AutoCloner

Multiple sequence alignment - TraesCS1D01G213400

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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	TraesCS1D01G213400	chr1D	100.000	2596	0	0	1	2596	298634506	298637101	0.000000e+00	4795.0
1	TraesCS1D01G213400	chr1D	84.795	855	84	29	614	1449	422820589	422819762	0.000000e+00	817.0
2	TraesCS1D01G213400	chr1D	84.888	847	68	32	739	1539	422737365	422736533	0.000000e+00	800.0
3	TraesCS1D01G213400	chr1D	91.341	589	39	5	1	577	23324124	23323536	0.000000e+00	795.0
4	TraesCS1D01G213400	chr1D	85.019	514	52	7	1047	1554	298265134	298264640	1.390000e-137	499.0
5	TraesCS1D01G213400	chr1D	78.927	261	47	5	1189	1445	298620029	298619773	1.240000e-38	171.0
6	TraesCS1D01G213400	chr1A	93.443	854	44	7	1750	2596	372531079	372531927	0.000000e+00	1256.0
7	TraesCS1D01G213400	chr1A	94.487	653	27	4	614	1258	372524517	372525168	0.000000e+00	998.0
8	TraesCS1D01G213400	chr1A	87.137	723	56	25	753	1449	518683279	518682568	0.000000e+00	785.0
9	TraesCS1D01G213400	chr1A	89.619	472	22	6	1253	1723	372530472	372530917	2.240000e-160	575.0
10	TraesCS1D01G213400	chr1B	95.324	556	15	6	641	1194	402066642	402067188	0.000000e+00	872.0
11	TraesCS1D01G213400	chr1B	89.286	644	48	12	1657	2292	402068663	402069293	0.000000e+00	787.0
12	TraesCS1D01G213400	chr1B	80.923	975	102	41	614	1539	571502159	571501220	0.000000e+00	693.0
13	TraesCS1D01G213400	chr1B	87.925	588	50	9	4	577	667044929	667044349	0.000000e+00	673.0
14	TraesCS1D01G213400	chr1B	97.101	276	8	0	1190	1465	402068109	402068384	1.410000e-127	466.0
15	TraesCS1D01G213400	chr1B	89.342	319	31	3	2281	2596	402094794	402095112	5.210000e-107	398.0
16	TraesCS1D01G213400	chr1B	91.855	221	7	4	1453	1668	402068401	402068615	5.430000e-77	298.0
17	TraesCS1D01G213400	chr1B	88.293	205	21	3	1004	1206	401190773	401190570	2.580000e-60	243.0
18	TraesCS1D01G213400	chr1B	79.231	260	48	4	1189	1445	402051012	402050756	2.660000e-40	176.0
19	TraesCS1D01G213400	chr5D	91.341	589	37	5	1	577	21254334	21253748	0.000000e+00	793.0
20	TraesCS1D01G213400	chr5D	91.252	583	37	6	1	571	543622127	543622707	0.000000e+00	782.0
21	TraesCS1D01G213400	chr7B	90.306	588	44	4	2	577	579567500	579566914	0.000000e+00	758.0
22	TraesCS1D01G213400	chr7B	85.455	165	22	2	2433	2596	722335279	722335116	1.240000e-38	171.0
23	TraesCS1D01G213400	chr7B	85.455	165	22	2	2433	2596	722592515	722592352	1.240000e-38	171.0
24	TraesCS1D01G213400	chr7B	90.698	43	4	0	575	617	615192960	615192918	1.000000e-04	58.4
25	TraesCS1D01G213400	chr7B	100.000	28	0	0	588	615	220880961	220880934	5.000000e-03	52.8
26	TraesCS1D01G213400	chr7D	89.761	586	47	5	1	577	590597644	590597063	0.000000e+00	737.0
27	TraesCS1D01G213400	chr7D	87.366	372	36	4	164	526	110655067	110654698	1.440000e-112	416.0
28	TraesCS1D01G213400	chr6D	88.448	580	52	6	1	571	322244704	322245277	0.000000e+00	686.0
29	TraesCS1D01G213400	chr3B	89.258	512	45	3	1	503	817248139	817247629	1.310000e-177	632.0
30	TraesCS1D01G213400	chr3B	86.667	270	32	1	312	577	778541474	778541205	1.950000e-76	296.0
31	TraesCS1D01G213400	chr3B	90.244	41	4	0	575	615	807226372	807226332	1.000000e-03	54.7
32	TraesCS1D01G213400	chr4A	88.915	433	38	3	1	423	651109421	651108989	2.290000e-145	525.0
33	TraesCS1D01G213400	chr4A	91.954	261	20	1	1	261	651131226	651130967	5.280000e-97	364.0
34	TraesCS1D01G213400	chr3A	82.815	611	63	13	1	571	564414021	564414629	2.300000e-140	508.0
35	TraesCS1D01G213400	chr2A	89.975	399	30	3	1	390	74098406	74098803	8.290000e-140	507.0
36	TraesCS1D01G213400	chr2B	85.714	84	7	4	2455	2536	3204270	3204190	1.660000e-12	84.2
37	TraesCS1D01G213400	chrUn	90.476	42	4	0	576	617	457566731	457566772	3.610000e-04	56.5

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	TraesCS1D01G213400	chr1D	298634506	298637101	2595	False	4795.00	4795	100.0000	1	2596	1	chr1D.!!$F1	2595
1	TraesCS1D01G213400	chr1D	422819762	422820589	827	True	817.00	817	84.7950	614	1449	1	chr1D.!!$R5	835
2	TraesCS1D01G213400	chr1D	422736533	422737365	832	True	800.00	800	84.8880	739	1539	1	chr1D.!!$R4	800
3	TraesCS1D01G213400	chr1D	23323536	23324124	588	True	795.00	795	91.3410	1	577	1	chr1D.!!$R1	576
4	TraesCS1D01G213400	chr1A	372524517	372525168	651	False	998.00	998	94.4870	614	1258	1	chr1A.!!$F1	644
5	TraesCS1D01G213400	chr1A	372530472	372531927	1455	False	915.50	1256	91.5310	1253	2596	2	chr1A.!!$F2	1343
6	TraesCS1D01G213400	chr1A	518682568	518683279	711	True	785.00	785	87.1370	753	1449	1	chr1A.!!$R1	696
7	TraesCS1D01G213400	chr1B	571501220	571502159	939	True	693.00	693	80.9230	614	1539	1	chr1B.!!$R3	925
8	TraesCS1D01G213400	chr1B	667044349	667044929	580	True	673.00	673	87.9250	4	577	1	chr1B.!!$R4	573
9	TraesCS1D01G213400	chr1B	402066642	402069293	2651	False	605.75	872	93.3915	641	2292	4	chr1B.!!$F2	1651
10	TraesCS1D01G213400	chr5D	21253748	21254334	586	True	793.00	793	91.3410	1	577	1	chr5D.!!$R1	576
11	TraesCS1D01G213400	chr5D	543622127	543622707	580	False	782.00	782	91.2520	1	571	1	chr5D.!!$F1	570
12	TraesCS1D01G213400	chr7B	579566914	579567500	586	True	758.00	758	90.3060	2	577	1	chr7B.!!$R2	575
13	TraesCS1D01G213400	chr7D	590597063	590597644	581	True	737.00	737	89.7610	1	577	1	chr7D.!!$R2	576
14	TraesCS1D01G213400	chr6D	322244704	322245277	573	False	686.00	686	88.4480	1	571	1	chr6D.!!$F1	570
15	TraesCS1D01G213400	chr3B	817247629	817248139	510	True	632.00	632	89.2580	1	503	1	chr3B.!!$R3	502
16	TraesCS1D01G213400	chr3A	564414021	564414629	608	False	508.00	508	82.8150	1	571	1	chr3A.!!$F1	570

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
270	295	0.465705	GATCCGATCTGAACCCAGCA	59.534	55.0	0.75	0.0	40.2	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1624	2714	1.230324	AAGTGCCAAAAGCTCGACTC	58.77	50.0	0.0	0.0	44.23	3.36	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
72	73	2.105993	GTCCCCATCCTATACCACCAAC	59.894	54.545	0.00	0.00	0.00	3.77
94	95	3.209812	CGTCTGCTCCGGATCCGA	61.210	66.667	35.42	19.41	42.83	4.55
137	145	6.445451	ACCTACATAGATGAGATTGCCATT	57.555	37.500	0.00	0.00	0.00	3.16
172	197	3.801307	TCCGTAGTAGATATCCAGGCA	57.199	47.619	0.00	0.00	0.00	4.75
201	226	4.819761	GATCCGACGCAGCCAGCA	62.820	66.667	0.00	0.00	46.13	4.41
270	295	0.465705	GATCCGATCTGAACCCAGCA	59.534	55.000	0.75	0.00	40.20	4.41
404	453	3.905678	CCCAGCGGCTCCTCGTAG	61.906	72.222	0.00	0.00	0.00	3.51
428	477	4.129737	CGTCCTGCGTCGGTGGAT	62.130	66.667	0.00	0.00	35.54	3.41
539	590	2.245438	GAGGGCTCGAAGGGAAGTGG	62.245	65.000	0.00	0.00	0.00	4.00
591	645	3.532501	CGCCTTGGGTGGTTTGTT	58.467	55.556	0.00	0.00	0.00	2.83
592	646	1.067250	CGCCTTGGGTGGTTTGTTG	59.933	57.895	0.00	0.00	0.00	3.33
593	647	1.445518	GCCTTGGGTGGTTTGTTGG	59.554	57.895	0.00	0.00	0.00	3.77
594	648	2.038814	GCCTTGGGTGGTTTGTTGGG	62.039	60.000	0.00	0.00	0.00	4.12
595	649	1.406860	CCTTGGGTGGTTTGTTGGGG	61.407	60.000	0.00	0.00	0.00	4.96
596	650	1.383248	TTGGGTGGTTTGTTGGGGG	60.383	57.895	0.00	0.00	0.00	5.40
597	651	3.238497	GGGTGGTTTGTTGGGGGC	61.238	66.667	0.00	0.00	0.00	5.80
598	652	3.611674	GGTGGTTTGTTGGGGGCG	61.612	66.667	0.00	0.00	0.00	6.13
599	653	4.293648	GTGGTTTGTTGGGGGCGC	62.294	66.667	0.00	0.00	0.00	6.53
600	654	4.531426	TGGTTTGTTGGGGGCGCT	62.531	61.111	7.64	0.00	0.00	5.92
601	655	3.989787	GGTTTGTTGGGGGCGCTG	61.990	66.667	7.64	0.00	0.00	5.18
602	656	4.662961	GTTTGTTGGGGGCGCTGC	62.663	66.667	7.64	0.00	0.00	5.25
603	657	4.912395	TTTGTTGGGGGCGCTGCT	62.912	61.111	7.64	0.00	0.00	4.24
612	666	4.853050	GGCGCTGCTGGAGATGCT	62.853	66.667	7.64	0.00	0.00	3.79
627	681	5.297029	TGGAGATGCTCTAATATATCGGACG	59.703	44.000	0.00	0.00	0.00	4.79
646	700	1.329906	CGAGGCTGTGATCTGATTTGC	59.670	52.381	0.00	0.00	0.00	3.68
672	730	1.207089	TGTAGGTTGAAGCCCTGATCG	59.793	52.381	0.00	0.00	33.35	3.69
829	893	1.234821	GAACTGGACGGAACATGCAA	58.765	50.000	0.00	0.00	0.00	4.08
1108	1213	4.357947	GCACGACCTGCTCCGTCA	62.358	66.667	0.00	0.00	43.33	4.35
1150	1255	3.249189	TTGCTCCTCCTGGCCGTT	61.249	61.111	0.00	0.00	0.00	4.44
1376	2406	2.922503	TGCTCGGCCTCAACCTCA	60.923	61.111	0.00	0.00	0.00	3.86
1465	2543	2.619177	CCCACACCACTAGATCGAGTAG	59.381	54.545	8.26	3.99	0.00	2.57
1490	2568	3.193903	TGATGTTGTCATGCCTGGATTTG	59.806	43.478	0.00	0.00	34.06	2.32
1548	2635	9.271828	GTTGTATTCTTTTGTTTCCCATGATTT	57.728	29.630	0.00	0.00	0.00	2.17
1624	2714	5.224562	TCAAAAGGTAATTTGTATCGCGG	57.775	39.130	6.13	0.00	40.40	6.46
1670	2819	7.882791	TGATATCGCCATTGTTAATTACCTGAT	59.117	33.333	0.00	0.00	0.00	2.90
1730	2880	5.310720	ACCTGAAAAGTGAAAACACTCAC	57.689	39.130	3.38	0.00	45.10	3.51
1762	2912	3.871006	TCTTGCGATCATGTATGAACCAC	59.129	43.478	0.00	0.00	40.69	4.16
1822	3111	5.784750	TGTTTCTAAGCAACATGAGATCG	57.215	39.130	0.00	0.00	0.00	3.69
1911	3200	6.436843	TTTCTCGGGAAAAAGAAGATATGC	57.563	37.500	8.32	0.00	38.35	3.14
1938	3227	2.754472	GGAGGAAATTGCACAAACCAC	58.246	47.619	0.00	0.00	0.00	4.16
2027	3316	8.035394	CCATCTATTAGTATAATCCGTTGCAGT	58.965	37.037	0.00	0.00	0.00	4.40
2029	3318	9.998106	ATCTATTAGTATAATCCGTTGCAGTTT	57.002	29.630	0.00	0.00	0.00	2.66
2151	3443	1.101049	AAAGCGGCCAATATCACCCG	61.101	55.000	2.24	0.00	43.38	5.28
2248	3542	9.528018	GTATTTTCTTGAAAACATGGAACTTCA	57.472	29.630	10.24	0.00	0.00	3.02
2414	3711	6.036577	ACAAAAGTTTGAATGTTGGTCAGT	57.963	33.333	10.66	0.00	40.55	3.41
2441	3738	0.955919	GTCAGCGGAGGAAAACCCAG	60.956	60.000	0.00	0.00	37.41	4.45
2451	3748	1.202348	GGAAAACCCAGCTACATGTGC	59.798	52.381	9.11	10.27	34.14	4.57
2465	3762	4.576216	ACATGTGCGGAAACATAAACAA	57.424	36.364	0.00	0.00	38.75	2.83
2474	3771	6.535150	TGCGGAAACATAAACAACAAATTGAA	59.465	30.769	0.00	0.00	39.30	2.69
2507	3804	3.452474	CCTCTGCAACTAGCTCATGTAC	58.548	50.000	0.00	0.00	45.94	2.90
2527	3824	5.597594	TGTACTGATGATGATCTTGCTCTCT	59.402	40.000	0.00	0.00	0.00	3.10
2557	3854	9.665719	TCATGAGCATTGTTATAGTAACAAAGA	57.334	29.630	16.41	6.43	42.57	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	73	2.356818	GATCCGGAGCAGACGAAGGG	62.357	65.000	16.44	0.00	0.00	3.95
94	95	2.357517	CGGTTCTTGGCTCGCTGT	60.358	61.111	0.00	0.00	0.00	4.40
137	145	0.611062	ACGGATGTCTTCTCGACCCA	60.611	55.000	0.00	0.00	42.13	4.51
201	226	3.637273	GGGGTGGTGGTCTTCGCT	61.637	66.667	0.00	0.00	0.00	4.93
270	295	4.452733	GCTACGCGGCAGGAGGTT	62.453	66.667	12.47	0.00	0.00	3.50
335	384	1.337821	CTACCTTTGTCGACGCTGTC	58.662	55.000	11.62	0.00	0.00	3.51
339	388	2.098831	GGGCTACCTTTGTCGACGC	61.099	63.158	11.62	5.93	0.00	5.19
428	477	3.054361	GGACTTCTTCCCCTTCAAGCATA	60.054	47.826	0.00	0.00	38.70	3.14
530	581	0.496841	AACCCTAGTCCCACTTCCCT	59.503	55.000	0.00	0.00	0.00	4.20
571	625	4.218686	AAACCACCCAAGGCGGCT	62.219	61.111	5.25	5.25	0.00	5.52
574	628	1.067250	CAACAAACCACCCAAGGCG	59.933	57.895	0.00	0.00	0.00	5.52
577	631	1.406860	CCCCCAACAAACCACCCAAG	61.407	60.000	0.00	0.00	0.00	3.61
578	632	1.383248	CCCCCAACAAACCACCCAA	60.383	57.895	0.00	0.00	0.00	4.12
579	633	2.283809	CCCCCAACAAACCACCCA	59.716	61.111	0.00	0.00	0.00	4.51
580	634	3.238497	GCCCCCAACAAACCACCC	61.238	66.667	0.00	0.00	0.00	4.61
581	635	3.611674	CGCCCCCAACAAACCACC	61.612	66.667	0.00	0.00	0.00	4.61
582	636	4.293648	GCGCCCCCAACAAACCAC	62.294	66.667	0.00	0.00	0.00	4.16
583	637	4.531426	AGCGCCCCCAACAAACCA	62.531	61.111	2.29	0.00	0.00	3.67
584	638	3.989787	CAGCGCCCCCAACAAACC	61.990	66.667	2.29	0.00	0.00	3.27
585	639	4.662961	GCAGCGCCCCCAACAAAC	62.663	66.667	2.29	0.00	0.00	2.93
586	640	4.912395	AGCAGCGCCCCCAACAAA	62.912	61.111	2.29	0.00	0.00	2.83
595	649	4.853050	AGCATCTCCAGCAGCGCC	62.853	66.667	2.29	0.00	0.00	6.53
596	650	3.270839	GAGCATCTCCAGCAGCGC	61.271	66.667	0.00	0.00	0.00	5.92
607	661	5.753744	CCTCGTCCGATATATTAGAGCATC	58.246	45.833	0.00	0.00	0.00	3.91
608	662	4.036971	GCCTCGTCCGATATATTAGAGCAT	59.963	45.833	0.00	0.00	0.00	3.79
609	663	3.377485	GCCTCGTCCGATATATTAGAGCA	59.623	47.826	0.00	0.00	0.00	4.26
610	664	3.628487	AGCCTCGTCCGATATATTAGAGC	59.372	47.826	0.00	0.00	0.00	4.09
611	665	4.636648	ACAGCCTCGTCCGATATATTAGAG	59.363	45.833	0.00	0.00	0.00	2.43
612	666	4.395231	CACAGCCTCGTCCGATATATTAGA	59.605	45.833	0.00	0.00	0.00	2.10
627	681	1.329906	CGCAAATCAGATCACAGCCTC	59.670	52.381	0.00	0.00	0.00	4.70
646	700	1.068541	GGGCTTCAACCTACAAAAGCG	60.069	52.381	0.00	0.00	43.91	4.68
672	730	3.485463	TTGATGACCGGGGATCAATAC	57.515	47.619	20.69	7.29	34.40	1.89
829	893	8.225603	AGCTTCAAATGTGTTTATATTCCGAT	57.774	30.769	0.00	0.00	0.00	4.18
1012	1092	2.983030	GGGTGTGTGCATGGCGAA	60.983	61.111	0.00	0.00	0.00	4.70
1108	1213	2.648143	CGGTGCCATGGCCATTTGT	61.648	57.895	33.44	0.00	41.09	2.83
1150	1255	4.408821	GCCACGACCATGAGCCCA	62.409	66.667	0.00	0.00	0.00	5.36
1376	2406	1.680314	GTAGGTCGACGGGGAGGTT	60.680	63.158	9.92	0.00	0.00	3.50
1490	2568	7.276878	ACCAACAAATAAACAAACAGTGCTTAC	59.723	33.333	0.00	0.00	0.00	2.34
1624	2714	1.230324	AAGTGCCAAAAGCTCGACTC	58.770	50.000	0.00	0.00	44.23	3.36
1670	2819	1.277326	GACGCACGCATGAGTATTGA	58.723	50.000	0.39	0.00	39.19	2.57
1822	3111	4.820894	ATACCCTTGTAGAACAGTCCAC	57.179	45.455	0.00	0.00	0.00	4.02
1911	3200	2.423185	TGTGCAATTTCCTCCGCATTAG	59.577	45.455	0.00	0.00	36.64	1.73
2027	3316	6.127842	GGAATTAAACGGTGGATTAGAGCAAA	60.128	38.462	0.00	0.00	0.00	3.68
2029	3318	4.879545	GGAATTAAACGGTGGATTAGAGCA	59.120	41.667	0.00	0.00	0.00	4.26
2107	3396	1.602237	CTGACCGGTGTGGCCTATT	59.398	57.895	14.63	0.00	43.94	1.73
2108	3397	3.031417	GCTGACCGGTGTGGCCTAT	62.031	63.158	14.63	0.00	43.94	2.57
2109	3398	3.702048	GCTGACCGGTGTGGCCTA	61.702	66.667	14.63	0.00	43.94	3.93
2151	3443	8.655651	TTTTGGTTAATTTTGACCACTGATTC	57.344	30.769	6.45	0.00	45.18	2.52
2397	3694	5.459762	CACATCAACTGACCAACATTCAAAC	59.540	40.000	0.00	0.00	0.00	2.93
2406	3703	2.849942	CTGACCACATCAACTGACCAA	58.150	47.619	0.00	0.00	36.69	3.67
2414	3711	1.191489	TCCTCCGCTGACCACATCAA	61.191	55.000	0.00	0.00	36.69	2.57
2441	3738	4.095610	GTTTATGTTTCCGCACATGTAGC	58.904	43.478	0.00	4.03	37.93	3.58
2451	3748	7.341446	GGTTCAATTTGTTGTTTATGTTTCCG	58.659	34.615	0.00	0.00	0.00	4.30
2465	3762	3.763897	GGCATGACTAGGGTTCAATTTGT	59.236	43.478	0.00	0.00	0.00	2.83
2474	3771	2.216148	GCAGAGGCATGACTAGGGT	58.784	57.895	0.00	0.00	40.72	4.34
2507	3804	5.602628	TCAAGAGAGCAAGATCATCATCAG	58.397	41.667	0.00	0.00	0.00	2.90
2527	3824	9.612066	TGTTACTATAACAATGCTCATGATCAA	57.388	29.630	2.91	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.