AutoCloner

Multiple sequence alignment - TraesCS6D01G211600

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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	TraesCS6D01G211600	chr6D	100.000	3602	0	0	1	3602	298923492	298927093	0.000000e+00	6652.0
1	TraesCS6D01G211600	chr6A	95.773	2626	89	14	33	2646	420823387	420820772	0.000000e+00	4215.0
2	TraesCS6D01G211600	chr6B	96.268	2197	73	7	455	2646	462034569	462036761	0.000000e+00	3594.0
3	TraesCS6D01G211600	chr6B	89.831	295	24	3	6	295	462033953	462034246	1.220000e-99	374.0
4	TraesCS6D01G211600	chr6B	90.625	96	7	2	285	378	462034343	462034438	3.780000e-25	126.0
5	TraesCS6D01G211600	chr6B	94.118	51	3	0	367	417	462034453	462034503	1.070000e-10	78.7
6	TraesCS6D01G211600	chr4D	97.228	974	15	7	2639	3602	449187469	449186498	0.000000e+00	1639.0
7	TraesCS6D01G211600	chr4D	96.804	970	20	2	2643	3602	407129295	407130263	0.000000e+00	1609.0
8	TraesCS6D01G211600	chr4D	74.560	1592	344	50	991	2552	479540646	479542206	1.090000e-179	640.0
9	TraesCS6D01G211600	chr4D	91.111	315	13	4	2640	2944	489247499	489247808	2.590000e-111	412.0
10	TraesCS6D01G211600	chr4D	74.003	577	130	15	1008	1571	5290361	5289792	2.180000e-52	217.0
11	TraesCS6D01G211600	chr5D	97.314	968	16	1	2645	3602	556870410	556871377	0.000000e+00	1635.0
12	TraesCS6D01G211600	chr5D	76.264	1563	319	47	1015	2552	537088077	537089612	0.000000e+00	784.0
13	TraesCS6D01G211600	chr5D	75.721	1561	330	45	1015	2552	537162874	537161340	0.000000e+00	737.0
14	TraesCS6D01G211600	chr5D	75.158	1421	298	43	998	2380	512534343	512535746	5.110000e-173	617.0
15	TraesCS6D01G211600	chr7D	97.020	973	17	3	2640	3602	26594875	26595845	0.000000e+00	1626.0
16	TraesCS6D01G211600	chr7D	96.807	971	20	2	2642	3602	13186866	13187835	0.000000e+00	1611.0
17	TraesCS6D01G211600	chr7D	96.798	968	19	3	2645	3602	564962673	564961708	0.000000e+00	1605.0
18	TraesCS6D01G211600	chr7D	96.281	968	22	4	2645	3602	69722330	69723293	0.000000e+00	1576.0
19	TraesCS6D01G211600	chr1D	96.591	968	21	3	2646	3602	259685532	259686498	0.000000e+00	1594.0
20	TraesCS6D01G211600	chr3D	96.491	969	22	3	2644	3602	553520626	553521592	0.000000e+00	1591.0
21	TraesCS6D01G211600	chr3D	96.281	968	24	3	2645	3602	609395105	609396070	0.000000e+00	1578.0
22	TraesCS6D01G211600	chr4A	76.221	1556	323	41	1015	2548	632999852	632998322	0.000000e+00	780.0
23	TraesCS6D01G211600	chr4A	76.099	1569	323	45	1009	2552	632989700	632991241	0.000000e+00	773.0
24	TraesCS6D01G211600	chr4A	74.826	1581	338	49	998	2548	685834797	685836347	0.000000e+00	660.0
25	TraesCS6D01G211600	chr5B	76.115	1570	324	45	1009	2552	677537448	677538992	0.000000e+00	774.0
26	TraesCS6D01G211600	chr5B	76.074	1559	323	44	1015	2548	677545043	677543510	0.000000e+00	767.0
27	TraesCS6D01G211600	chr5B	75.403	1427	288	51	996	2380	643460738	643462143	1.820000e-177	632.0
28	TraesCS6D01G211600	chr2A	73.772	1567	353	48	1014	2548	18358274	18359814	6.750000e-157	564.0
29	TraesCS6D01G211600	chr7B	91.967	361	18	2	2639	2989	117744421	117744062	2.500000e-136	496.0
30	TraesCS6D01G211600	chr3B	92.157	357	17	2	2643	2989	43352297	43352652	8.980000e-136	494.0
31	TraesCS6D01G211600	chrUn	91.597	357	18	3	2643	2989	70528601	70528247	1.940000e-132	483.0
32	TraesCS6D01G211600	chrUn	90.675	311	16	3	2643	2943	63016588	63016281	5.600000e-108	401.0
33	TraesCS6D01G211600	chr7A	89.970	329	21	3	2627	2944	499580955	499581282	7.200000e-112	414.0
34	TraesCS6D01G211600	chr4B	74.806	516	116	11	1008	1513	9385831	9386342	1.680000e-53	220.0

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	TraesCS6D01G211600	chr6D	298923492	298927093	3601	False	6652.000	6652	100.0000	1	3602	1	chr6D.!!$F1	3601
1	TraesCS6D01G211600	chr6A	420820772	420823387	2615	True	4215.000	4215	95.7730	33	2646	1	chr6A.!!$R1	2613
2	TraesCS6D01G211600	chr6B	462033953	462036761	2808	False	1043.175	3594	92.7105	6	2646	4	chr6B.!!$F1	2640
3	TraesCS6D01G211600	chr4D	449186498	449187469	971	True	1639.000	1639	97.2280	2639	3602	1	chr4D.!!$R2	963
4	TraesCS6D01G211600	chr4D	407129295	407130263	968	False	1609.000	1609	96.8040	2643	3602	1	chr4D.!!$F1	959
5	TraesCS6D01G211600	chr4D	479540646	479542206	1560	False	640.000	640	74.5600	991	2552	1	chr4D.!!$F2	1561
6	TraesCS6D01G211600	chr4D	5289792	5290361	569	True	217.000	217	74.0030	1008	1571	1	chr4D.!!$R1	563
7	TraesCS6D01G211600	chr5D	556870410	556871377	967	False	1635.000	1635	97.3140	2645	3602	1	chr5D.!!$F3	957
8	TraesCS6D01G211600	chr5D	537088077	537089612	1535	False	784.000	784	76.2640	1015	2552	1	chr5D.!!$F2	1537
9	TraesCS6D01G211600	chr5D	537161340	537162874	1534	True	737.000	737	75.7210	1015	2552	1	chr5D.!!$R1	1537
10	TraesCS6D01G211600	chr5D	512534343	512535746	1403	False	617.000	617	75.1580	998	2380	1	chr5D.!!$F1	1382
11	TraesCS6D01G211600	chr7D	26594875	26595845	970	False	1626.000	1626	97.0200	2640	3602	1	chr7D.!!$F2	962
12	TraesCS6D01G211600	chr7D	13186866	13187835	969	False	1611.000	1611	96.8070	2642	3602	1	chr7D.!!$F1	960
13	TraesCS6D01G211600	chr7D	564961708	564962673	965	True	1605.000	1605	96.7980	2645	3602	1	chr7D.!!$R1	957
14	TraesCS6D01G211600	chr7D	69722330	69723293	963	False	1576.000	1576	96.2810	2645	3602	1	chr7D.!!$F3	957
15	TraesCS6D01G211600	chr1D	259685532	259686498	966	False	1594.000	1594	96.5910	2646	3602	1	chr1D.!!$F1	956
16	TraesCS6D01G211600	chr3D	553520626	553521592	966	False	1591.000	1591	96.4910	2644	3602	1	chr3D.!!$F1	958
17	TraesCS6D01G211600	chr3D	609395105	609396070	965	False	1578.000	1578	96.2810	2645	3602	1	chr3D.!!$F2	957
18	TraesCS6D01G211600	chr4A	632998322	632999852	1530	True	780.000	780	76.2210	1015	2548	1	chr4A.!!$R1	1533
19	TraesCS6D01G211600	chr4A	632989700	632991241	1541	False	773.000	773	76.0990	1009	2552	1	chr4A.!!$F1	1543
20	TraesCS6D01G211600	chr4A	685834797	685836347	1550	False	660.000	660	74.8260	998	2548	1	chr4A.!!$F2	1550
21	TraesCS6D01G211600	chr5B	677537448	677538992	1544	False	774.000	774	76.1150	1009	2552	1	chr5B.!!$F2	1543
22	TraesCS6D01G211600	chr5B	677543510	677545043	1533	True	767.000	767	76.0740	1015	2548	1	chr5B.!!$R1	1533
23	TraesCS6D01G211600	chr5B	643460738	643462143	1405	False	632.000	632	75.4030	996	2380	1	chr5B.!!$F1	1384
24	TraesCS6D01G211600	chr2A	18358274	18359814	1540	False	564.000	564	73.7720	1014	2548	1	chr2A.!!$F1	1534
25	TraesCS6D01G211600	chr4B	9385831	9386342	511	False	220.000	220	74.8060	1008	1513	1	chr4B.!!$F1	505

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
890	1064	0.392060	GCCGGCTTATATAACCCCCG	60.392	60.000	22.15	13.58	35.74	5.73	F
985	1159	1.227853	GGCCAAGAAGTGTGGACGT	60.228	57.895	0.00	0.00	38.54	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2559	2776	0.03601	CACCCAAATCTGCGTCCTCT	60.036	55.0	0.0	0.00	0.00	3.69	R
2658	2875	0.73288	GTCCATATCGTCCGGATGCG	60.733	60.0	19.4	13.56	36.55	4.73	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
36	37	3.182572	GTGTCGATGAATAATGCTCCGTC	59.817	47.826	0.00	0.00	0.00	4.79
68	69	6.946340	TGATCTAAAAGTAGTCATGGAAGCA	58.054	36.000	0.00	0.00	0.00	3.91
93	94	3.588569	AGATAGGAGGGTGGTATCCAAC	58.411	50.000	0.00	0.00	41.21	3.77
94	95	2.953093	TAGGAGGGTGGTATCCAACA	57.047	50.000	6.17	0.00	44.30	3.33
204	206	1.143684	ACCTGGTTGACTGATGTTGCT	59.856	47.619	0.00	0.00	0.00	3.91
240	242	4.671766	CGATTTTCTAGCCGGGTTTTCTTG	60.672	45.833	13.43	0.00	0.00	3.02
384	499	5.242171	CCATTTGGTCGGTTATATTAACCCC	59.758	44.000	10.13	7.53	36.99	4.95
417	558	2.036733	CTGGGTTGACCGAGTCTGTTTA	59.963	50.000	4.22	0.00	44.64	2.01
418	559	2.435069	TGGGTTGACCGAGTCTGTTTAA	59.565	45.455	5.77	0.00	44.64	1.52
419	560	3.118334	TGGGTTGACCGAGTCTGTTTAAA	60.118	43.478	5.77	0.00	44.64	1.52
420	561	3.878699	GGGTTGACCGAGTCTGTTTAAAA	59.121	43.478	5.77	0.00	36.71	1.52
477	647	4.790718	AAAACTAGGGAAGAACACCTGT	57.209	40.909	0.00	0.00	37.72	4.00
511	681	3.056250	ACTGAAAACACATGCAACACCAA	60.056	39.130	0.00	0.00	0.00	3.67
529	699	4.598257	CCAACCAGGTGCTCTACG	57.402	61.111	0.00	0.00	0.00	3.51
579	749	4.895668	TGGACGGTACCAGATTTAACTT	57.104	40.909	13.54	0.00	34.77	2.66
587	757	6.592607	CGGTACCAGATTTAACTTGAAAGCTA	59.407	38.462	13.54	0.00	33.42	3.32
592	762	9.750125	ACCAGATTTAACTTGAAAGCTAAAAAG	57.250	29.630	3.50	0.00	33.42	2.27
622	792	3.243569	TGCCTCACAAATAAAACCGGTTG	60.244	43.478	23.08	10.70	0.00	3.77
657	827	4.123497	TCAACAAGACACTATCATCCCG	57.877	45.455	0.00	0.00	0.00	5.14
707	881	1.091771	CGATGAACCCTTCGCTGCAT	61.092	55.000	0.00	0.00	34.09	3.96
710	884	0.613260	TGAACCCTTCGCTGCATACT	59.387	50.000	0.00	0.00	0.00	2.12
741	915	0.671796	GTTTCCACCCCCTTTGTTCG	59.328	55.000	0.00	0.00	0.00	3.95
808	982	0.666913	CAAGATAGCCACATGCAGCC	59.333	55.000	4.04	0.00	44.83	4.85
836	1010	4.876107	CACCCTCGTATCTTGCTATTGTTT	59.124	41.667	0.00	0.00	0.00	2.83
856	1030	2.905075	TCCATTTGGCACATCTAGACG	58.095	47.619	0.00	0.00	39.30	4.18
879	1053	1.134175	GCAAAGCAATAAGCCGGCTTA	59.866	47.619	42.37	42.37	46.39	3.09
884	1058	6.569610	GCAAAGCAATAAGCCGGCTTATATAA	60.570	38.462	45.74	30.95	46.39	0.98
890	1064	0.392060	GCCGGCTTATATAACCCCCG	60.392	60.000	22.15	13.58	35.74	5.73
948	1122	4.570663	CACGATCGAGGGCCGTCC	62.571	72.222	24.34	5.06	39.75	4.79
958	1132	2.670148	GGGCCGTCCTGAATCCTGT	61.670	63.158	0.00	0.00	0.00	4.00
985	1159	1.227853	GGCCAAGAAGTGTGGACGT	60.228	57.895	0.00	0.00	38.54	4.34
1131	1310	2.101415	CGACATCTTCTGCATCACCCTA	59.899	50.000	0.00	0.00	0.00	3.53
2264	2481	2.361610	CTTCGGGCCCAACAGCAT	60.362	61.111	24.92	0.00	0.00	3.79
2559	2776	4.467084	GGCGAGCCCATCAACGGA	62.467	66.667	1.97	0.00	0.00	4.69
2609	2826	1.275291	TCTTCCCTTGTAGAACCTGCG	59.725	52.381	0.00	0.00	0.00	5.18
2658	2875	7.370383	TCCATGAAAAAGAGTCATTTTACAGC	58.630	34.615	6.09	0.00	33.37	4.40
2794	3022	4.383552	CGAACTGATCTGATTTTCCCTCCT	60.384	45.833	6.60	0.00	0.00	3.69
2813	3041	7.957448	TCCCTCCTAAATATTTCGAGGGTATTA	59.043	37.037	35.42	25.06	46.78	0.98
3326	3556	2.505982	CATTCGTCCAGCCCCGAT	59.494	61.111	0.00	0.00	32.44	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.612604	TCGACACATTCCACATTACCG	58.387	47.619	0.00	0.00	0.00	4.02
1	2	4.188462	TCATCGACACATTCCACATTACC	58.812	43.478	0.00	0.00	0.00	2.85
3	4	8.558700	CATTATTCATCGACACATTCCACATTA	58.441	33.333	0.00	0.00	0.00	1.90
4	5	7.420002	CATTATTCATCGACACATTCCACATT	58.580	34.615	0.00	0.00	0.00	2.71
68	69	4.360140	TGGATACCACCCTCCTATCTACAT	59.640	45.833	0.00	0.00	32.47	2.29
186	188	3.607775	CGAAAGCAACATCAGTCAACCAG	60.608	47.826	0.00	0.00	0.00	4.00
204	206	6.799925	GGCTAGAAAATCGATTGAAAACGAAA	59.200	34.615	12.25	0.00	41.65	3.46
240	242	2.601367	ACCATGGCCCAACTGCAC	60.601	61.111	13.04	0.00	0.00	4.57
318	433	1.959282	GCATGATTGGTGAGAATCCCC	59.041	52.381	0.00	0.00	32.20	4.81
381	496	1.152963	CCAGCCCTTTGTATCGGGG	60.153	63.158	0.00	0.00	40.95	5.73
384	499	1.094785	CAACCCAGCCCTTTGTATCG	58.905	55.000	0.00	0.00	0.00	2.92
463	604	4.618920	TTTCTAGACAGGTGTTCTTCCC	57.381	45.455	0.00	0.00	0.00	3.97
477	647	7.571244	GCATGTGTTTTCAGTCGATTTTCTAGA	60.571	37.037	0.00	0.00	0.00	2.43
529	699	2.095567	ACTTTGTGATTCGTGCTCATGC	60.096	45.455	0.00	0.00	40.20	4.06
657	827	1.133363	CAATGCGCAACATACGGCAC	61.133	55.000	17.11	0.00	38.34	5.01
707	881	0.321298	GAAACTCCAAGGCGCCAGTA	60.321	55.000	31.54	10.04	0.00	2.74
710	884	2.282180	GGAAACTCCAAGGCGCCA	60.282	61.111	31.54	6.61	36.28	5.69
741	915	1.471684	CTTGCTGAATGCTGGGAGAAC	59.528	52.381	0.00	0.00	43.37	3.01
808	982	2.365617	AGCAAGATACGAGGGTGGTATG	59.634	50.000	0.00	0.00	31.01	2.39
836	1010	2.499693	TCGTCTAGATGTGCCAAATGGA	59.500	45.455	11.71	0.00	37.39	3.41
856	1030	1.913317	CCGGCTTATTGCTTTGCTTC	58.087	50.000	0.00	0.00	42.39	3.86
879	1053	1.370064	GCGAGCACGGGGGTTATAT	59.630	57.895	5.52	0.00	40.15	0.86
890	1064	1.933853	CAAGTAACCATAGGCGAGCAC	59.066	52.381	0.00	0.00	0.00	4.40
948	1122	1.068333	CCGGTGCAAAACAGGATTCAG	60.068	52.381	0.00	0.00	46.30	3.02
955	1129	1.300080	CTTGGCCGGTGCAAAACAG	60.300	57.895	1.90	0.00	40.13	3.16
958	1132	1.040339	ACTTCTTGGCCGGTGCAAAA	61.040	50.000	1.90	0.00	40.13	2.44
1131	1310	1.228894	TCCGAGGAGCTTGGTGACT	60.229	57.895	0.00	0.00	36.45	3.41
1377	1564	1.153369	GAAGCAGAGCGTGGCCATA	60.153	57.895	9.72	0.00	0.00	2.74
1587	1774	3.057548	TCTTCTGCGTACGCCGGA	61.058	61.111	35.11	28.26	41.09	5.14
2264	2481	0.468226	GGCCGGTATGATGAAGGTGA	59.532	55.000	1.90	0.00	0.00	4.02
2313	2530	1.543208	GCTGATGATATCCCGTGGCAA	60.543	52.381	0.00	0.00	0.00	4.52
2559	2776	0.036010	CACCCAAATCTGCGTCCTCT	60.036	55.000	0.00	0.00	0.00	3.69
2609	2826	3.011760	GCGCACAGCCTACGTTCAC	62.012	63.158	0.30	0.00	40.81	3.18
2635	2852	6.183359	GCGCTGTAAAATGACTCTTTTTCATG	60.183	38.462	0.00	0.00	33.84	3.07
2658	2875	0.732880	GTCCATATCGTCCGGATGCG	60.733	60.000	19.40	13.56	36.55	4.73
2813	3041	1.485066	AGCCCTGAAATTCGTACCGAT	59.515	47.619	0.00	0.00	35.23	4.18
3326	3556	3.644823	TGAACGTTCGTAGATCAAGCAA	58.355	40.909	22.48	0.00	35.04	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.