AutoCloner

Multiple sequence alignment - TraesCS3B01G273200

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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	TraesCS3B01G273200	chr3B	100.000	4460	0	0	1	4460	440227856	440232315	0.000000e+00	8237
1	TraesCS3B01G273200	chr3A	94.089	3434	155	24	111	3533	461842562	461839166	0.000000e+00	5173
2	TraesCS3B01G273200	chr3D	94.850	2660	117	15	938	3584	341493355	341496007	0.000000e+00	4135
3	TraesCS3B01G273200	chr3D	87.044	849	96	9	3619	4460	82426364	82425523	0.000000e+00	946
4	TraesCS3B01G273200	chr3D	87.044	849	96	9	3619	4460	580361788	580360947	0.000000e+00	946
5	TraesCS3B01G273200	chr3D	93.366	618	19	4	1	614	341491871	341492470	0.000000e+00	894
6	TraesCS3B01G273200	chr3D	91.391	302	13	4	618	906	341492780	341493081	6.950000e-108	401
7	TraesCS3B01G273200	chr1D	85.726	2424	274	33	1066	3475	443552710	443555075	0.000000e+00	2494
8	TraesCS3B01G273200	chr1D	85.004	2394	297	31	1094	3470	443716412	443718760	0.000000e+00	2375
9	TraesCS3B01G273200	chr1D	84.506	2388	287	35	1094	3453	443467359	443465027	0.000000e+00	2283
10	TraesCS3B01G273200	chr1D	85.655	1694	200	27	1093	2770	443429533	443427867	0.000000e+00	1742
11	TraesCS3B01G273200	chr1D	87.545	835	90	9	3621	4448	439248240	439249067	0.000000e+00	953
12	TraesCS3B01G273200	chr1A	85.520	2424	288	31	1066	3475	539616534	539614160	0.000000e+00	2473
13	TraesCS3B01G273200	chr1A	85.607	2390	284	26	1094	3470	539428196	539425854	0.000000e+00	2453
14	TraesCS3B01G273200	chr1A	82.647	801	100	19	1990	2773	539721587	539722365	0.000000e+00	673
15	TraesCS3B01G273200	chr1A	83.745	486	61	8	2854	3339	535481108	535481575	1.140000e-120	444
16	TraesCS3B01G273200	chr4B	85.637	2409	265	41	1079	3475	660197465	660195126	0.000000e+00	2457
17	TraesCS3B01G273200	chr1B	85.460	2414	273	41	1079	3468	603149402	603147043	0.000000e+00	2442
18	TraesCS3B01G273200	chr1B	85.528	2377	297	25	1094	3463	603093688	603091352	0.000000e+00	2440
19	TraesCS3B01G273200	chr1B	83.997	2487	309	37	996	3454	603261306	603263731	0.000000e+00	2305
20	TraesCS3B01G273200	chr6B	89.568	834	79	6	3623	4452	667070165	667069336	0.000000e+00	1051
21	TraesCS3B01G273200	chr5B	89.247	837	86	4	3622	4456	670507331	670506497	0.000000e+00	1044
22	TraesCS3B01G273200	chr7D	88.639	845	83	8	3620	4460	618244410	618243575	0.000000e+00	1016
23	TraesCS3B01G273200	chr7B	88.402	845	94	4	3619	4460	553131526	553130683	0.000000e+00	1014
24	TraesCS3B01G273200	chr4A	87.603	847	92	11	3619	4460	647019071	647018233	0.000000e+00	970
25	TraesCS3B01G273200	chr2B	87.802	828	94	7	3637	4460	729491828	729492652	0.000000e+00	963

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	TraesCS3B01G273200	chr3B	440227856	440232315	4459	False	8237	8237	100.000000	1	4460	1	chr3B.!!$F1	4459
1	TraesCS3B01G273200	chr3A	461839166	461842562	3396	True	5173	5173	94.089000	111	3533	1	chr3A.!!$R1	3422
2	TraesCS3B01G273200	chr3D	341491871	341496007	4136	False	1810	4135	93.202333	1	3584	3	chr3D.!!$F1	3583
3	TraesCS3B01G273200	chr3D	82425523	82426364	841	True	946	946	87.044000	3619	4460	1	chr3D.!!$R1	841
4	TraesCS3B01G273200	chr3D	580360947	580361788	841	True	946	946	87.044000	3619	4460	1	chr3D.!!$R2	841
5	TraesCS3B01G273200	chr1D	443552710	443555075	2365	False	2494	2494	85.726000	1066	3475	1	chr1D.!!$F2	2409
6	TraesCS3B01G273200	chr1D	443716412	443718760	2348	False	2375	2375	85.004000	1094	3470	1	chr1D.!!$F3	2376
7	TraesCS3B01G273200	chr1D	443465027	443467359	2332	True	2283	2283	84.506000	1094	3453	1	chr1D.!!$R2	2359
8	TraesCS3B01G273200	chr1D	443427867	443429533	1666	True	1742	1742	85.655000	1093	2770	1	chr1D.!!$R1	1677
9	TraesCS3B01G273200	chr1D	439248240	439249067	827	False	953	953	87.545000	3621	4448	1	chr1D.!!$F1	827
10	TraesCS3B01G273200	chr1A	539614160	539616534	2374	True	2473	2473	85.520000	1066	3475	1	chr1A.!!$R2	2409
11	TraesCS3B01G273200	chr1A	539425854	539428196	2342	True	2453	2453	85.607000	1094	3470	1	chr1A.!!$R1	2376
12	TraesCS3B01G273200	chr1A	539721587	539722365	778	False	673	673	82.647000	1990	2773	1	chr1A.!!$F2	783
13	TraesCS3B01G273200	chr4B	660195126	660197465	2339	True	2457	2457	85.637000	1079	3475	1	chr4B.!!$R1	2396
14	TraesCS3B01G273200	chr1B	603147043	603149402	2359	True	2442	2442	85.460000	1079	3468	1	chr1B.!!$R2	2389
15	TraesCS3B01G273200	chr1B	603091352	603093688	2336	True	2440	2440	85.528000	1094	3463	1	chr1B.!!$R1	2369
16	TraesCS3B01G273200	chr1B	603261306	603263731	2425	False	2305	2305	83.997000	996	3454	1	chr1B.!!$F1	2458
17	TraesCS3B01G273200	chr6B	667069336	667070165	829	True	1051	1051	89.568000	3623	4452	1	chr6B.!!$R1	829
18	TraesCS3B01G273200	chr5B	670506497	670507331	834	True	1044	1044	89.247000	3622	4456	1	chr5B.!!$R1	834
19	TraesCS3B01G273200	chr7D	618243575	618244410	835	True	1016	1016	88.639000	3620	4460	1	chr7D.!!$R1	840
20	TraesCS3B01G273200	chr7B	553130683	553131526	843	True	1014	1014	88.402000	3619	4460	1	chr7B.!!$R1	841
21	TraesCS3B01G273200	chr4A	647018233	647019071	838	True	970	970	87.603000	3619	4460	1	chr4A.!!$R1	841
22	TraesCS3B01G273200	chr2B	729491828	729492652	824	False	963	963	87.802000	3637	4460	1	chr2B.!!$F1	823

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	Hairpin	End Stability	Orientation
926	1252	0.822164	GCATGCTTGATTGCTTCCCT	59.178	50.0	11.37	35.95	4.20	F
936	1504	0.843309	TTGCTTCCCTTGTCCTGACA	59.157	50.0	0.00	39.98	3.58	F
2541	3215	0.036875	CCCAGTTCAGGAGGTTCACC	59.963	60.0	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2541	3215	0.179134	CGTTCTTGAGCTCCCGGTAG	60.179	60.0	12.15	0.00	3.18	R
2862	3539	1.026182	TGCCAAGCGCGATCTTGAAT	61.026	50.0	22.85	44.61	2.57	R
3667	4353	0.105039	CTCCTACTCGGTTGATGGCC	59.895	60.0	0.00	0.00	5.36	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
40	41	4.904253	TCAAACACTAAAGGAAAACCCG	57.096	40.909	0.00	0.00	40.87	5.28
43	44	5.066764	TCAAACACTAAAGGAAAACCCGAAG	59.933	40.000	0.00	0.00	40.87	3.79
335	338	1.334160	AATTTCCCAACCGTTGACCC	58.666	50.000	13.04	0.00	0.00	4.46
409	412	1.269206	ACGCCATTGCAAGAACACAAG	60.269	47.619	4.94	0.00	37.32	3.16
415	418	5.346822	GCCATTGCAAGAACACAAGAATAAG	59.653	40.000	4.94	0.00	37.47	1.73
433	436	6.493458	AGAATAAGGACTAAAGCTTGCCAAAA	59.507	34.615	0.00	0.00	0.00	2.44
481	484	8.548877	TGTCCTTGAATAAGAGCTTATAAGGTT	58.451	33.333	17.80	6.39	39.72	3.50
773	1096	6.127647	ACAACAAGATTTGCAGAAACTTGAGA	60.128	34.615	24.34	0.00	39.84	3.27
814	1140	3.395671	CGATAAAACACTTTGCGTCTCG	58.604	45.455	0.00	0.00	0.00	4.04
885	1211	1.002087	GAAGAACACCGGTGACCTGAT	59.998	52.381	40.21	20.34	0.00	2.90
919	1245	5.967469	CGTAAGTACTAGCATGCTTGATTG	58.033	41.667	31.42	16.61	0.00	2.67
920	1246	4.889832	AAGTACTAGCATGCTTGATTGC	57.110	40.909	31.42	15.91	39.17	3.56
922	1248	4.521146	AGTACTAGCATGCTTGATTGCTT	58.479	39.130	31.42	13.34	46.71	3.91
923	1249	4.574013	AGTACTAGCATGCTTGATTGCTTC	59.426	41.667	31.42	9.98	46.71	3.86
924	1250	2.686915	ACTAGCATGCTTGATTGCTTCC	59.313	45.455	31.42	0.00	46.71	3.46
926	1252	0.822164	GCATGCTTGATTGCTTCCCT	59.178	50.000	11.37	0.00	35.95	4.20
927	1253	1.206371	GCATGCTTGATTGCTTCCCTT	59.794	47.619	11.37	0.00	35.95	3.95
930	1498	1.888512	TGCTTGATTGCTTCCCTTGTC	59.111	47.619	0.00	0.00	0.00	3.18
932	1500	2.800250	CTTGATTGCTTCCCTTGTCCT	58.200	47.619	0.00	0.00	0.00	3.85
936	1504	0.843309	TTGCTTCCCTTGTCCTGACA	59.157	50.000	0.00	0.00	39.98	3.58
983	1554	1.136305	TCCCTTGTCGATCGATCAACC	59.864	52.381	22.50	8.45	0.00	3.77
1035	1618	1.379642	CCAATCTGGCGCTCCTTTCC	61.380	60.000	7.64	0.00	0.00	3.13
1179	1765	4.021925	GCCACCTTCTCCTGCGGT	62.022	66.667	0.00	0.00	0.00	5.68
1584	2198	3.834799	CTCCTGTACGACGGCCCC	61.835	72.222	0.00	0.00	0.00	5.80
1665	2279	2.370281	ACTACAACAGCTCACGGATG	57.630	50.000	0.00	0.00	37.36	3.51
1693	2307	2.202518	ACGACACCGGCGTATTCG	60.203	61.111	16.46	16.46	40.65	3.34
2541	3215	0.036875	CCCAGTTCAGGAGGTTCACC	59.963	60.000	0.00	0.00	0.00	4.02
3025	3702	0.250295	CAAGCTGTCCGGGAGAAACA	60.250	55.000	0.00	0.00	0.00	2.83
3360	4037	6.388100	TGGAAATGGTGAAGATCTCCTTATCT	59.612	38.462	0.00	0.00	37.84	1.98
3458	4141	0.241749	CACCCTGCGTACTTGTCGTA	59.758	55.000	0.00	0.00	0.00	3.43
3492	4175	1.572941	TCGATAGTCGATTCCCGCG	59.427	57.895	0.00	0.00	44.82	6.46
3501	4184	1.721664	CGATTCCCGCGTCTCTACCA	61.722	60.000	4.92	0.00	0.00	3.25
3507	4190	0.172578	CCGCGTCTCTACCATTGTCA	59.827	55.000	4.92	0.00	0.00	3.58
3549	4232	6.423862	TGTTGTAGCGTGTAATTTGAACTTC	58.576	36.000	0.00	0.00	0.00	3.01
3551	4234	5.057819	TGTAGCGTGTAATTTGAACTTCCA	58.942	37.500	0.00	0.00	0.00	3.53
3565	4248	1.067635	ACTTCCATTGCGCCATTTCAC	60.068	47.619	4.18	0.00	0.00	3.18
3592	4278	7.559590	AAAAATGTAACTCTAGCCTGCTATG	57.440	36.000	0.00	0.00	0.00	2.23
3593	4279	6.485830	AAATGTAACTCTAGCCTGCTATGA	57.514	37.500	0.00	0.00	0.00	2.15
3594	4280	6.485830	AATGTAACTCTAGCCTGCTATGAA	57.514	37.500	0.00	0.00	0.00	2.57
3595	4281	6.678568	ATGTAACTCTAGCCTGCTATGAAT	57.321	37.500	0.00	0.00	0.00	2.57
3596	4282	6.090483	TGTAACTCTAGCCTGCTATGAATC	57.910	41.667	0.00	0.00	0.00	2.52
3597	4283	5.598417	TGTAACTCTAGCCTGCTATGAATCA	59.402	40.000	0.00	0.00	0.00	2.57
3598	4284	4.870123	ACTCTAGCCTGCTATGAATCAG	57.130	45.455	0.00	0.00	0.00	2.90
3599	4285	4.478203	ACTCTAGCCTGCTATGAATCAGA	58.522	43.478	0.00	0.00	32.26	3.27
3600	4286	5.085920	ACTCTAGCCTGCTATGAATCAGAT	58.914	41.667	0.00	0.00	32.26	2.90
3601	4287	6.252233	ACTCTAGCCTGCTATGAATCAGATA	58.748	40.000	0.00	0.00	32.26	1.98
3602	4288	6.152661	ACTCTAGCCTGCTATGAATCAGATAC	59.847	42.308	0.00	0.00	32.26	2.24
3603	4289	4.550076	AGCCTGCTATGAATCAGATACC	57.450	45.455	0.00	0.00	32.26	2.73
3604	4290	3.056250	AGCCTGCTATGAATCAGATACCG	60.056	47.826	0.00	0.00	32.26	4.02
3605	4291	3.854666	CCTGCTATGAATCAGATACCGG	58.145	50.000	0.00	0.00	32.26	5.28
3606	4292	3.257393	CTGCTATGAATCAGATACCGGC	58.743	50.000	0.00	0.00	32.26	6.13
3607	4293	2.899900	TGCTATGAATCAGATACCGGCT	59.100	45.455	0.00	0.00	0.00	5.52
3608	4294	3.324846	TGCTATGAATCAGATACCGGCTT	59.675	43.478	0.00	0.00	0.00	4.35
3609	4295	3.681897	GCTATGAATCAGATACCGGCTTG	59.318	47.826	0.00	0.00	0.00	4.01
3610	4296	2.620251	TGAATCAGATACCGGCTTGG	57.380	50.000	0.00	0.00	46.41	3.61
3611	4297	2.115427	TGAATCAGATACCGGCTTGGA	58.885	47.619	0.00	0.00	42.00	3.53
3612	4298	2.103094	TGAATCAGATACCGGCTTGGAG	59.897	50.000	0.00	0.00	42.00	3.86
3613	4299	0.394565	ATCAGATACCGGCTTGGAGC	59.605	55.000	0.00	0.00	42.00	4.70
3667	4353	4.766404	AGCCCGACTTTGAATTAACAAG	57.234	40.909	0.00	0.00	0.00	3.16
3679	4365	2.570415	TTAACAAGGCCATCAACCGA	57.430	45.000	5.01	0.00	0.00	4.69
3680	4366	2.107950	TAACAAGGCCATCAACCGAG	57.892	50.000	5.01	0.00	0.00	4.63
3681	4367	0.110486	AACAAGGCCATCAACCGAGT	59.890	50.000	5.01	0.00	0.00	4.18
3725	4412	7.800015	TTACAACACGAAAGAAAAAGGAAAC	57.200	32.000	0.00	0.00	0.00	2.78
3857	4551	0.546122	GGAGGACACCACCATGCATA	59.454	55.000	0.00	0.00	34.35	3.14
3874	4568	5.431420	TGCATATTTTGTGTCGTTGACTT	57.569	34.783	0.00	0.00	33.15	3.01
3917	4612	0.959553	AACACGTGATCTGACTCCGT	59.040	50.000	25.01	0.00	0.00	4.69
4016	4712	1.416030	ACCCAAATCAAAGTGCCCAAC	59.584	47.619	0.00	0.00	0.00	3.77
4019	4715	2.896685	CCAAATCAAAGTGCCCAACCTA	59.103	45.455	0.00	0.00	0.00	3.08
4056	4752	5.185635	CACAAGGAACATACCCACATGAAAT	59.814	40.000	0.00	0.00	0.00	2.17
4076	4774	1.064825	AGAGAACCGACCACCCAATT	58.935	50.000	0.00	0.00	0.00	2.32
4077	4775	1.165270	GAGAACCGACCACCCAATTG	58.835	55.000	0.00	0.00	0.00	2.32
4133	4831	3.678072	CGAGAGTTATCAAACAAAGGCGA	59.322	43.478	0.00	0.00	38.12	5.54
4176	4876	2.684655	ATGCAACACCATGCCCCC	60.685	61.111	0.00	0.00	45.83	5.40
4198	4899	2.158813	GGTCAAGGATAGGAATCGCCAA	60.159	50.000	0.00	0.00	40.02	4.52
4199	4900	2.872858	GTCAAGGATAGGAATCGCCAAC	59.127	50.000	0.00	0.00	40.02	3.77
4200	4901	1.867233	CAAGGATAGGAATCGCCAACG	59.133	52.381	0.00	0.00	40.02	4.10
4202	4903	1.228657	GGATAGGAATCGCCAACGCC	61.229	60.000	0.00	0.00	40.02	5.68
4203	4904	1.557443	GATAGGAATCGCCAACGCCG	61.557	60.000	0.00	0.00	40.02	6.46
4245	4946	3.407967	GCGACCCCAATCCCCTCA	61.408	66.667	0.00	0.00	0.00	3.86
4256	4957	4.256180	CCCCTCATACCAGCGGCC	62.256	72.222	0.00	0.00	0.00	6.13
4257	4958	3.479203	CCCTCATACCAGCGGCCA	61.479	66.667	2.24	0.00	0.00	5.36
4269	4970	4.760047	CGGCCAGAACCCTCCACG	62.760	72.222	2.24	0.00	0.00	4.94
4270	4971	3.637273	GGCCAGAACCCTCCACGT	61.637	66.667	0.00	0.00	0.00	4.49
4330	5032	2.514592	ATGCCGCCATCGAACCAG	60.515	61.111	0.00	0.00	38.10	4.00
4366	5069	4.770362	TCGAGCCATCCCCGGACA	62.770	66.667	0.73	0.00	0.00	4.02
4368	5071	2.919043	GAGCCATCCCCGGACAAT	59.081	61.111	0.73	0.00	0.00	2.71
4407	5110	1.601914	GCCACCAAAATGTCGTTGTCC	60.602	52.381	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	6.042143	CCTTTAGTGTTTGAACATTTGCTGT	58.958	36.000	0.00	0.00	41.59	4.40
25	26	2.107726	AGGCTTCGGGTTTTCCTTTAGT	59.892	45.455	0.00	0.00	40.46	2.24
55	56	7.308348	GCATATATTGTTGTACATACACCCCAC	60.308	40.741	0.00	0.00	35.64	4.61
233	235	0.396811	AACGACAAGGGCTGCTAAGT	59.603	50.000	0.00	0.00	0.00	2.24
409	412	5.897377	TTGGCAAGCTTTAGTCCTTATTC	57.103	39.130	0.00	0.00	0.00	1.75
433	436	4.436242	TCGAGTGACGAGCTAGAATTTT	57.564	40.909	0.00	0.00	46.45	1.82
481	484	7.004086	TCTTATTCTTTCTTTTTCTGCTGGGA	58.996	34.615	0.00	0.00	0.00	4.37
543	549	6.537660	GGTGACAACCATTATACCTTACTGTC	59.462	42.308	0.00	0.00	46.75	3.51
773	1096	1.149854	GGGGAAACACCGTTGACCT	59.850	57.895	0.00	0.00	40.11	3.85
793	1119	3.120616	TCGAGACGCAAAGTGTTTTATCG	59.879	43.478	0.00	0.00	0.00	2.92
814	1140	2.271800	CATTGACCCAACTAGAGCGTC	58.728	52.381	0.00	0.00	0.00	5.19
820	1146	1.338674	TGACGGCATTGACCCAACTAG	60.339	52.381	0.00	0.00	0.00	2.57
885	1211	5.469760	TGCTAGTACTTACGTGTCAGTTACA	59.530	40.000	0.00	0.00	35.06	2.41
907	1233	0.822164	AGGGAAGCAATCAAGCATGC	59.178	50.000	10.51	10.51	42.87	4.06
909	1235	2.494870	GACAAGGGAAGCAATCAAGCAT	59.505	45.455	0.00	0.00	36.85	3.79
910	1236	1.888512	GACAAGGGAAGCAATCAAGCA	59.111	47.619	0.00	0.00	36.85	3.91
911	1237	1.203287	GGACAAGGGAAGCAATCAAGC	59.797	52.381	0.00	0.00	0.00	4.01
912	1238	2.490903	CAGGACAAGGGAAGCAATCAAG	59.509	50.000	0.00	0.00	0.00	3.02
913	1239	2.108075	TCAGGACAAGGGAAGCAATCAA	59.892	45.455	0.00	0.00	0.00	2.57
915	1241	2.087646	GTCAGGACAAGGGAAGCAATC	58.912	52.381	0.00	0.00	0.00	2.67
916	1242	1.425066	TGTCAGGACAAGGGAAGCAAT	59.575	47.619	0.00	0.00	38.56	3.56
919	1245	3.567478	ATATGTCAGGACAAGGGAAGC	57.433	47.619	6.17	0.00	45.41	3.86
920	1246	7.995488	AGAATTTATATGTCAGGACAAGGGAAG	59.005	37.037	6.17	0.00	45.41	3.46
922	1248	7.451731	AGAATTTATATGTCAGGACAAGGGA	57.548	36.000	6.17	0.00	45.41	4.20
923	1249	7.389053	GCTAGAATTTATATGTCAGGACAAGGG	59.611	40.741	6.17	0.00	45.41	3.95
924	1250	7.933577	TGCTAGAATTTATATGTCAGGACAAGG	59.066	37.037	6.17	0.00	45.41	3.61
926	1252	9.276590	CATGCTAGAATTTATATGTCAGGACAA	57.723	33.333	6.17	0.00	45.41	3.18
927	1253	7.388776	GCATGCTAGAATTTATATGTCAGGACA	59.611	37.037	11.37	4.37	46.44	4.02
930	1498	7.918536	AGCATGCTAGAATTTATATGTCAGG	57.081	36.000	21.21	0.00	0.00	3.86
932	1500	8.907222	TCAAGCATGCTAGAATTTATATGTCA	57.093	30.769	23.00	0.00	0.00	3.58
983	1554	5.049336	GCCATCATGAATGTGAGATCTTCTG	60.049	44.000	0.00	0.00	33.13	3.02
1019	1602	1.997874	AGGGAAAGGAGCGCCAGAT	60.998	57.895	9.88	0.00	36.29	2.90
1023	1606	1.524849	GATCAGGGAAAGGAGCGCC	60.525	63.158	2.29	0.00	0.00	6.53
1035	1618	3.305539	GCAGCAGTAGATGAGAGATCAGG	60.306	52.174	0.00	0.00	31.30	3.86
1077	1663	2.106683	GTGCTGTACCGATGGTGCC	61.107	63.158	0.00	0.00	37.51	5.01
1112	1698	1.481871	GTCTTCCACCGACAGGGATA	58.518	55.000	0.00	0.00	43.47	2.59
1584	2198	0.595588	AGTAGATGCTGGCGATCTCG	59.404	55.000	9.50	0.00	43.27	4.04
1689	2303	0.389948	GGTTGTCGCTGGAGACGAAT	60.390	55.000	0.00	0.00	43.70	3.34
1693	2307	2.029844	GCAGGTTGTCGCTGGAGAC	61.030	63.158	0.00	0.00	41.30	3.36
1968	2582	2.288025	GGTGGGGAGGCTGAACGTA	61.288	63.158	0.00	0.00	0.00	3.57
2223	2861	5.056480	CGCACCTTGAGATATATGTTTCCA	58.944	41.667	0.00	0.00	0.00	3.53
2541	3215	0.179134	CGTTCTTGAGCTCCCGGTAG	60.179	60.000	12.15	0.00	0.00	3.18
2796	3470	1.421268	TGCCTGTCCAGTGACTCATTT	59.579	47.619	0.00	0.00	42.28	2.32
2862	3539	1.026182	TGCCAAGCGCGATCTTGAAT	61.026	50.000	22.85	0.00	44.61	2.57
2961	3638	1.499056	GTCGAGGTCGCGTGTTAGA	59.501	57.895	5.77	0.00	39.60	2.10
3163	3840	4.021544	GCTCCCAATCACGATCTCTAGAAT	60.022	45.833	0.00	0.00	0.00	2.40
3197	3874	4.415332	CGTCCGTGGTCGTCTGGG	62.415	72.222	0.00	0.00	35.01	4.45
3360	4037	0.911045	TGCTCCTCTCCTCCATGCAA	60.911	55.000	0.00	0.00	0.00	4.08
3458	4141	5.003804	ACTATCGAGCATGAAACCAAAGTT	58.996	37.500	0.00	0.00	38.03	2.66
3492	4175	5.934625	AGAACAACATGACAATGGTAGAGAC	59.065	40.000	0.00	0.00	38.19	3.36
3501	4184	7.280876	ACAATATAGCGAGAACAACATGACAAT	59.719	33.333	0.00	0.00	0.00	2.71
3507	4190	6.985188	ACAACAATATAGCGAGAACAACAT	57.015	33.333	0.00	0.00	0.00	2.71
3549	4232	0.109365	TTCGTGAAATGGCGCAATGG	60.109	50.000	10.83	0.00	0.00	3.16
3551	4234	2.430546	TTTTCGTGAAATGGCGCAAT	57.569	40.000	10.83	0.00	0.00	3.56
3584	4270	3.854666	CCGGTATCTGATTCATAGCAGG	58.145	50.000	0.00	0.00	38.33	4.85
3585	4271	3.056250	AGCCGGTATCTGATTCATAGCAG	60.056	47.826	1.90	0.00	39.15	4.24
3586	4272	2.899900	AGCCGGTATCTGATTCATAGCA	59.100	45.455	1.90	0.00	0.00	3.49
3587	4273	3.601443	AGCCGGTATCTGATTCATAGC	57.399	47.619	1.90	0.00	0.00	2.97
3588	4274	4.021104	TCCAAGCCGGTATCTGATTCATAG	60.021	45.833	1.90	0.00	35.57	2.23
3589	4275	3.901222	TCCAAGCCGGTATCTGATTCATA	59.099	43.478	1.90	0.00	35.57	2.15
3590	4276	2.705658	TCCAAGCCGGTATCTGATTCAT	59.294	45.455	1.90	0.00	35.57	2.57
3591	4277	2.103094	CTCCAAGCCGGTATCTGATTCA	59.897	50.000	1.90	0.00	35.57	2.57
3592	4278	2.760374	CTCCAAGCCGGTATCTGATTC	58.240	52.381	1.90	0.00	35.57	2.52
3593	4279	1.202698	GCTCCAAGCCGGTATCTGATT	60.203	52.381	1.90	0.00	34.48	2.57
3594	4280	0.394565	GCTCCAAGCCGGTATCTGAT	59.605	55.000	1.90	0.00	34.48	2.90
3595	4281	1.823295	GCTCCAAGCCGGTATCTGA	59.177	57.895	1.90	0.00	34.48	3.27
3596	4282	4.445699	GCTCCAAGCCGGTATCTG	57.554	61.111	1.90	0.00	34.48	2.90
3667	4353	0.105039	CTCCTACTCGGTTGATGGCC	59.895	60.000	0.00	0.00	0.00	5.36
3679	4365	5.746990	ATTTGCAGTCTTGTACTCCTACT	57.253	39.130	0.00	0.00	35.76	2.57
3680	4366	6.872020	TGTAATTTGCAGTCTTGTACTCCTAC	59.128	38.462	0.00	0.00	35.76	3.18
3681	4367	6.999950	TGTAATTTGCAGTCTTGTACTCCTA	58.000	36.000	0.00	0.00	35.76	2.94
3700	4387	7.490079	GGTTTCCTTTTTCTTTCGTGTTGTAAT	59.510	33.333	0.00	0.00	0.00	1.89
3725	4412	6.038161	TGAGCACATTGTATCTTTATTTCCGG	59.962	38.462	0.00	0.00	0.00	5.14
3835	4529	1.557269	GCATGGTGGTGTCCTCCTCT	61.557	60.000	8.11	0.00	37.97	3.69
3857	4551	3.066203	GGTGGAAGTCAACGACACAAAAT	59.934	43.478	0.00	0.00	34.60	1.82
3874	4568	1.410932	CCTGTTTGGTCCTTTGGTGGA	60.411	52.381	0.00	0.00	0.00	4.02
3977	4673	3.764237	GTTCTAGGGTGAACCACTTCA	57.236	47.619	1.16	0.00	43.89	3.02
4016	4712	0.984230	TGTGCCTCTCCTTTGGTAGG	59.016	55.000	0.00	0.00	46.27	3.18
4019	4715	0.111253	CCTTGTGCCTCTCCTTTGGT	59.889	55.000	0.00	0.00	0.00	3.67
4056	4752	1.946984	ATTGGGTGGTCGGTTCTCTA	58.053	50.000	0.00	0.00	0.00	2.43
4122	4820	2.955660	TGAGGTTTCATCGCCTTTGTTT	59.044	40.909	0.00	0.00	34.81	2.83
4123	4821	2.554032	CTGAGGTTTCATCGCCTTTGTT	59.446	45.455	0.00	0.00	34.81	2.83
4126	4824	2.303022	TCTCTGAGGTTTCATCGCCTTT	59.697	45.455	4.59	0.00	34.81	3.11
4133	4831	1.988107	TGGCCTTCTCTGAGGTTTCAT	59.012	47.619	3.32	0.00	39.11	2.57
4176	4876	1.605712	GGCGATTCCTATCCTTGACCG	60.606	57.143	0.00	0.00	0.00	4.79
4218	4919	1.558167	TTGGGGTCGCTGCCTCAATA	61.558	55.000	4.81	0.00	43.54	1.90
4229	4930	0.396811	GTATGAGGGGATTGGGGTCG	59.603	60.000	0.00	0.00	0.00	4.79
4245	4946	2.590092	GGTTCTGGCCGCTGGTAT	59.410	61.111	0.00	0.00	0.00	2.73
4256	4957	4.996976	CAGACGTGGAGGGTTCTG	57.003	61.111	0.00	0.00	0.00	3.02
4269	4970	2.888414	GGCATCCTACTCTAGTCCAGAC	59.112	54.545	0.00	0.00	0.00	3.51
4270	4971	2.487445	CGGCATCCTACTCTAGTCCAGA	60.487	54.545	0.00	0.00	0.00	3.86
4330	5032	1.228154	GTGGTGGTGGAGTTGGGTC	60.228	63.158	0.00	0.00	0.00	4.46
4407	5110	0.252193	TCATGCCCCTTTTTCCTGGG	60.252	55.000	0.00	0.00	42.98	4.45
4421	5124	1.093159	CTCAGGTGAAAGCCTCATGC	58.907	55.000	0.00	0.00	36.58	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.