AutoCloner

Multiple sequence alignment - TraesCS5B01G318500

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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	TraesCS5B01G318500	chr5B	100.000	3623	0	0	1	3623	503076770	503080392	0.000000e+00	6691.0
1	TraesCS5B01G318500	chr5B	84.956	1602	197	28	1031	2597	502376272	502377864	0.000000e+00	1583.0
2	TraesCS5B01G318500	chr5B	84.722	1584	208	18	1030	2597	502264842	502266407	0.000000e+00	1554.0
3	TraesCS5B01G318500	chr5B	81.281	609	112	2	1986	2593	503085917	503086524	3.250000e-135	492.0
4	TraesCS5B01G318500	chr5D	91.489	2761	169	18	830	3575	416172774	416175483	0.000000e+00	3736.0
5	TraesCS5B01G318500	chr5D	85.836	1645	192	22	996	2619	468340468	468342092	0.000000e+00	1709.0
6	TraesCS5B01G318500	chr5D	85.315	1539	189	27	1086	2597	415768273	415769801	0.000000e+00	1555.0
7	TraesCS5B01G318500	chr5D	84.955	1542	206	14	1068	2597	415746270	415747797	0.000000e+00	1539.0
8	TraesCS5B01G318500	chr5D	86.057	918	116	8	997	1909	416199522	416200432	0.000000e+00	976.0
9	TraesCS5B01G318500	chr5D	94.173	635	33	2	3	634	416171675	416172308	0.000000e+00	965.0
10	TraesCS5B01G318500	chr5D	98.352	182	3	0	650	831	416172563	416172744	1.620000e-83	320.0
11	TraesCS5B01G318500	chr5A	95.253	1917	71	7	833	2737	528890609	528892517	0.000000e+00	3018.0
12	TraesCS5B01G318500	chr5A	84.200	1538	207	27	1086	2597	528490021	528488494	0.000000e+00	1461.0
13	TraesCS5B01G318500	chr5A	95.506	890	36	4	2737	3623	528894874	528895762	0.000000e+00	1419.0
14	TraesCS5B01G318500	chr5A	91.681	601	33	2	3	603	528889441	528890024	0.000000e+00	817.0
15	TraesCS5B01G318500	chr5A	83.191	351	57	2	1986	2335	528912290	528912639	1.620000e-83	320.0
16	TraesCS5B01G318500	chr5A	95.745	188	6	2	644	831	528890392	528890577	5.880000e-78	302.0
17	TraesCS5B01G318500	chr5A	98.611	72	1	0	563	634	528890027	528890098	1.060000e-25	128.0
18	TraesCS5B01G318500	chr5A	74.545	165	34	7	2285	2445	495587144	495586984	8.400000e-07	65.8
19	TraesCS5B01G318500	chr1D	73.899	318	68	6	311	615	490573781	490574096	2.960000e-21	113.0
20	TraesCS5B01G318500	chr7D	82.400	125	20	2	345	469	126064721	126064599	1.380000e-19	108.0
21	TraesCS5B01G318500	chr7D	84.722	72	10	1	3059	3130	214991469	214991539	1.800000e-08	71.3
22	TraesCS5B01G318500	chr2B	75.107	233	48	9	327	557	424333838	424333614	2.300000e-17	100.0
23	TraesCS5B01G318500	chr7A	91.837	49	4	0	143	191	719970014	719969966	6.490000e-08	69.4
24	TraesCS5B01G318500	chr4A	91.837	49	4	0	143	191	738403321	738403273	6.490000e-08	69.4
25	TraesCS5B01G318500	chr3B	83.099	71	9	3	400	470	770957843	770957910	1.090000e-05	62.1
26	TraesCS5B01G318500	chr2A	100.000	28	0	0	531	558	93997285	93997258	7.000000e-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	TraesCS5B01G318500	chr5B	503076770	503080392	3622	False	6691.000000	6691	100.000000	1	3623	1	chr5B.!!$F3	3622
1	TraesCS5B01G318500	chr5B	502376272	502377864	1592	False	1583.000000	1583	84.956000	1031	2597	1	chr5B.!!$F2	1566
2	TraesCS5B01G318500	chr5B	502264842	502266407	1565	False	1554.000000	1554	84.722000	1030	2597	1	chr5B.!!$F1	1567
3	TraesCS5B01G318500	chr5B	503085917	503086524	607	False	492.000000	492	81.281000	1986	2593	1	chr5B.!!$F4	607
4	TraesCS5B01G318500	chr5D	468340468	468342092	1624	False	1709.000000	1709	85.836000	996	2619	1	chr5D.!!$F4	1623
5	TraesCS5B01G318500	chr5D	416171675	416175483	3808	False	1673.666667	3736	94.671333	3	3575	3	chr5D.!!$F5	3572
6	TraesCS5B01G318500	chr5D	415768273	415769801	1528	False	1555.000000	1555	85.315000	1086	2597	1	chr5D.!!$F2	1511
7	TraesCS5B01G318500	chr5D	415746270	415747797	1527	False	1539.000000	1539	84.955000	1068	2597	1	chr5D.!!$F1	1529
8	TraesCS5B01G318500	chr5D	416199522	416200432	910	False	976.000000	976	86.057000	997	1909	1	chr5D.!!$F3	912
9	TraesCS5B01G318500	chr5A	528488494	528490021	1527	True	1461.000000	1461	84.200000	1086	2597	1	chr5A.!!$R2	1511
10	TraesCS5B01G318500	chr5A	528889441	528895762	6321	False	1136.800000	3018	95.359200	3	3623	5	chr5A.!!$F2	3620

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
964	1327	0.321653	AATCGGACAACACAGCCTCC	60.322	55.0	0.00	0.0	0.00	4.3	F
1731	2100	0.323542	AGAGGATCGACGTCCAGGTT	60.324	55.0	10.58	0.0	42.67	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2153	2567	0.743345	CAGCACCGCCTTAAGGTACC	60.743	60.0	22.55	2.73	40.59	3.34	R
2985	5765	1.032014	TGATGATCTCGTGGCGATGA	58.968	50.0	0.00	0.00	34.61	2.92	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
29	30	1.177401	GCCACCAAATCCAGTTCCTC	58.823	55.000	0.00	0.00	0.00	3.71
32	33	0.400213	ACCAAATCCAGTTCCTCGCA	59.600	50.000	0.00	0.00	0.00	5.10
45	46	1.077501	CTCGCACATCCCACCCATT	60.078	57.895	0.00	0.00	0.00	3.16
67	68	4.610333	TCCAGTCCTCAGATTTGCTACTA	58.390	43.478	0.00	0.00	0.00	1.82
85	86	0.685097	TAATGCCTCCATAGTCGGCC	59.315	55.000	0.00	0.00	43.12	6.13
194	195	0.622665	CCTGGATGGCCTTGAGAACT	59.377	55.000	3.32	0.00	34.31	3.01
213	214	1.598132	CTACGGTGATGTCGTCGATCT	59.402	52.381	0.00	0.00	41.38	2.75
315	316	4.782019	TCATGGCCATACAAAGAACAAC	57.218	40.909	20.30	0.00	0.00	3.32
319	320	3.568007	TGGCCATACAAAGAACAACAGAC	59.432	43.478	0.00	0.00	0.00	3.51
382	386	0.814457	CTAGAAGCACTGGAGCGAGT	59.186	55.000	0.00	0.00	40.15	4.18
393	397	0.674895	GGAGCGAGTTGAAGGCACAT	60.675	55.000	0.00	0.00	0.00	3.21
417	421	0.684805	GTCATCGTCCCTCCCTCACT	60.685	60.000	0.00	0.00	0.00	3.41
431	435	1.621814	CCTCACTGGAGACGGGTAAAA	59.378	52.381	0.00	0.00	44.26	1.52
441	445	2.946990	AGACGGGTAAAACCTTGTTGTG	59.053	45.455	0.00	0.00	38.64	3.33
463	467	4.343814	TGGTAGACAGTTGAGACATTGTCA	59.656	41.667	18.57	0.00	41.74	3.58
471	475	5.410746	CAGTTGAGACATTGTCATGCTAAGT	59.589	40.000	18.57	6.37	34.60	2.24
514	518	3.944422	ACAACAACTGTCGTCAATGAC	57.056	42.857	2.75	2.75	39.37	3.06
634	681	4.717877	TCCGTCGGAGTTGTATATAGGAA	58.282	43.478	10.71	0.00	0.00	3.36
637	968	5.334724	CCGTCGGAGTTGTATATAGGAAGAC	60.335	48.000	4.91	0.00	0.00	3.01
642	973	6.294065	CGGAGTTGTATATAGGAAGACTGACC	60.294	46.154	0.00	0.00	0.00	4.02
643	974	6.778559	GGAGTTGTATATAGGAAGACTGACCT	59.221	42.308	6.68	6.68	39.95	3.85
644	975	7.943447	GGAGTTGTATATAGGAAGACTGACCTA	59.057	40.741	10.00	10.00	41.99	3.08
646	977	9.884814	AGTTGTATATAGGAAGACTGACCTATT	57.115	33.333	19.77	13.11	44.13	1.73
660	992	7.554476	AGACTGACCTATTTCTTTTGATTAGCC	59.446	37.037	0.00	0.00	0.00	3.93
662	994	7.554476	ACTGACCTATTTCTTTTGATTAGCCTC	59.446	37.037	0.00	0.00	0.00	4.70
824	1156	1.454847	TTGGCCTCGTTGCAAAGGT	60.455	52.632	16.71	0.00	34.96	3.50
863	1226	0.635731	GACGAAATCACGAGCGACAG	59.364	55.000	0.00	0.00	37.03	3.51
962	1325	0.606401	CCAATCGGACAACACAGCCT	60.606	55.000	0.00	0.00	0.00	4.58
963	1326	0.798776	CAATCGGACAACACAGCCTC	59.201	55.000	0.00	0.00	0.00	4.70
964	1327	0.321653	AATCGGACAACACAGCCTCC	60.322	55.000	0.00	0.00	0.00	4.30
965	1328	1.480212	ATCGGACAACACAGCCTCCA	61.480	55.000	0.00	0.00	0.00	3.86
966	1329	1.669115	CGGACAACACAGCCTCCAG	60.669	63.158	0.00	0.00	0.00	3.86
967	1330	1.451936	GGACAACACAGCCTCCAGT	59.548	57.895	0.00	0.00	0.00	4.00
968	1331	0.685097	GGACAACACAGCCTCCAGTA	59.315	55.000	0.00	0.00	0.00	2.74
969	1332	1.338200	GGACAACACAGCCTCCAGTAG	60.338	57.143	0.00	0.00	0.00	2.57
1076	1439	1.003580	TGTTGTCATCAGGAAGGCTCC	59.996	52.381	0.00	0.00	42.81	4.70
1191	1560	1.730487	CGAGCTGCACTCTCGGTAT	59.270	57.895	20.17	0.00	46.82	2.73
1215	1584	1.366366	CGACGGTGGTCTCCTGTTT	59.634	57.895	0.00	0.00	41.16	2.83
1614	1983	2.200899	GCGGAGAAGATGAAAGAGCTC	58.799	52.381	5.27	5.27	0.00	4.09
1650	2019	1.002624	GTTCATGTCGGGGCTCCAA	60.003	57.895	1.96	0.00	0.00	3.53
1698	2067	1.890573	GCAAAGATGGTTAGGTGGGCA	60.891	52.381	0.00	0.00	0.00	5.36
1731	2100	0.323542	AGAGGATCGACGTCCAGGTT	60.324	55.000	10.58	0.00	42.67	3.50
2147	2561	2.158740	TCGAGGAAGACGATCTGAGGAT	60.159	50.000	0.00	0.00	34.85	3.24
2153	2567	2.246469	AGACGATCTGAGGATGATGGG	58.754	52.381	0.00	0.00	31.46	4.00
2718	3132	6.925165	AGAATGTAATGCAAAAAGTGTCCTTG	59.075	34.615	0.00	0.00	0.00	3.61
2729	3143	7.518848	GCAAAAAGTGTCCTTGGAAATGATTTC	60.519	37.037	9.36	9.36	38.94	2.17
2805	5576	6.500684	TTCATTCCTCGAAATTCCTTTGAG	57.499	37.500	0.00	0.00	43.05	3.02
2914	5692	0.615331	AAGATTCAGAGAAGCGCCCA	59.385	50.000	2.29	0.00	0.00	5.36
2936	5714	2.611518	GCCTCCTATCGATTCCATTCG	58.388	52.381	1.71	0.00	40.46	3.34
2941	5719	1.006825	TATCGATTCCATTCGCGCCG	61.007	55.000	1.71	0.00	38.97	6.46
2985	5765	3.819877	GACCGTTGACGCAACCCCT	62.820	63.158	14.31	1.07	40.82	4.79
3043	5823	2.415491	CCTCCGGCGAAATTTTTCTTCC	60.415	50.000	9.30	2.43	35.07	3.46
3066	5849	0.988063	TCCCATCCGGTCATTGTTGA	59.012	50.000	0.00	0.00	0.00	3.18
3171	5954	1.601903	CACGTACACAACAACCTGCAT	59.398	47.619	0.00	0.00	0.00	3.96
3176	5959	4.024387	CGTACACAACAACCTGCATAAAGT	60.024	41.667	0.00	0.00	0.00	2.66
3199	5982	6.071616	AGTGACCTAGAGAAAAGCTTCTACAG	60.072	42.308	0.00	0.00	42.19	2.74
3230	6013	1.202915	ACATGACAACAGGCACCATCA	60.203	47.619	0.00	0.00	0.00	3.07
3233	6016	0.250901	GACAACAGGCACCATCACCT	60.251	55.000	0.00	0.00	36.45	4.00
3239	6022	1.942657	CAGGCACCATCACCTATTTCG	59.057	52.381	0.00	0.00	33.38	3.46
3325	6108	9.108284	ACATTCAAACAAAGAATTACCCAAAAG	57.892	29.630	0.00	0.00	33.64	2.27
3341	6124	2.119484	AAAGGTCGCCCGTGGATGAA	62.119	55.000	0.00	0.00	35.12	2.57
3417	6201	8.680903	CACAGAGCCTCTATCAAATTATTTTGT	58.319	33.333	0.00	1.87	42.37	2.83
3487	6271	1.537202	AGAAGTCATTGTTCGCCTTGC	59.463	47.619	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.736192	GGATTTGGTGGCACGAAATTTG	59.264	45.455	31.88	0.00	36.80	2.32
1	2	2.366916	TGGATTTGGTGGCACGAAATTT	59.633	40.909	31.88	18.40	36.80	1.82
20	21	1.450312	GGGATGTGCGAGGAACTGG	60.450	63.158	0.00	0.00	41.55	4.00
29	30	2.120909	GGAATGGGTGGGATGTGCG	61.121	63.158	0.00	0.00	0.00	5.34
32	33	0.625849	GACTGGAATGGGTGGGATGT	59.374	55.000	0.00	0.00	0.00	3.06
45	46	3.445008	AGTAGCAAATCTGAGGACTGGA	58.555	45.455	0.00	0.00	0.00	3.86
85	86	0.543749	GGAGGAGTTGACCCATGGAG	59.456	60.000	15.22	5.95	0.00	3.86
138	139	0.677288	TAGAAGGTGGTGACGGTGTG	59.323	55.000	0.00	0.00	0.00	3.82
194	195	1.329599	CAGATCGACGACATCACCGTA	59.670	52.381	0.00	0.00	40.67	4.02
213	214	5.391843	CGTCAAACCATCATATGAAGCAACA	60.392	40.000	9.99	0.00	0.00	3.33
315	316	3.425227	GGGCGTAATTTTTGGTACGTCTG	60.425	47.826	7.63	0.00	40.01	3.51
319	320	3.768468	ATGGGCGTAATTTTTGGTACG	57.232	42.857	0.00	0.00	38.76	3.67
366	370	0.319900	TCAACTCGCTCCAGTGCTTC	60.320	55.000	0.00	0.00	0.00	3.86
382	386	0.032815	TGACGACGATGTGCCTTCAA	59.967	50.000	0.00	0.00	0.00	2.69
393	397	2.110967	GGAGGGACGATGACGACGA	61.111	63.158	0.00	0.00	42.66	4.20
417	421	1.770061	ACAAGGTTTTACCCGTCTCCA	59.230	47.619	0.00	0.00	39.75	3.86
431	435	3.199071	TCAACTGTCTACCACAACAAGGT	59.801	43.478	0.00	0.00	43.14	3.50
441	445	4.883083	TGACAATGTCTCAACTGTCTACC	58.117	43.478	14.97	0.00	39.15	3.18
463	467	3.742640	GCTGATCCTTTCGGACTTAGCAT	60.743	47.826	0.00	0.00	43.51	3.79
471	475	0.036388	GGTGTGCTGATCCTTTCGGA	60.036	55.000	0.00	0.00	45.16	4.55
514	518	2.031807	TCCTTCTTATCGACGCTTCTCG	59.968	50.000	0.00	0.00	45.38	4.04
634	681	7.554476	GGCTAATCAAAAGAAATAGGTCAGTCT	59.446	37.037	0.00	0.00	0.00	3.24
637	968	7.554118	TGAGGCTAATCAAAAGAAATAGGTCAG	59.446	37.037	0.00	0.00	0.00	3.51
646	977	8.739972	GGTAAAATCTGAGGCTAATCAAAAGAA	58.260	33.333	0.00	0.00	0.00	2.52
648	980	8.286191	AGGTAAAATCTGAGGCTAATCAAAAG	57.714	34.615	0.00	0.00	0.00	2.27
863	1226	3.766151	TCCTGATCGTCACGTTGTAATC	58.234	45.455	0.00	0.00	0.00	1.75
962	1325	3.561528	CCTCACTACACTGGACTACTGGA	60.562	52.174	0.00	0.00	0.00	3.86
963	1326	2.755655	CCTCACTACACTGGACTACTGG	59.244	54.545	0.00	0.00	0.00	4.00
964	1327	3.440872	GTCCTCACTACACTGGACTACTG	59.559	52.174	0.00	0.00	43.91	2.74
965	1328	3.688235	GTCCTCACTACACTGGACTACT	58.312	50.000	0.00	0.00	43.91	2.57
969	1332	2.490115	CTCAGTCCTCACTACACTGGAC	59.510	54.545	0.00	0.00	46.67	4.02
1052	1415	3.776969	AGCCTTCCTGATGACAACATAGA	59.223	43.478	0.00	0.00	36.82	1.98
1076	1439	2.201436	CTTGCTGCTGCTTCTGCCTG	62.201	60.000	17.00	0.00	40.48	4.85
1112	1481	4.695231	CGACCAACGGACGCGACT	62.695	66.667	15.93	0.00	34.05	4.18
1206	1575	0.037882	CGAGCTGCAGAAACAGGAGA	60.038	55.000	20.43	0.00	38.16	3.71
1266	1635	1.764134	TGGTTCTTGTACAGGTCCGTT	59.236	47.619	4.75	0.00	0.00	4.44
1267	1636	1.069668	GTGGTTCTTGTACAGGTCCGT	59.930	52.381	4.75	0.00	0.00	4.69
1650	2019	4.070552	GGAAGCACGTCCTCCGCT	62.071	66.667	0.00	0.00	41.42	5.52
1680	2049	2.525368	GTTGCCCACCTAACCATCTTT	58.475	47.619	0.00	0.00	0.00	2.52
1698	2067	2.294078	CCTCTTCTCCAGCCCCGTT	61.294	63.158	0.00	0.00	0.00	4.44
1731	2100	0.468226	AGAACTTGTCCCACGCTTCA	59.532	50.000	0.00	0.00	0.00	3.02
1946	2345	2.622436	CAGAGGATCAAGGGAAACGAC	58.378	52.381	0.00	0.00	37.82	4.34
2121	2535	2.099921	CAGATCGTCTTCCTCGATGGTT	59.900	50.000	5.58	0.00	45.90	3.67
2147	2561	0.834612	CGCCTTAAGGTACCCCATCA	59.165	55.000	22.55	0.00	37.57	3.07
2153	2567	0.743345	CAGCACCGCCTTAAGGTACC	60.743	60.000	22.55	2.73	40.59	3.34
2493	2907	3.649277	CTCCCAGTCGAAGTGGCGG	62.649	68.421	9.22	1.58	37.37	6.13
2778	5549	5.741388	AGGAATTTCGAGGAATGAAATCG	57.259	39.130	1.84	0.00	43.35	3.34
2805	5576	8.467598	AGGAGTTTAAGGTTTTGAAAGTTCTTC	58.532	33.333	0.00	0.00	0.00	2.87
2853	5625	5.487488	TGGCTACTCAAATTAGGAAGAAGGA	59.513	40.000	0.00	0.00	0.00	3.36
2914	5692	1.633774	ATGGAATCGATAGGAGGCGT	58.366	50.000	0.00	0.00	0.00	5.68
2923	5701	2.310233	CGGCGCGAATGGAATCGAT	61.310	57.895	12.10	0.00	45.48	3.59
2985	5765	1.032014	TGATGATCTCGTGGCGATGA	58.968	50.000	0.00	0.00	34.61	2.92
3043	5823	2.378038	ACAATGACCGGATGGGAAATG	58.622	47.619	9.46	0.00	40.75	2.32
3066	5849	3.069318	GAACGACGGGGAGGAGCT	61.069	66.667	0.00	0.00	0.00	4.09
3171	5954	7.304497	AGAAGCTTTTCTCTAGGTCACTTTA	57.696	36.000	0.00	0.00	0.00	1.85
3176	5959	6.010850	TCTGTAGAAGCTTTTCTCTAGGTCA	58.989	40.000	0.00	0.00	32.72	4.02
3199	5982	3.664107	TGTTGTCATGTAAGTGCTCCTC	58.336	45.455	0.00	0.00	0.00	3.71
3341	6124	4.455877	AGTTGAGAAAATCGGCGAAATTCT	59.544	37.500	28.95	28.95	33.28	2.40
3417	6201	1.203313	GGGCCTAGGATGGATGACCTA	60.203	57.143	14.75	0.00	37.68	3.08
3499	6286	7.926018	GTCTCTCTCCATCTTATTCTTTCTTCC	59.074	40.741	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.