AutoCloner

Multiple sequence alignment - TraesCS5D01G105800

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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	TraesCS5D01G105800	chr5D	100.000	3446	0	0	1	3446	119658149	119661594	0.000000e+00	6364.0
1	TraesCS5D01G105800	chr5B	93.533	2768	131	15	1	2767	132587165	132589885	0.000000e+00	4076.0
2	TraesCS5D01G105800	chr5B	93.501	677	41	2	2766	3440	132595229	132595904	0.000000e+00	1003.0
3	TraesCS5D01G105800	chr5B	95.000	40	2	0	1896	1935	132589085	132589124	2.870000e-06	63.9
4	TraesCS5D01G105800	chr5A	91.835	2768	185	13	1	2767	129748463	129751190	0.000000e+00	3821.0
5	TraesCS5D01G105800	chr5A	97.500	40	1	0	1896	1935	129750398	129750437	6.170000e-08	69.4
6	TraesCS5D01G105800	chr6D	85.587	2130	246	31	648	2767	1540282	1538204	0.000000e+00	2176.0
7	TraesCS5D01G105800	chr6D	84.956	1828	197	41	615	2433	8140100	8141858	0.000000e+00	1781.0
8	TraesCS5D01G105800	chr6D	80.565	283	45	7	1221	1500	803690	803965	3.480000e-50	209.0
9	TraesCS5D01G105800	chr6D	100.000	31	0	0	1905	1935	8141408	8141438	1.340000e-04	58.4
10	TraesCS5D01G105800	chr6B	83.906	2125	274	32	649	2767	5715712	5713650	0.000000e+00	1967.0
11	TraesCS5D01G105800	chr6B	84.792	1828	207	34	615	2438	15105596	15107356	0.000000e+00	1770.0
12	TraesCS5D01G105800	chr6B	85.882	680	90	6	2769	3446	437548838	437548163	0.000000e+00	719.0
13	TraesCS5D01G105800	chr6B	85.169	681	90	10	2770	3446	435842805	435842132	0.000000e+00	688.0
14	TraesCS5D01G105800	chr6A	84.314	1836	209	38	615	2438	8608597	8610365	0.000000e+00	1722.0
15	TraesCS5D01G105800	chr6A	83.933	1861	205	39	615	2438	8387490	8389293	0.000000e+00	1694.0
16	TraesCS5D01G105800	chr6A	79.643	280	50	5	1221	1500	286421	286693	9.760000e-46	195.0
17	TraesCS5D01G105800	chr6A	100.000	32	0	0	1904	1935	8388827	8388858	3.710000e-05	60.2
18	TraesCS5D01G105800	chr6A	100.000	31	0	0	1905	1935	8609907	8609937	1.340000e-04	58.4
19	TraesCS5D01G105800	chr7D	84.665	1402	162	26	648	2047	558888744	558887394	0.000000e+00	1349.0
20	TraesCS5D01G105800	chr7D	87.704	675	81	2	2093	2767	558848876	558848204	0.000000e+00	785.0
21	TraesCS5D01G105800	chr7D	88.871	638	69	2	2807	3443	378179826	378180462	0.000000e+00	784.0
22	TraesCS5D01G105800	chr7D	85.441	680	95	3	2769	3446	332729804	332729127	0.000000e+00	704.0
23	TraesCS5D01G105800	chr4D	89.065	631	65	2	2817	3446	98583822	98584449	0.000000e+00	780.0
24	TraesCS5D01G105800	chr2B	86.087	690	86	9	2761	3445	313203156	313203840	0.000000e+00	734.0
25	TraesCS5D01G105800	chr3B	87.112	644	74	6	2806	3446	431187227	431186590	0.000000e+00	721.0
26	TraesCS5D01G105800	chr7A	86.625	643	82	3	2807	3446	205515060	205515701	0.000000e+00	708.0
27	TraesCS5D01G105800	chr7A	80.072	276	43	8	1220	1495	8381342	8381605	9.760000e-46	195.0
28	TraesCS5D01G105800	chr7A	75.463	216	37	12	985	1194	8381133	8381338	1.320000e-14	91.6
29	TraesCS5D01G105800	chr4A	72.031	1044	209	52	219	1224	657194227	657195225	2.070000e-57	233.0

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	TraesCS5D01G105800	chr5D	119658149	119661594	3445	False	6364.00	6364	100.0000	1	3446	1	chr5D.!!$F1	3445
1	TraesCS5D01G105800	chr5B	132587165	132589885	2720	False	2069.95	4076	94.2665	1	2767	2	chr5B.!!$F2	2766
2	TraesCS5D01G105800	chr5B	132595229	132595904	675	False	1003.00	1003	93.5010	2766	3440	1	chr5B.!!$F1	674
3	TraesCS5D01G105800	chr5A	129748463	129751190	2727	False	1945.20	3821	94.6675	1	2767	2	chr5A.!!$F1	2766
4	TraesCS5D01G105800	chr6D	1538204	1540282	2078	True	2176.00	2176	85.5870	648	2767	1	chr6D.!!$R1	2119
5	TraesCS5D01G105800	chr6D	8140100	8141858	1758	False	919.70	1781	92.4780	615	2433	2	chr6D.!!$F2	1818
6	TraesCS5D01G105800	chr6B	5713650	5715712	2062	True	1967.00	1967	83.9060	649	2767	1	chr6B.!!$R1	2118
7	TraesCS5D01G105800	chr6B	15105596	15107356	1760	False	1770.00	1770	84.7920	615	2438	1	chr6B.!!$F1	1823
8	TraesCS5D01G105800	chr6B	437548163	437548838	675	True	719.00	719	85.8820	2769	3446	1	chr6B.!!$R3	677
9	TraesCS5D01G105800	chr6B	435842132	435842805	673	True	688.00	688	85.1690	2770	3446	1	chr6B.!!$R2	676
10	TraesCS5D01G105800	chr6A	8608597	8610365	1768	False	890.20	1722	92.1570	615	2438	2	chr6A.!!$F3	1823
11	TraesCS5D01G105800	chr6A	8387490	8389293	1803	False	877.10	1694	91.9665	615	2438	2	chr6A.!!$F2	1823
12	TraesCS5D01G105800	chr7D	558887394	558888744	1350	True	1349.00	1349	84.6650	648	2047	1	chr7D.!!$R3	1399
13	TraesCS5D01G105800	chr7D	558848204	558848876	672	True	785.00	785	87.7040	2093	2767	1	chr7D.!!$R2	674
14	TraesCS5D01G105800	chr7D	378179826	378180462	636	False	784.00	784	88.8710	2807	3443	1	chr7D.!!$F1	636
15	TraesCS5D01G105800	chr7D	332729127	332729804	677	True	704.00	704	85.4410	2769	3446	1	chr7D.!!$R1	677
16	TraesCS5D01G105800	chr4D	98583822	98584449	627	False	780.00	780	89.0650	2817	3446	1	chr4D.!!$F1	629
17	TraesCS5D01G105800	chr2B	313203156	313203840	684	False	734.00	734	86.0870	2761	3445	1	chr2B.!!$F1	684
18	TraesCS5D01G105800	chr3B	431186590	431187227	637	True	721.00	721	87.1120	2806	3446	1	chr3B.!!$R1	640
19	TraesCS5D01G105800	chr7A	205515060	205515701	641	False	708.00	708	86.6250	2807	3446	1	chr7A.!!$F1	639
20	TraesCS5D01G105800	chr4A	657194227	657195225	998	False	233.00	233	72.0310	219	1224	1	chr4A.!!$F1	1005

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
573	586	0.332972	GATGGCAGAAGAAGGGGGTT	59.667	55.0	0.0	0.0	0.0	4.11	F
1305	1356	0.890683	CCCAACATCAACTCCAAGGC	59.109	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1578	1630	0.739813	AATCGTAGCAAGACGGGCAC	60.740	55.0	6.07	0.0	43.12	5.01	R
3265	3369	1.237285	TTGCGAGCCTCCAAAGCTTC	61.237	55.0	0.00	0.0	41.75	3.86	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
63	64	8.997323	GCAATGAGCACTTCTTATCATAAGTAT	58.003	33.333	4.28	0.00	44.79	2.12
252	253	2.667470	GACACTCTATCCTACCAGGCA	58.333	52.381	0.00	0.00	34.61	4.75
285	286	4.107961	CCTCCCCCATTAAATATCCCAACT	59.892	45.833	0.00	0.00	0.00	3.16
301	302	1.321074	AACTCGGACCCTAGAAGCCG	61.321	60.000	9.84	9.84	44.83	5.52
318	319	1.232119	CCGAACCCACCTTACAACAC	58.768	55.000	0.00	0.00	0.00	3.32
475	486	1.550976	GGAACAGAGGAGGACATTCGT	59.449	52.381	0.00	0.00	0.00	3.85
506	517	2.168936	AGGAACTACAACGTTGGTCACA	59.831	45.455	30.34	10.27	36.02	3.58
541	553	2.711922	CGTTGGAGGAGACGGGGAG	61.712	68.421	0.00	0.00	35.74	4.30
573	586	0.332972	GATGGCAGAAGAAGGGGGTT	59.667	55.000	0.00	0.00	0.00	4.11
671	684	1.826385	CTAAATCGGGATCCATGGCC	58.174	55.000	15.23	2.88	0.00	5.36
689	703	2.936032	GGCTGGAGGAGGTTGGGT	60.936	66.667	0.00	0.00	0.00	4.51
901	924	7.747155	TCGATTTGGTTTTGGTAATACTTGA	57.253	32.000	0.00	0.00	0.00	3.02
906	929	7.883391	TTGGTTTTGGTAATACTTGACTTCA	57.117	32.000	0.00	0.00	0.00	3.02
944	968	4.893524	ACGATAGATAGGTGTCCATTCACA	59.106	41.667	0.00	0.00	38.84	3.58
1041	1081	2.739996	CCTCTCCTCTGCCGCCATT	61.740	63.158	0.00	0.00	0.00	3.16
1042	1082	1.523258	CTCTCCTCTGCCGCCATTG	60.523	63.158	0.00	0.00	0.00	2.82
1119	1169	1.524002	CGGATCCAGCAGTGATGGT	59.476	57.895	25.99	14.05	40.37	3.55
1212	1263	2.887568	GTCGCCATGGAGTCGCAG	60.888	66.667	18.40	0.00	0.00	5.18
1213	1264	3.068064	TCGCCATGGAGTCGCAGA	61.068	61.111	18.40	0.00	0.00	4.26
1224	1275	3.469970	TCGCAGACCATCCGCCAT	61.470	61.111	0.00	0.00	0.00	4.40
1225	1276	3.274586	CGCAGACCATCCGCCATG	61.275	66.667	0.00	0.00	0.00	3.66
1268	1319	2.355445	GATCGAGGATGACTGCGCCA	62.355	60.000	4.18	0.00	0.00	5.69
1305	1356	0.890683	CCCAACATCAACTCCAAGGC	59.109	55.000	0.00	0.00	0.00	4.35
1360	1411	0.904649	TCATGGCCAAGACAGTCGAT	59.095	50.000	10.96	0.00	0.00	3.59
1393	1444	1.582968	CACAGGTGTTGCTGCATCC	59.417	57.895	1.84	7.03	0.00	3.51
1477	1528	1.052124	TCGACCCTGACACCCACTTT	61.052	55.000	0.00	0.00	0.00	2.66
1563	1615	1.059584	TGTTCCCCTTCTGGCACTCA	61.060	55.000	0.00	0.00	0.00	3.41
1578	1630	2.289002	GCACTCAAATCTAGATTGGGCG	59.711	50.000	18.61	12.31	0.00	6.13
1594	1646	3.179265	CGTGCCCGTCTTGCTACG	61.179	66.667	0.00	0.00	42.49	3.51
1900	1957	5.589855	TGATTAACATGCGGAAACATCAGAT	59.410	36.000	0.00	0.00	0.00	2.90
1985	2065	3.190744	TCTCACACGATAGGTCACTTCAC	59.809	47.826	0.00	0.00	43.77	3.18
1992	2072	1.860676	TAGGTCACTTCACGTGTTGC	58.139	50.000	16.51	7.68	44.16	4.17
2037	2117	6.822667	ACACATCTTAATGCAAGACAATCA	57.177	33.333	0.00	0.00	46.01	2.57
2039	2119	7.660112	ACACATCTTAATGCAAGACAATCAAA	58.340	30.769	0.00	0.00	46.01	2.69
2109	2189	1.065418	ACCCTATGGTTCTTTCTGCCG	60.065	52.381	0.00	0.00	44.75	5.69
2186	2273	4.744137	CAGACTACTGCAGACATGATTAGC	59.256	45.833	23.35	6.22	37.33	3.09
2189	2276	1.482182	ACTGCAGACATGATTAGCGGA	59.518	47.619	23.35	0.00	35.62	5.54
2222	2310	6.019479	CGGAGGAGATTCGTAATTTCTTCAAG	60.019	42.308	10.12	0.00	32.05	3.02
2307	2407	3.203263	TCAGTAGAGGAGCATCTAGGTGT	59.797	47.826	4.60	0.00	32.49	4.16
2625	2726	8.547967	TGTTTTATCTTCAAGGTAGATGACAC	57.452	34.615	0.00	0.00	34.35	3.67
2647	2748	5.060816	CACGATGTTGCATAAACCATTTGAC	59.939	40.000	0.00	0.00	38.06	3.18
2725	2826	0.620556	GTGGCTCATCTCCTGGGAAA	59.379	55.000	0.00	0.00	0.00	3.13
2786	2887	2.159057	GGCTAAACCAATGCAATGGAGG	60.159	50.000	27.62	13.67	43.54	4.30
2790	2891	0.974010	ACCAATGCAATGGAGGCCAG	60.974	55.000	27.62	0.00	43.54	4.85
2863	2967	6.834451	TGGACTACTTGACCAAATAAAAACCA	59.166	34.615	0.00	0.00	37.54	3.67
2960	3064	4.977347	GTCTAGATAGTAGGCAGCGAAAAC	59.023	45.833	0.00	0.00	0.00	2.43
3039	3143	4.702131	AGATACAGAGATTTTTGGTGTGGC	59.298	41.667	0.00	0.00	0.00	5.01
3043	3147	2.158475	AGAGATTTTTGGTGTGGCTCCA	60.158	45.455	0.00	0.00	0.00	3.86
3118	3222	2.046892	GGCTGCACGAGTCCATGT	60.047	61.111	0.50	0.00	0.00	3.21
3211	3315	2.464796	TAGCCTCAATCGGGGTAGAA	57.535	50.000	0.00	0.00	35.98	2.10
3265	3369	0.689623	ACTCCTTGGCTCAACTCCAG	59.310	55.000	0.00	0.00	34.66	3.86
3281	3388	1.023513	CCAGAAGCTTTGGAGGCTCG	61.024	60.000	17.72	0.00	39.30	5.03
3291	3398	1.123077	TGGAGGCTCGCAAGTGATAT	58.877	50.000	8.69	0.00	39.48	1.63
3319	3427	4.019858	CAATCTAGGAGACACCACTCTCA	58.980	47.826	0.00	0.00	38.84	3.27
3419	3527	4.467438	TCACTCTCTCACAGATTTGGCATA	59.533	41.667	0.00	0.00	0.00	3.14
3432	3540	0.618458	TGGCATAGTGGTGGGAGAAC	59.382	55.000	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
252	253	3.090532	GGGGGAGGGTCGAGCAAT	61.091	66.667	17.59	3.89	0.00	3.56
301	302	5.506815	GCTTTTAGTGTTGTAAGGTGGGTTC	60.507	44.000	0.00	0.00	0.00	3.62
318	319	8.688747	AAGATAGGAAAGATGGATGCTTTTAG	57.311	34.615	0.00	0.00	35.83	1.85
385	386	4.587189	GTGGTAGCGGCTAGGCGG	62.587	72.222	35.68	19.86	38.18	6.13
475	486	3.521560	GTTGTAGTTCCTCGATGCATCA	58.478	45.455	25.70	12.22	0.00	3.07
506	517	1.518572	CGCCGACCTTCGCAAGTAT	60.519	57.895	0.00	0.00	38.82	2.12
541	553	1.130054	TGCCATCTCCTCTATGCCCC	61.130	60.000	0.00	0.00	0.00	5.80
655	668	2.431683	CGGCCATGGATCCCGATT	59.568	61.111	20.96	0.00	44.55	3.34
671	684	4.101448	CCCAACCTCCTCCAGCCG	62.101	72.222	0.00	0.00	0.00	5.52
689	703	2.763215	GTGCAACCCCATCCCTCA	59.237	61.111	0.00	0.00	0.00	3.86
759	781	4.973317	CCAGTGGTGGCACTTTTACAAAAG	60.973	45.833	18.45	11.90	43.01	2.27
886	909	9.362151	AGGAAATGAAGTCAAGTATTACCAAAA	57.638	29.630	0.00	0.00	0.00	2.44
901	924	5.547465	TCGTACATCACAAGGAAATGAAGT	58.453	37.500	0.00	0.00	32.05	3.01
906	929	8.307483	CCTATCTATCGTACATCACAAGGAAAT	58.693	37.037	0.00	0.00	0.00	2.17
944	968	2.799126	TTATTGAGTCGGGGCAACAT	57.201	45.000	0.00	0.00	39.74	2.71
1119	1169	4.007644	CACCTGCCTCTGCGGTCA	62.008	66.667	0.00	0.00	42.66	4.02
1220	1271	2.512515	GGTCTGCGACTCCATGGC	60.513	66.667	6.96	0.00	32.47	4.40
1221	1272	0.531532	GATGGTCTGCGACTCCATGG	60.532	60.000	4.97	4.97	41.33	3.66
1222	1273	0.531532	GGATGGTCTGCGACTCCATG	60.532	60.000	7.14	0.00	41.33	3.66
1223	1274	1.826024	GGATGGTCTGCGACTCCAT	59.174	57.895	8.26	5.64	43.54	3.41
1224	1275	2.710902	CGGATGGTCTGCGACTCCA	61.711	63.158	13.37	5.41	41.93	3.86
1225	1276	2.105128	CGGATGGTCTGCGACTCC	59.895	66.667	8.26	7.46	41.93	3.85
1226	1277	2.583593	GCGGATGGTCTGCGACTC	60.584	66.667	8.26	0.70	41.93	3.36
1232	1283	0.179037	ATCATGTGGCGGATGGTCTG	60.179	55.000	0.00	0.00	0.00	3.51
1233	1284	0.107456	GATCATGTGGCGGATGGTCT	59.893	55.000	0.00	0.00	29.62	3.85
1268	1319	0.395724	GGGATCGGGATGCCTTTGTT	60.396	55.000	11.51	0.00	44.78	2.83
1360	1411	2.043115	ACCTGTGGATCCACTAGAGACA	59.957	50.000	37.92	19.93	46.30	3.41
1383	1434	1.002257	ATGGTGTCGGATGCAGCAA	60.002	52.632	3.51	0.00	45.53	3.91
1422	1473	0.833949	GTCCCAGATCTTGAGGTCCC	59.166	60.000	0.00	0.00	0.00	4.46
1563	1615	1.680338	GGCACGCCCAATCTAGATTT	58.320	50.000	15.49	0.00	0.00	2.17
1578	1630	0.739813	AATCGTAGCAAGACGGGCAC	60.740	55.000	6.07	0.00	43.12	5.01
1985	2065	5.685511	AGCTAATAAAACACAAAGCAACACG	59.314	36.000	0.00	0.00	32.42	4.49
2074	2154	1.722034	AGGGTGTCAGAGAGAAGCAA	58.278	50.000	0.00	0.00	0.00	3.91
2207	2294	6.310467	CGTTCTGGATCTTGAAGAAATTACGA	59.690	38.462	0.00	0.00	32.03	3.43
2222	2310	2.094182	TGGCAAGTAGTCGTTCTGGATC	60.094	50.000	0.00	0.00	0.00	3.36
2307	2407	8.039603	ACGAATACTAAGCATTCATTCAACAA	57.960	30.769	0.00	0.00	32.92	2.83
2625	2726	5.159925	TGTCAAATGGTTTATGCAACATCG	58.840	37.500	0.00	0.00	37.07	3.84
2696	2797	1.970640	AGATGAGCCACACACAGTACA	59.029	47.619	0.00	0.00	0.00	2.90
2725	2826	2.015587	GAAGTCGGTCTATCGTCTGGT	58.984	52.381	0.00	0.00	0.00	4.00
2767	2868	2.159057	GGCCTCCATTGCATTGGTTTAG	60.159	50.000	23.40	15.09	38.01	1.85
2786	2887	2.935201	CAAGTTGTATGAGAGCTCTGGC	59.065	50.000	23.91	8.39	39.06	4.85
2790	2891	5.584253	TCCTACAAGTTGTATGAGAGCTC	57.416	43.478	15.91	5.27	31.66	4.09
2813	2914	3.574826	CACCCCTCTAGACCTACTTATGC	59.425	52.174	0.00	0.00	0.00	3.14
2863	2967	6.153942	AGAACTAAAATAGGGAAAAGGCCT	57.846	37.500	0.00	0.00	0.00	5.19
3043	3147	2.459644	TGTACGGTAGCACCACCTATT	58.540	47.619	6.21	0.00	38.47	1.73
3137	3241	5.902431	AGATAAGGTAGCTTCTTCATGGACT	59.098	40.000	11.11	0.00	0.00	3.85
3265	3369	1.237285	TTGCGAGCCTCCAAAGCTTC	61.237	55.000	0.00	0.00	41.75	3.86
3281	3388	7.671302	TCCTAGATTGGTTAGATATCACTTGC	58.329	38.462	5.32	0.00	0.00	4.01
3291	3398	4.710375	GTGGTGTCTCCTAGATTGGTTAGA	59.290	45.833	0.00	0.00	37.07	2.10
3419	3527	0.324943	CCAATCGTTCTCCCACCACT	59.675	55.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.