AutoCloner

Multiple sequence alignment - TraesCS6A01G032300

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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	TraesCS6A01G032300	chr6A	100.000	2171	0	0	985	3155	15940118	15937948	0.000000e+00	4010.0
1	TraesCS6A01G032300	chr6A	100.000	568	0	0	1	568	15941102	15940535	0.000000e+00	1050.0
2	TraesCS6A01G032300	chr6A	78.165	1264	246	24	985	2234	15914155	15912908	0.000000e+00	778.0
3	TraesCS6A01G032300	chr6A	76.180	869	168	30	1576	2424	15717384	15718233	3.760000e-114	422.0
4	TraesCS6A01G032300	chr6A	100.000	31	0	0	391	421	15940672	15940642	1.220000e-04	58.4
5	TraesCS6A01G032300	chr6A	100.000	31	0	0	431	461	15940712	15940682	1.220000e-04	58.4
6	TraesCS6A01G032300	chr6D	97.378	2174	51	4	985	3155	15358333	15356163	0.000000e+00	3694.0
7	TraesCS6A01G032300	chr6D	77.417	1169	246	16	1075	2234	7994185	7993026	0.000000e+00	680.0
8	TraesCS6A01G032300	chr6D	76.190	1218	255	28	1071	2267	18001535	18000332	7.480000e-171	610.0
9	TraesCS6A01G032300	chr6D	90.437	366	30	4	4	365	15359233	15358869	7.920000e-131	477.0
10	TraesCS6A01G032300	chr6B	96.425	2182	67	5	985	3155	27076982	27074801	0.000000e+00	3587.0
11	TraesCS6A01G032300	chr6B	82.061	1310	202	25	985	2268	26389194	26390496	0.000000e+00	1086.0
12	TraesCS6A01G032300	chr6B	78.411	1334	267	17	1072	2394	26500599	26501922	0.000000e+00	848.0
13	TraesCS6A01G032300	chr6B	76.935	1318	265	34	1086	2379	26841855	26840553	0.000000e+00	713.0
14	TraesCS6A01G032300	chr6B	90.137	365	32	3	4	365	27077609	27077246	3.680000e-129	472.0
15	TraesCS6A01G032300	chr6B	77.112	651	122	22	1743	2379	28495978	28496615	5.010000e-93	351.0
16	TraesCS6A01G032300	chr5D	79.858	1410	273	10	992	2394	27985489	27984084	0.000000e+00	1020.0
17	TraesCS6A01G032300	chr1A	78.696	1150	234	10	1072	2216	589248426	589247283	0.000000e+00	756.0
18	TraesCS6A01G032300	chr3B	77.475	1212	246	26	1070	2268	761047672	761046475	0.000000e+00	701.0
19	TraesCS6A01G032300	chr3B	91.566	83	7	0	1968	2050	819481780	819481862	7.150000e-22	115.0
20	TraesCS6A01G032300	chr3A	79.634	383	55	18	2254	2631	748565127	748565491	1.450000e-63	254.0

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	TraesCS6A01G032300	chr6A	15937948	15941102	3154	True	1294.2	4010	100.0000	1	3155	4	chr6A.!!$R2	3154
1	TraesCS6A01G032300	chr6A	15912908	15914155	1247	True	778.0	778	78.1650	985	2234	1	chr6A.!!$R1	1249
2	TraesCS6A01G032300	chr6A	15717384	15718233	849	False	422.0	422	76.1800	1576	2424	1	chr6A.!!$F1	848
3	TraesCS6A01G032300	chr6D	15356163	15359233	3070	True	2085.5	3694	93.9075	4	3155	2	chr6D.!!$R3	3151
4	TraesCS6A01G032300	chr6D	7993026	7994185	1159	True	680.0	680	77.4170	1075	2234	1	chr6D.!!$R1	1159
5	TraesCS6A01G032300	chr6D	18000332	18001535	1203	True	610.0	610	76.1900	1071	2267	1	chr6D.!!$R2	1196
6	TraesCS6A01G032300	chr6B	27074801	27077609	2808	True	2029.5	3587	93.2810	4	3155	2	chr6B.!!$R2	3151
7	TraesCS6A01G032300	chr6B	26389194	26390496	1302	False	1086.0	1086	82.0610	985	2268	1	chr6B.!!$F1	1283
8	TraesCS6A01G032300	chr6B	26500599	26501922	1323	False	848.0	848	78.4110	1072	2394	1	chr6B.!!$F2	1322
9	TraesCS6A01G032300	chr6B	26840553	26841855	1302	True	713.0	713	76.9350	1086	2379	1	chr6B.!!$R1	1293
10	TraesCS6A01G032300	chr6B	28495978	28496615	637	False	351.0	351	77.1120	1743	2379	1	chr6B.!!$F3	636
11	TraesCS6A01G032300	chr5D	27984084	27985489	1405	True	1020.0	1020	79.8580	992	2394	1	chr5D.!!$R1	1402
12	TraesCS6A01G032300	chr1A	589247283	589248426	1143	True	756.0	756	78.6960	1072	2216	1	chr1A.!!$R1	1144
13	TraesCS6A01G032300	chr3B	761046475	761047672	1197	True	701.0	701	77.4750	1070	2268	1	chr3B.!!$R1	1198

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
409	416	0.110056	CACTCAACGGTTGCATGAGC	60.11	55.0	15.89	0.0	43.41	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2340	2699	1.699634	ACATCATATCGGGGTTCAGGG	59.3	52.381	0.0	0.0	0.0	4.45	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
32	33	6.371809	GTTCATTTGAACCTACAACACTCA	57.628	37.500	11.54	0.00	46.42	3.41
65	66	9.528018	ACATTTTACAACCACTTGTTTTATCTG	57.472	29.630	0.00	0.00	41.15	2.90
75	76	6.039047	CCACTTGTTTTATCTGCTATCATGCT	59.961	38.462	0.00	0.00	0.00	3.79
89	90	3.535280	TCATGCTTGTATGCGGAGTTA	57.465	42.857	0.00	0.00	35.36	2.24
103	104	3.606687	CGGAGTTAATTGTTGGCTACCT	58.393	45.455	0.00	0.00	0.00	3.08
104	105	4.007659	CGGAGTTAATTGTTGGCTACCTT	58.992	43.478	0.00	0.00	0.00	3.50
156	157	1.237533	TGCGTTGAACATGCACTGAT	58.762	45.000	0.00	0.00	42.91	2.90
163	164	5.625251	GTTGAACATGCACTGATCACTAAG	58.375	41.667	8.04	0.00	36.50	2.18
176	177	8.773645	CACTGATCACTAAGTATTGTTTGTTGA	58.226	33.333	0.00	0.00	0.00	3.18
373	380	9.993454	AAAATAATAAATAGTACTCCCTCCGTC	57.007	33.333	0.00	0.00	0.00	4.79
375	382	8.896722	ATAATAAATAGTACTCCCTCCGTCAT	57.103	34.615	0.00	0.00	0.00	3.06
378	385	4.719026	ATAGTACTCCCTCCGTCATGTA	57.281	45.455	0.00	0.00	0.00	2.29
379	386	2.652590	AGTACTCCCTCCGTCATGTAC	58.347	52.381	0.00	0.00	0.00	2.90
380	387	2.241685	AGTACTCCCTCCGTCATGTACT	59.758	50.000	0.00	0.00	36.70	2.73
381	388	1.765230	ACTCCCTCCGTCATGTACTC	58.235	55.000	0.00	0.00	0.00	2.59
382	389	1.005569	ACTCCCTCCGTCATGTACTCA	59.994	52.381	0.00	0.00	0.00	3.41
383	390	2.100197	CTCCCTCCGTCATGTACTCAA	58.900	52.381	0.00	0.00	0.00	3.02
385	392	2.693591	TCCCTCCGTCATGTACTCAATC	59.306	50.000	0.00	0.00	0.00	2.67
386	393	2.430694	CCCTCCGTCATGTACTCAATCA	59.569	50.000	0.00	0.00	0.00	2.57
388	395	4.115516	CCTCCGTCATGTACTCAATCAAG	58.884	47.826	0.00	0.00	0.00	3.02
389	396	4.142160	CCTCCGTCATGTACTCAATCAAGA	60.142	45.833	0.00	0.00	0.00	3.02
390	397	4.744570	TCCGTCATGTACTCAATCAAGAC	58.255	43.478	0.00	0.00	0.00	3.01
391	398	4.219725	TCCGTCATGTACTCAATCAAGACA	59.780	41.667	0.00	0.00	33.67	3.41
392	399	4.327357	CCGTCATGTACTCAATCAAGACAC	59.673	45.833	0.00	0.00	33.67	3.67
393	400	5.164233	CGTCATGTACTCAATCAAGACACT	58.836	41.667	0.00	0.00	33.67	3.55
394	401	5.287274	CGTCATGTACTCAATCAAGACACTC	59.713	44.000	0.00	0.00	33.67	3.51
395	402	6.159293	GTCATGTACTCAATCAAGACACTCA	58.841	40.000	0.00	0.00	34.05	3.41
396	403	6.646653	GTCATGTACTCAATCAAGACACTCAA	59.353	38.462	0.00	0.00	34.05	3.02
397	404	6.646653	TCATGTACTCAATCAAGACACTCAAC	59.353	38.462	0.00	0.00	0.00	3.18
398	405	4.982295	TGTACTCAATCAAGACACTCAACG	59.018	41.667	0.00	0.00	0.00	4.10
399	406	3.393800	ACTCAATCAAGACACTCAACGG	58.606	45.455	0.00	0.00	0.00	4.44
400	407	3.181465	ACTCAATCAAGACACTCAACGGT	60.181	43.478	0.00	0.00	0.00	4.83
401	408	3.804036	TCAATCAAGACACTCAACGGTT	58.196	40.909	0.00	0.00	0.00	4.44
402	409	3.559655	TCAATCAAGACACTCAACGGTTG	59.440	43.478	14.62	14.62	0.00	3.77
403	410	1.295792	TCAAGACACTCAACGGTTGC	58.704	50.000	15.89	1.87	0.00	4.17
404	411	1.013596	CAAGACACTCAACGGTTGCA	58.986	50.000	15.89	4.67	0.00	4.08
405	412	1.603802	CAAGACACTCAACGGTTGCAT	59.396	47.619	15.89	3.59	0.00	3.96
408	415	1.195448	GACACTCAACGGTTGCATGAG	59.805	52.381	22.75	15.41	44.77	2.90
409	416	0.110056	CACTCAACGGTTGCATGAGC	60.110	55.000	15.89	0.00	43.41	4.26
410	417	1.237285	ACTCAACGGTTGCATGAGCC	61.237	55.000	15.89	1.32	43.41	4.70
411	418	1.926511	CTCAACGGTTGCATGAGCCC	61.927	60.000	15.89	0.00	41.13	5.19
439	741	1.535462	CAAACTAAGCCCACTCAACGG	59.465	52.381	0.00	0.00	0.00	4.44
468	770	0.816825	CCCAAGATGGCATCGTCCAG	60.817	60.000	21.01	9.25	39.89	3.86
504	806	0.807667	AGCAGAAACGCGAGCCATAG	60.808	55.000	15.93	0.00	36.85	2.23
550	856	2.821366	CTACGGCAGCCAAGCAGG	60.821	66.667	13.30	0.00	41.84	4.85
1037	1358	2.808315	CATCGTCTCCCACCTCCG	59.192	66.667	0.00	0.00	0.00	4.63
1344	1680	2.738521	CTGGCCTCCAACGTCGTG	60.739	66.667	3.32	0.00	30.80	4.35
1972	2312	3.008049	CAGGCCCAGGTACTATGTTATCC	59.992	52.174	0.00	0.00	36.02	2.59
2313	2661	1.538047	TGCCAGTTTCCTCATTGCTC	58.462	50.000	0.00	0.00	0.00	4.26
2436	2800	7.007723	TGTGTTTCTAACTAATGTTGGGGATT	58.992	34.615	0.00	0.00	37.59	3.01
2456	2820	2.127271	ATGGAAATCGGATGTGTGCA	57.873	45.000	0.00	0.00	0.00	4.57
2483	2847	3.993920	CAACTTTTGGATCAAACCAGGG	58.006	45.455	0.00	0.00	41.19	4.45
2641	3006	4.081586	AGGTAGTACTAAGCTTGCAGTTCC	60.082	45.833	9.86	6.81	0.00	3.62
2716	3081	5.590530	ACCAAGTTTGCAGTTCAATGTTA	57.409	34.783	0.00	0.00	34.12	2.41
2805	3170	9.822727	TTCTTTCCCCTTATTGTTCTAAAGATT	57.177	29.630	0.00	0.00	33.24	2.40
2806	3171	9.462606	TCTTTCCCCTTATTGTTCTAAAGATTC	57.537	33.333	0.00	0.00	29.39	2.52
2807	3172	9.243105	CTTTCCCCTTATTGTTCTAAAGATTCA	57.757	33.333	0.00	0.00	0.00	2.57
2978	3347	3.010027	TGGAGGTGCCATGAATAACAAGA	59.990	43.478	0.00	0.00	43.33	3.02
3081	3450	1.077644	AGCTTGCATGGAGCCAGAG	60.078	57.895	5.25	0.00	44.83	3.35
3082	3451	2.772691	GCTTGCATGGAGCCAGAGC	61.773	63.158	9.12	9.12	44.83	4.09
3150	3519	2.857152	CCGTTGTTCACAAAACCACATG	59.143	45.455	0.00	0.00	37.63	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	6.959639	ATGTTTTGATTGAGTGTTGTAGGT	57.040	33.333	0.00	0.00	0.00	3.08
32	33	8.785329	ACAAGTGGTTGTAAAATGTTTTGATT	57.215	26.923	1.16	0.00	45.48	2.57
64	65	2.145536	CCGCATACAAGCATGATAGCA	58.854	47.619	0.00	0.00	36.85	3.49
65	66	2.414481	CTCCGCATACAAGCATGATAGC	59.586	50.000	0.00	0.00	0.00	2.97
75	76	4.380023	GCCAACAATTAACTCCGCATACAA	60.380	41.667	0.00	0.00	0.00	2.41
89	90	6.987403	TTAGGAAAAAGGTAGCCAACAATT	57.013	33.333	0.00	0.00	0.00	2.32
124	125	8.379161	GCATGTTCAACGCAAAAATATGATTAA	58.621	29.630	0.00	0.00	0.00	1.40
130	131	5.118971	CAGTGCATGTTCAACGCAAAAATAT	59.881	36.000	0.00	0.00	37.41	1.28
137	138	1.197492	GATCAGTGCATGTTCAACGCA	59.803	47.619	0.00	0.00	0.00	5.24
139	140	2.481568	AGTGATCAGTGCATGTTCAACG	59.518	45.455	1.14	0.00	38.92	4.10
156	157	7.766738	TGTCACTCAACAAACAATACTTAGTGA	59.233	33.333	0.00	0.00	38.68	3.41
163	164	8.345565	AGAGAAATGTCACTCAACAAACAATAC	58.654	33.333	0.00	0.00	35.83	1.89
197	201	7.500559	AGGAGAAGACACCATATTAATTTGCTC	59.499	37.037	0.00	0.00	0.00	4.26
358	365	3.457380	AGTACATGACGGAGGGAGTACTA	59.543	47.826	0.00	0.00	40.02	1.82
360	367	2.617774	GAGTACATGACGGAGGGAGTAC	59.382	54.545	0.00	0.00	33.80	2.73
365	372	2.430694	TGATTGAGTACATGACGGAGGG	59.569	50.000	0.00	0.00	0.00	4.30
366	373	3.801114	TGATTGAGTACATGACGGAGG	57.199	47.619	0.00	0.00	0.00	4.30
367	374	4.800993	GTCTTGATTGAGTACATGACGGAG	59.199	45.833	0.00	0.00	33.80	4.63
368	375	4.219725	TGTCTTGATTGAGTACATGACGGA	59.780	41.667	0.00	0.00	41.11	4.69
369	376	4.327357	GTGTCTTGATTGAGTACATGACGG	59.673	45.833	0.00	0.00	41.11	4.79
370	377	5.164233	AGTGTCTTGATTGAGTACATGACG	58.836	41.667	0.00	0.00	41.11	4.35
371	378	6.159293	TGAGTGTCTTGATTGAGTACATGAC	58.841	40.000	0.00	0.00	39.74	3.06
372	379	6.345096	TGAGTGTCTTGATTGAGTACATGA	57.655	37.500	0.00	0.00	0.00	3.07
373	380	6.400409	CGTTGAGTGTCTTGATTGAGTACATG	60.400	42.308	0.00	0.00	0.00	3.21
375	382	4.982295	CGTTGAGTGTCTTGATTGAGTACA	59.018	41.667	0.00	0.00	0.00	2.90
378	385	3.181465	ACCGTTGAGTGTCTTGATTGAGT	60.181	43.478	0.00	0.00	0.00	3.41
379	386	3.393800	ACCGTTGAGTGTCTTGATTGAG	58.606	45.455	0.00	0.00	0.00	3.02
380	387	3.469008	ACCGTTGAGTGTCTTGATTGA	57.531	42.857	0.00	0.00	0.00	2.57
381	388	3.849645	GCAACCGTTGAGTGTCTTGATTG	60.850	47.826	15.63	0.00	0.00	2.67
382	389	2.290641	GCAACCGTTGAGTGTCTTGATT	59.709	45.455	15.63	0.00	0.00	2.57
383	390	1.873591	GCAACCGTTGAGTGTCTTGAT	59.126	47.619	15.63	0.00	0.00	2.57
385	392	1.013596	TGCAACCGTTGAGTGTCTTG	58.986	50.000	15.63	0.00	0.00	3.02
386	393	1.603802	CATGCAACCGTTGAGTGTCTT	59.396	47.619	15.63	0.00	0.00	3.01
388	395	1.195448	CTCATGCAACCGTTGAGTGTC	59.805	52.381	15.63	0.00	33.72	3.67
389	396	1.229428	CTCATGCAACCGTTGAGTGT	58.771	50.000	15.63	0.00	33.72	3.55
390	397	0.110056	GCTCATGCAACCGTTGAGTG	60.110	55.000	15.63	11.75	39.24	3.51
391	398	1.237285	GGCTCATGCAACCGTTGAGT	61.237	55.000	15.63	0.00	39.24	3.41
392	399	1.503542	GGCTCATGCAACCGTTGAG	59.496	57.895	15.63	9.46	41.91	3.02
393	400	1.971167	GGGCTCATGCAACCGTTGA	60.971	57.895	15.63	0.98	41.91	3.18
394	401	1.804396	TTGGGCTCATGCAACCGTTG	61.804	55.000	6.91	6.91	41.91	4.10
395	402	1.526575	CTTGGGCTCATGCAACCGTT	61.527	55.000	0.00	0.00	41.91	4.44
396	403	1.973281	CTTGGGCTCATGCAACCGT	60.973	57.895	0.00	0.00	41.91	4.83
397	404	1.033746	ATCTTGGGCTCATGCAACCG	61.034	55.000	0.00	0.00	41.91	4.44
398	405	0.458669	CATCTTGGGCTCATGCAACC	59.541	55.000	0.00	0.00	41.91	3.77
399	406	0.458669	CCATCTTGGGCTCATGCAAC	59.541	55.000	0.00	0.00	41.91	4.17
400	407	2.890612	CCATCTTGGGCTCATGCAA	58.109	52.632	0.00	0.00	41.91	4.08
401	408	4.670199	CCATCTTGGGCTCATGCA	57.330	55.556	0.00	0.00	41.91	3.96
409	416	2.947448	GCTTAGTTTGCCATCTTGGG	57.053	50.000	0.00	0.00	38.19	4.12
421	470	0.763035	ACCGTTGAGTGGGCTTAGTT	59.237	50.000	0.00	0.00	0.00	2.24
422	471	0.763035	AACCGTTGAGTGGGCTTAGT	59.237	50.000	0.00	0.00	0.00	2.24
439	741	0.458669	CCATCTTGGGCTCATGCAAC	59.541	55.000	0.00	0.00	41.91	4.17
504	806	1.375551	CCCGTACAGTTATGTTGGCC	58.624	55.000	0.00	0.00	41.01	5.36
507	809	1.392168	CGTGCCCGTACAGTTATGTTG	59.608	52.381	0.00	0.00	41.01	3.33
533	835	2.821366	CCTGCTTGGCTGCCGTAG	60.821	66.667	14.98	14.58	0.00	3.51
1014	1320	3.002583	TGGGAGACGATGCAGCCA	61.003	61.111	0.00	0.00	0.00	4.75
1584	1924	1.820519	ACCATACACAGCTTGGCAATG	59.179	47.619	0.00	0.00	33.66	2.82
1737	2077	2.100991	GCTTTGGCGGCGATCTTG	59.899	61.111	12.98	0.00	0.00	3.02
1972	2312	5.413499	CAATCCATTTGCCTTAAGGAACTG	58.587	41.667	26.21	17.74	40.86	3.16
2340	2699	1.699634	ACATCATATCGGGGTTCAGGG	59.300	52.381	0.00	0.00	0.00	4.45
2436	2800	3.274095	TGCACACATCCGATTTCCATA	57.726	42.857	0.00	0.00	0.00	2.74
2483	2847	3.153919	TGTTATGTCTGGTTTTCTGGGC	58.846	45.455	0.00	0.00	0.00	5.36
2764	3129	6.053005	GGGGAAAGAAAACAAAAGGTTAAGG	58.947	40.000	0.00	0.00	39.29	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.