAAGCACCAC	58.659	40.000	0.00	0.00	0.00	4.16
244	262	2.040278	TGCTAGCCACTGTTTTGAGGAT	59.960	45.455	13.29	0.00	0.00	3.24
246	264	1.896220	TGCTAGCCACTGTTTTGAGG	58.104	50.000	13.29	0.00	0.00	3.86
278	297	0.544357	ACTCAAGGATGGACCGTGGA	60.544	55.000	0.00	0.00	45.72	4.02
279	298	0.324943	AACTCAAGGATGGACCGTGG	59.675	55.000	0.00	0.00	45.72	4.94
280	299	2.185004	AAACTCAAGGATGGACCGTG	57.815	50.000	0.00	0.00	46.75	4.94
281	300	3.775316	AGATAAACTCAAGGATGGACCGT	59.225	43.478	0.00	0.00	44.74	4.83
282	301	4.408182	AGATAAACTCAAGGATGGACCG	57.592	45.455	0.00	0.00	44.74	4.79
283	302	7.125792	TCTAAGATAAACTCAAGGATGGACC	57.874	40.000	0.00	0.00	39.35	4.46
316	335	1.012086	CCGTCATGCTCAAGGATGTG	58.988	55.000	10.74	5.73	43.25	3.21
317	336	0.904649	TCCGTCATGCTCAAGGATGT	59.095	50.000	10.74	0.00	43.25	3.06
331	350	5.398416	GCTTTCTGTTGTGTATTTTTCCGTC	59.602	40.000	0.00	0.00	0.00	4.79
368	388	1.542915	GATGCTTTCCACTGCACACAT	59.457	47.619	0.00	0.00	42.26	3.21
407	427	4.965158	GCGAAGAGATATATAGCTGCGTAC	59.035	45.833	4.97	0.00	0.00	3.67
408	428	4.260253	CGCGAAGAGATATATAGCTGCGTA	60.260	45.833	17.45	0.00	37.34	4.42
409	429	3.486043	CGCGAAGAGATATATAGCTGCGT	60.486	47.826	17.45	4.63	37.34	5.24
410	430	3.032498	CGCGAAGAGATATATAGCTGCG	58.968	50.000	13.68	13.68	35.74	5.18
411	431	3.367607	CCGCGAAGAGATATATAGCTGC	58.632	50.000	8.23	1.70	0.00	5.25
412	432	3.367607	GCCGCGAAGAGATATATAGCTG	58.632	50.000	8.23	0.00	0.00	4.24
413	433	2.032302	CGCCGCGAAGAGATATATAGCT	59.968	50.000	8.23	0.00	0.00	3.32
415	435	3.609475	GACGCCGCGAAGAGATATATAG	58.391	50.000	21.79	0.00	0.00	1.31
416	436	2.030091	CGACGCCGCGAAGAGATATATA	59.970	50.000	21.79	0.00	0.00	0.86
417	437	1.202043	CGACGCCGCGAAGAGATATAT	60.202	52.381	21.79	0.00	0.00	0.86
418	438	0.165295	CGACGCCGCGAAGAGATATA	59.835	55.000	21.79	0.00	0.00	0.86
419	439	1.082038	CGACGCCGCGAAGAGATAT	60.082	57.895	21.79	0.00	0.00	1.63
420	440	1.985447	AACGACGCCGCGAAGAGATA	61.985	55.000	21.79	0.00	39.95	1.98
551	595	3.043713	CAGCGCTCTTCCGTTGCA	61.044	61.111	7.13	0.00	32.99	4.08
556	600	2.884685	CTCTGCAGCGCTCTTCCG	60.885	66.667	7.13	0.00	0.00	4.30
563	607	4.724602	TCACCGTCTCTGCAGCGC	62.725	66.667	9.47	0.00	0.00	5.92
639	683	7.806487	CCTCGTGTTAAAATCTTAAAAAGGTCC	59.194	37.037	0.00	0.00	0.00	4.46
688	736	3.295228	CTTTTGTCTCCACGCGCGG	62.295	63.158	35.22	22.11	0.00	6.46
730	778	5.221362	TGCTTTAGCCTTAGCATCACGTATA	60.221	40.000	0.00	0.00	42.12	1.47
755	803	0.721718	GCCAGTATGAACTCACGTGC	59.278	55.000	11.67	0.00	39.69	5.34
760	808	1.281577	TGCCATGCCAGTATGAACTCA	59.718	47.619	0.00	0.00	39.69	3.41
848	896	2.096248	CTCGGAGTAGAGTTGGAAGCT	58.904	52.381	0.00	0.00	33.75	3.74
857	905	0.814457	ACTGCAAGCTCGGAGTAGAG	59.186	55.000	0.00	0.00	35.58	2.43
862	910	0.386478	GCAAAACTGCAAGCTCGGAG	60.386	55.000	0.00	0.00	37.60	4.63
863	911	0.819259	AGCAAAACTGCAAGCTCGGA	60.819	50.000	0.00	0.00	37.60	4.55
933	997	6.551385	AATCGATCAGTTAATGCTCAATCC	57.449	37.500	0.00	0.00	0.00	3.01
974	1038	0.043138	GCGTTTGTGTTTGCATGCAC	60.043	50.000	22.58	10.94	36.26	4.57
975	1039	0.459063	TGCGTTTGTGTTTGCATGCA	60.459	45.000	18.46	18.46	31.31	3.96
976	1040	0.230260	CTGCGTTTGTGTTTGCATGC	59.770	50.000	11.82	11.82	36.64	4.06
977	1041	0.854062	CCTGCGTTTGTGTTTGCATG	59.146	50.000	0.00	0.00	36.64	4.06
1316	1381	3.349006	CCAGTATGATGCGGCGGC	61.349	66.667	9.78	9.68	39.69	6.53
1354	1419	4.509737	GGACTCGGTGTAGGCGGC	62.510	72.222	0.00	0.00	0.00	6.53
1355	1420	1.452651	TAGGACTCGGTGTAGGCGG	60.453	63.158	0.00	0.00	0.00	6.13
1470	1538	0.833287	GCTTCCTGGTGATGAGCCTA	59.167	55.000	0.00	0.00	0.00	3.93
1872	1949	1.012086	CATCAGGATCTGTGTTGCCG	58.988	55.000	0.00	0.00	32.61	5.69
1881	1958	2.053244	GGTGGGATGACATCAGGATCT	58.947	52.381	17.08	0.00	0.00	2.75
2371	2448	9.436957	AATAGTATAAATTCAGGGCGAACTATG	57.563	33.333	0.00	0.00	36.12	2.23
2374	2451	6.204882	GCAATAGTATAAATTCAGGGCGAACT	59.795	38.462	0.00	0.00	36.12	3.01
2392	2469	7.824289	ACAATCACGGCTATATATTGCAATAGT	59.176	33.333	22.76	16.24	32.10	2.12
2393	2470	8.118607	CACAATCACGGCTATATATTGCAATAG	58.881	37.037	22.76	13.01	32.10	1.73
2519	2606	2.594592	GGCTGGAAACGTGTGCCT	60.595	61.111	0.00	0.00	40.36	4.75
2552	2639	0.467804	ATTTTTGTGCGTTTGGGGCT	59.532	45.000	0.00	0.00	0.00	5.19
2603	2693	2.880963	TGATGATCGCCGAACATGTA	57.119	45.000	14.83	1.01	0.00	2.29
2828	2972	4.789075	CTGCAACTGCGCCCATGC	62.789	66.667	18.07	18.07	45.83	4.06
2829	2973	4.789075	GCTGCAACTGCGCCCATG	62.789	66.667	4.18	1.40	45.83	3.66
2883	3027	1.079336	GAAGACGTGGTACCTGGCC	60.079	63.158	14.36	0.00	0.00	5.36
2912	3057	0.746659	ATCAGACATGGCGACGATGA	59.253	50.000	0.00	0.00	0.00	2.92
2930	3075	1.528824	CTGGCGTTCCTGATGGGAT	59.471	57.895	0.00	0.00	44.66	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.