AutoCloner

Multiple sequence alignment - TraesCS3A01G475200

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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	TraesCS3A01G475200	chr3A	100.000	4339	0	0	1	4339	706849189	706853527	0.000000e+00	8013.0
1	TraesCS3A01G475200	chr3A	87.920	1101	123	4	2234	3324	706922856	706923956	0.000000e+00	1288.0
2	TraesCS3A01G475200	chr3A	81.978	738	112	14	979	1704	706911341	706912069	1.330000e-169	606.0
3	TraesCS3A01G475200	chr3A	80.132	760	118	27	979	1717	706899631	706900378	1.780000e-148	536.0
4	TraesCS3A01G475200	chr3A	85.000	100	12	1	1566	1665	706850712	706850808	9.930000e-17	99.0
5	TraesCS3A01G475200	chr3A	85.000	100	12	1	1524	1620	706850754	706850853	9.930000e-17	99.0
6	TraesCS3A01G475200	chr3D	94.061	3654	162	16	708	4339	572103298	572099678	0.000000e+00	5494.0
7	TraesCS3A01G475200	chr3D	88.100	1084	129	0	2235	3318	572046026	572044943	0.000000e+00	1288.0
8	TraesCS3A01G475200	chr3D	85.069	1085	160	2	2235	3318	572085497	572084414	0.000000e+00	1105.0
9	TraesCS3A01G475200	chr3D	82.815	739	104	16	979	1704	572049408	572048680	1.320000e-179	640.0
10	TraesCS3A01G475200	chr3D	88.292	521	55	5	1	518	572114125	572113608	1.710000e-173	619.0
11	TraesCS3A01G475200	chr3D	94.706	170	9	0	535	704	572113434	572113265	9.250000e-67	265.0
12	TraesCS3A01G475200	chr3D	93.506	154	7	3	3587	3740	572081786	572081636	4.370000e-55	226.0
13	TraesCS3A01G475200	chr3D	85.567	97	11	1	1527	1620	572102434	572102338	9.930000e-17	99.0
14	TraesCS3A01G475200	chr3B	93.527	3507	188	26	862	4339	761900881	761904377	0.000000e+00	5182.0
15	TraesCS3A01G475200	chr3B	88.018	1085	130	0	2234	3318	761936925	761938009	0.000000e+00	1284.0
16	TraesCS3A01G475200	chr3B	80.580	448	68	7	3771	4208	54564785	54565223	1.160000e-85	327.0
17	TraesCS3A01G475200	chr3B	96.212	132	4	1	738	868	761899659	761899790	9.450000e-52	215.0
18	TraesCS3A01G475200	chr3B	76.385	343	58	11	3780	4109	584914324	584914656	3.470000e-36	163.0
19	TraesCS3A01G475200	chr3B	84.496	129	19	1	4212	4339	302116	301988	4.560000e-25	126.0
20	TraesCS3A01G475200	chr3B	88.172	93	8	2	1566	1658	761901547	761901636	1.650000e-19	108.0
21	TraesCS3A01G475200	chr3B	92.754	69	4	1	1524	1592	761901589	761901656	9.930000e-17	99.0
22	TraesCS3A01G475200	chr2B	83.333	1074	170	7	2259	3326	390925520	390926590	0.000000e+00	983.0
23	TraesCS3A01G475200	chr2B	86.567	134	17	1	4207	4339	150341124	150340991	3.500000e-31	147.0
24	TraesCS3A01G475200	chr2B	92.308	39	3	0	3571	3609	779107329	779107367	6.060000e-04	56.5
25	TraesCS3A01G475200	chr2D	83.038	1073	173	7	2260	3326	323076868	323077937	0.000000e+00	965.0
26	TraesCS3A01G475200	chr2D	86.567	134	17	1	4207	4339	98710683	98710550	3.500000e-31	147.0
27	TraesCS3A01G475200	chr2D	84.375	128	15	3	310	433	32507219	32507093	2.120000e-23	121.0
28	TraesCS3A01G475200	chr2A	82.698	1075	175	9	2259	3326	407740548	407739478	0.000000e+00	944.0
29	TraesCS3A01G475200	chr2A	92.308	39	3	0	3571	3609	196123936	196123974	6.060000e-04	56.5
30	TraesCS3A01G475200	chr5D	83.459	399	66	0	3810	4208	233950550	233950948	5.300000e-99	372.0
31	TraesCS3A01G475200	chr1A	79.481	424	73	6	3799	4208	515954821	515954398	5.490000e-74	289.0
32	TraesCS3A01G475200	chr7D	86.486	74	8	2	4136	4208	606815023	606815095	3.600000e-11	80.5
33	TraesCS3A01G475200	chr6B	94.286	35	2	0	459	493	642946266	642946300	2.000000e-03	54.7

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	TraesCS3A01G475200	chr3A	706849189	706853527	4338	False	2737.0	8013	90.00000	1	4339	3	chr3A.!!$F4	4338
1	TraesCS3A01G475200	chr3A	706922856	706923956	1100	False	1288.0	1288	87.92000	2234	3324	1	chr3A.!!$F3	1090
2	TraesCS3A01G475200	chr3A	706911341	706912069	728	False	606.0	606	81.97800	979	1704	1	chr3A.!!$F2	725
3	TraesCS3A01G475200	chr3A	706899631	706900378	747	False	536.0	536	80.13200	979	1717	1	chr3A.!!$F1	738
4	TraesCS3A01G475200	chr3D	572099678	572103298	3620	True	2796.5	5494	89.81400	708	4339	2	chr3D.!!$R3	3631
5	TraesCS3A01G475200	chr3D	572044943	572049408	4465	True	964.0	1288	85.45750	979	3318	2	chr3D.!!$R1	2339
6	TraesCS3A01G475200	chr3D	572081636	572085497	3861	True	665.5	1105	89.28750	2235	3740	2	chr3D.!!$R2	1505
7	TraesCS3A01G475200	chr3D	572113265	572114125	860	True	442.0	619	91.49900	1	704	2	chr3D.!!$R4	703
8	TraesCS3A01G475200	chr3B	761899659	761904377	4718	False	1401.0	5182	92.66625	738	4339	4	chr3B.!!$F4	3601
9	TraesCS3A01G475200	chr3B	761936925	761938009	1084	False	1284.0	1284	88.01800	2234	3318	1	chr3B.!!$F3	1084
10	TraesCS3A01G475200	chr2B	390925520	390926590	1070	False	983.0	983	83.33300	2259	3326	1	chr2B.!!$F1	1067
11	TraesCS3A01G475200	chr2D	323076868	323077937	1069	False	965.0	965	83.03800	2260	3326	1	chr2D.!!$F1	1066
12	TraesCS3A01G475200	chr2A	407739478	407740548	1070	True	944.0	944	82.69800	2259	3326	1	chr2A.!!$R1	1067

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
924	2187	0.461548	CTCTTCTCGGTGGCATGCTA	59.538	55.0	18.92	9.16	0.00	3.49	F
1299	2571	0.324614	TCATCGCCTCCTTCTTTGCA	59.675	50.0	0.00	0.00	0.00	4.08	F
1434	2706	0.457853	GACGCACATTGCTCGGAGTA	60.458	55.0	6.90	0.00	42.25	2.59	F
1859	3186	0.751452	TGCACCAACAGGTACGTACA	59.249	50.0	26.02	0.00	33.30	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2463	6059	0.411452	TCAGGGAGGAAGAGTGAGCT	59.589	55.000	0.00	0.00	0.00	4.09	R
3134	6733	0.975040	AGAGCATCGTGAGGAAGGCT	60.975	55.000	4.69	4.69	42.67	4.58	R
3296	6895	1.616865	TCGTCATCTCCGACAAACCTT	59.383	47.619	0.00	0.00	35.54	3.50	R
3767	9745	2.830317	TTTTTCGCGGAGGGGTCA	59.170	55.556	6.13	0.00	42.39	4.02	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
33	34	2.366837	TGTCCCCTCGGGCATGAT	60.367	61.111	0.00	0.00	39.48	2.45
35	36	1.526917	GTCCCCTCGGGCATGATTG	60.527	63.158	0.00	0.00	43.94	2.67
37	38	0.692756	TCCCCTCGGGCATGATTGTA	60.693	55.000	0.00	0.00	43.94	2.41
49	50	3.819337	GCATGATTGTATGCCAGAGTGAT	59.181	43.478	0.00	0.00	45.93	3.06
68	69	6.675987	AGTGATTCATGTTCTTTTTCTCAGC	58.324	36.000	0.00	0.00	0.00	4.26
119	120	3.143279	CGTGTGCGTTTTTATCGTTCTC	58.857	45.455	0.00	0.00	0.00	2.87
122	123	3.153735	GTGCGTTTTTATCGTTCTCAGC	58.846	45.455	0.00	0.00	0.00	4.26
161	162	8.860088	ACCTTTATGTTTGATCAGCTTTTTAGT	58.140	29.630	0.00	0.00	0.00	2.24
162	163	9.132521	CCTTTATGTTTGATCAGCTTTTTAGTG	57.867	33.333	0.00	0.00	0.00	2.74
167	168	7.542890	TGTTTGATCAGCTTTTTAGTGTTTCA	58.457	30.769	0.00	0.00	0.00	2.69
169	170	8.482429	GTTTGATCAGCTTTTTAGTGTTTCATG	58.518	33.333	0.00	0.00	0.00	3.07
170	171	6.680810	TGATCAGCTTTTTAGTGTTTCATGG	58.319	36.000	0.00	0.00	0.00	3.66
173	174	6.680810	TCAGCTTTTTAGTGTTTCATGGATG	58.319	36.000	0.00	0.00	0.00	3.51
193	194	4.987408	TGTCATGTATCATTTGGCCTTG	57.013	40.909	3.32	0.00	0.00	3.61
205	206	7.710676	TCATTTGGCCTTGTAGCTTTATTAA	57.289	32.000	3.32	0.00	0.00	1.40
402	405	3.312697	GGAAACAACTTCTCTGTGGTGTC	59.687	47.826	0.00	0.00	34.17	3.67
403	406	3.627395	AACAACTTCTCTGTGGTGTCA	57.373	42.857	0.00	0.00	0.00	3.58
410	413	3.949842	TCTCTGTGGTGTCAATCTCTG	57.050	47.619	0.00	0.00	0.00	3.35
416	419	3.056536	TGTGGTGTCAATCTCTGCTAGAC	60.057	47.826	0.00	0.00	36.93	2.59
430	433	4.098044	TCTGCTAGACGAAATACTCCCAAG	59.902	45.833	0.00	0.00	0.00	3.61
433	436	4.098196	GCTAGACGAAATACTCCCAAGACT	59.902	45.833	0.00	0.00	0.00	3.24
435	438	5.074584	AGACGAAATACTCCCAAGACTTC	57.925	43.478	0.00	0.00	0.00	3.01
440	443	5.348997	CGAAATACTCCCAAGACTTCTTCAC	59.651	44.000	0.00	0.00	33.11	3.18
441	444	4.828072	ATACTCCCAAGACTTCTTCACC	57.172	45.455	0.00	0.00	33.11	4.02
442	445	2.408565	ACTCCCAAGACTTCTTCACCA	58.591	47.619	0.00	0.00	33.11	4.17
443	446	2.370189	ACTCCCAAGACTTCTTCACCAG	59.630	50.000	0.00	0.00	33.11	4.00
444	447	2.370189	CTCCCAAGACTTCTTCACCAGT	59.630	50.000	0.00	0.00	33.11	4.00
446	449	3.971305	TCCCAAGACTTCTTCACCAGTAA	59.029	43.478	0.00	0.00	33.11	2.24
447	450	4.040461	TCCCAAGACTTCTTCACCAGTAAG	59.960	45.833	0.00	0.00	33.11	2.34
457	460	5.475719	TCTTCACCAGTAAGAACATTACGG	58.524	41.667	0.00	0.00	30.15	4.02
488	491	4.320608	TTTTGAAAGCCCATTGAGTCAC	57.679	40.909	0.00	0.00	0.00	3.67
502	505	4.487714	TGAGTCACCCATCCAGAAATAC	57.512	45.455	0.00	0.00	0.00	1.89
518	521	4.780021	AGAAATACTGGAAGCCTTGAGAGA	59.220	41.667	0.00	0.00	37.60	3.10
520	523	6.613271	AGAAATACTGGAAGCCTTGAGAGATA	59.387	38.462	0.00	0.00	37.60	1.98
523	526	5.505181	ACTGGAAGCCTTGAGAGATAAAA	57.495	39.130	0.00	0.00	37.60	1.52
524	527	5.495640	ACTGGAAGCCTTGAGAGATAAAAG	58.504	41.667	0.00	0.00	37.60	2.27
525	528	4.848357	TGGAAGCCTTGAGAGATAAAAGG	58.152	43.478	0.00	0.00	42.86	3.11
572	732	4.219115	TGGAACCACCAAATAGAAAAGCA	58.781	39.130	0.00	0.00	46.75	3.91
574	734	5.306678	TGGAACCACCAAATAGAAAAGCAAT	59.693	36.000	0.00	0.00	46.75	3.56
579	739	8.281212	ACCACCAAATAGAAAAGCAATAGTAG	57.719	34.615	0.00	0.00	0.00	2.57
595	755	9.810545	AGCAATAGTAGTTTACTCTTGAAGATC	57.189	33.333	14.70	0.00	42.26	2.75
602	762	1.490574	ACTCTTGAAGATCCGAGGGG	58.509	55.000	0.00	0.00	0.00	4.79
646	806	3.151022	GCAGGAGGAGAGGGGACG	61.151	72.222	0.00	0.00	0.00	4.79
662	822	1.598676	GGACGAAAAAGTTTCCGTGGC	60.599	52.381	17.13	7.02	35.22	5.01
679	839	4.181010	CGATGGTGGGGGCTGGAG	62.181	72.222	0.00	0.00	0.00	3.86
688	848	0.544697	GGGGGCTGGAGTTATTTCGA	59.455	55.000	0.00	0.00	0.00	3.71
704	864	2.776312	TCGATGCGATCTAGGTCAAC	57.224	50.000	3.42	0.00	0.00	3.18
705	865	2.021457	TCGATGCGATCTAGGTCAACA	58.979	47.619	3.42	0.78	0.00	3.33
706	866	2.623416	TCGATGCGATCTAGGTCAACAT	59.377	45.455	7.97	7.97	0.00	2.71
707	867	3.818773	TCGATGCGATCTAGGTCAACATA	59.181	43.478	3.42	0.00	0.00	2.29
708	868	4.277423	TCGATGCGATCTAGGTCAACATAA	59.723	41.667	3.42	0.00	0.00	1.90
709	869	4.982295	CGATGCGATCTAGGTCAACATAAA	59.018	41.667	3.42	0.00	0.00	1.40
710	870	5.462068	CGATGCGATCTAGGTCAACATAAAA	59.538	40.000	3.42	0.00	0.00	1.52
711	871	6.146184	CGATGCGATCTAGGTCAACATAAAAT	59.854	38.462	3.42	0.00	0.00	1.82
712	872	7.328493	CGATGCGATCTAGGTCAACATAAAATA	59.672	37.037	3.42	0.00	0.00	1.40
727	887	8.656849	CAACATAAAATAAGTAACTGTCGCTCT	58.343	33.333	0.00	0.00	0.00	4.09
924	2187	0.461548	CTCTTCTCGGTGGCATGCTA	59.538	55.000	18.92	9.16	0.00	3.49
1263	2535	0.617820	TACAGGCCTTCACCTCCTCC	60.618	60.000	0.00	0.00	38.26	4.30
1299	2571	0.324614	TCATCGCCTCCTTCTTTGCA	59.675	50.000	0.00	0.00	0.00	4.08
1434	2706	0.457853	GACGCACATTGCTCGGAGTA	60.458	55.000	6.90	0.00	42.25	2.59
1579	2900	5.257864	CGTATGCAAATATATGTCGCCATG	58.742	41.667	0.00	0.00	32.29	3.66
1704	3026	2.033801	TCAAAGAGCTTGACTGCTTTGC	59.966	45.455	15.10	0.00	44.17	3.68
1705	3027	0.957362	AAGAGCTTGACTGCTTTGCC	59.043	50.000	0.00	0.00	44.17	4.52
1859	3186	0.751452	TGCACCAACAGGTACGTACA	59.249	50.000	26.02	0.00	33.30	2.90
1860	3187	1.142474	GCACCAACAGGTACGTACAC	58.858	55.000	26.02	15.53	33.30	2.90
1882	4187	3.553511	CGAAATGGGAAGAGAATGAGACG	59.446	47.826	0.00	0.00	0.00	4.18
1952	4259	3.326588	TGGACCAACGGGGAAGATATATG	59.673	47.826	2.06	0.00	41.15	1.78
2063	4370	4.142160	TGCTAGGTGCTGTCTTGTAGTATG	60.142	45.833	0.00	0.00	43.37	2.39
2197	5786	3.057596	CGCCACATAATTTCGGGCATATT	60.058	43.478	0.00	0.00	44.82	1.28
2300	5891	1.221566	CATGTCGGAGATGGCACCA	59.778	57.895	7.22	0.00	40.67	4.17
2496	6092	1.500783	CCCTGACACCCCCAACTCAT	61.501	60.000	0.00	0.00	0.00	2.90
2766	6365	1.878948	CGCTCGGTTTTAAAGGGGACA	60.879	52.381	0.00	0.00	0.00	4.02
3134	6733	2.048597	ACCTTCGTCATCGCGCAA	60.049	55.556	8.75	0.00	36.96	4.85
3218	6817	2.738147	GGTCATGACCGTCTTCGTG	58.262	57.895	28.52	0.00	42.29	4.35
3251	6850	1.533469	CGGAGACCAAGAACGTCCCT	61.533	60.000	0.00	0.00	0.00	4.20
3296	6895	0.191064	AGGGACACTGGTTCTGGAGA	59.809	55.000	0.00	0.00	0.00	3.71
3354	9243	6.715718	AGAGCCTTGAATGGAGATGAATAATG	59.284	38.462	0.00	0.00	0.00	1.90
3355	9244	6.607970	AGCCTTGAATGGAGATGAATAATGA	58.392	36.000	0.00	0.00	0.00	2.57
3356	9245	7.064866	AGCCTTGAATGGAGATGAATAATGAA	58.935	34.615	0.00	0.00	0.00	2.57
3357	9246	7.562454	AGCCTTGAATGGAGATGAATAATGAAA	59.438	33.333	0.00	0.00	0.00	2.69
3358	9247	8.365647	GCCTTGAATGGAGATGAATAATGAAAT	58.634	33.333	0.00	0.00	0.00	2.17
3453	9364	3.949842	AAGTACGTTTAGGGGTCTGTC	57.050	47.619	0.00	0.00	0.00	3.51
3484	9395	5.245751	AGTTATTGGATTTGAATGGTGTGCA	59.754	36.000	0.00	0.00	0.00	4.57
3667	9645	2.978278	AGCCCCTGATATTCTCTCTTGG	59.022	50.000	0.00	0.00	0.00	3.61
3677	9655	4.751767	ATTCTCTCTTGGATGGTCAGAC	57.248	45.455	0.00	0.00	0.00	3.51
3767	9745	3.469008	TCATAACCAATCGATCGGCTT	57.531	42.857	16.41	6.65	0.00	4.35
3805	9783	2.879233	GCTCTTCCCACGTCACCCA	61.879	63.158	0.00	0.00	0.00	4.51
3811	9789	4.263572	CCACGTCACCCAGCCCAA	62.264	66.667	0.00	0.00	0.00	4.12
3929	9907	3.005539	GCCAGGCTCTCTCCCACA	61.006	66.667	3.29	0.00	0.00	4.17
3939	9917	3.710722	CTCCCACAGCGGCTTCCT	61.711	66.667	0.00	0.00	0.00	3.36
3964	9946	4.748144	GGGCAGCAGGTTGGGAGG	62.748	72.222	0.00	0.00	0.00	4.30
3969	9951	2.203480	GCAGGTTGGGAGGTGCAA	60.203	61.111	0.00	0.00	35.91	4.08
3973	9955	2.203294	GTTGGGAGGTGCAACGGT	60.203	61.111	0.00	0.00	38.12	4.83
4047	10029	3.702048	GTGTGGGAGCGGCTACCA	61.702	66.667	30.03	30.03	43.15	3.25
4088	10070	1.983119	GCATCGGGGGAGGATGTCAA	61.983	60.000	3.99	0.00	42.53	3.18
4094	10076	1.596934	GGGAGGATGTCAAGCGTGA	59.403	57.895	0.00	0.00	0.00	4.35
4102	10084	2.821685	TCAAGCGTGACACTGCCT	59.178	55.556	15.56	3.91	0.00	4.75
4126	10108	4.650377	GGCCATCGGGATCCAGGC	62.650	72.222	21.77	21.77	44.48	4.85
4149	10131	3.006728	CCGAGGTGGTTGGCCCTA	61.007	66.667	0.00	0.00	0.00	3.53
4188	10170	1.661341	ACTTCGATCTGCTTCATGCC	58.339	50.000	0.00	0.00	42.00	4.40
4197	10179	2.273449	CTTCATGCCGGCCTCCTT	59.727	61.111	26.77	0.00	0.00	3.36
4206	10188	1.144936	CGGCCTCCTTGATCTGGAC	59.855	63.158	0.00	0.00	0.00	4.02
4229	10212	2.927871	GCTTTTGGCGATTGCATCACTT	60.928	45.455	7.38	0.00	45.35	3.16
4285	10268	1.202557	CCTCATCTTCAGCCAGAGAGC	60.203	57.143	0.00	0.00	0.00	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.224066	CCGAGGGGACATAACACTCATC	60.224	54.545	0.00	0.00	34.06	2.92
33	34	4.847198	ACATGAATCACTCTGGCATACAA	58.153	39.130	0.00	0.00	0.00	2.41
35	36	5.121811	AGAACATGAATCACTCTGGCATAC	58.878	41.667	0.00	0.00	0.00	2.39
37	38	4.232188	AGAACATGAATCACTCTGGCAT	57.768	40.909	0.00	0.00	0.00	4.40
40	41	7.040892	TGAGAAAAAGAACATGAATCACTCTGG	60.041	37.037	0.00	0.00	0.00	3.86
49	50	4.816385	AGTCGCTGAGAAAAAGAACATGAA	59.184	37.500	0.00	0.00	0.00	2.57
78	79	1.202076	GCGTGCAGAACTAAATGCCTC	60.202	52.381	0.00	0.00	41.85	4.70
79	80	0.804989	GCGTGCAGAACTAAATGCCT	59.195	50.000	0.00	0.00	41.85	4.75
167	168	4.525487	GGCCAAATGATACATGACATCCAT	59.475	41.667	0.00	0.00	35.44	3.41
169	170	4.147321	AGGCCAAATGATACATGACATCC	58.853	43.478	5.01	0.53	0.00	3.51
170	171	5.068198	ACAAGGCCAAATGATACATGACATC	59.932	40.000	5.01	2.28	0.00	3.06
173	174	4.989279	ACAAGGCCAAATGATACATGAC	57.011	40.909	5.01	0.00	0.00	3.06
193	194	9.742552	GCGCACTTTCTATATTAATAAAGCTAC	57.257	33.333	0.30	0.00	33.25	3.58
205	206	2.544267	GGCTTTCGCGCACTTTCTATAT	59.456	45.455	8.75	0.00	36.88	0.86
208	209	0.320421	AGGCTTTCGCGCACTTTCTA	60.320	50.000	8.75	0.00	36.88	2.10
210	211	1.441016	CAGGCTTTCGCGCACTTTC	60.441	57.895	8.75	0.00	36.88	2.62
215	216	1.719725	TTGAAACAGGCTTTCGCGCA	61.720	50.000	8.75	0.00	36.88	6.09
218	219	2.202295	TTGTTGAAACAGGCTTTCGC	57.798	45.000	0.00	0.00	40.50	4.70
372	375	6.261826	CACAGAGAAGTTGTTTCCAAGAGATT	59.738	38.462	0.00	0.00	36.40	2.40
379	382	3.278574	CACCACAGAGAAGTTGTTTCCA	58.721	45.455	0.00	0.00	36.40	3.53
381	384	3.938963	TGACACCACAGAGAAGTTGTTTC	59.061	43.478	0.00	0.00	35.97	2.78
402	405	5.918011	GGAGTATTTCGTCTAGCAGAGATTG	59.082	44.000	0.00	0.00	36.29	2.67
403	406	5.010213	GGGAGTATTTCGTCTAGCAGAGATT	59.990	44.000	0.00	0.00	36.29	2.40
410	413	4.098196	AGTCTTGGGAGTATTTCGTCTAGC	59.902	45.833	0.00	0.00	0.00	3.42
416	419	5.348997	GTGAAGAAGTCTTGGGAGTATTTCG	59.651	44.000	0.00	0.00	36.11	3.46
430	433	7.148787	CGTAATGTTCTTACTGGTGAAGAAGTC	60.149	40.741	0.00	0.00	42.17	3.01
433	436	5.929992	CCGTAATGTTCTTACTGGTGAAGAA	59.070	40.000	0.00	0.00	39.92	2.52
435	438	5.475719	TCCGTAATGTTCTTACTGGTGAAG	58.524	41.667	0.00	0.00	0.00	3.02
502	505	4.880696	CCTTTTATCTCTCAAGGCTTCCAG	59.119	45.833	0.00	0.00	30.94	3.86
520	523	8.490311	AGCTAGAGAGTTTATATTGAGCCTTTT	58.510	33.333	0.00	0.00	0.00	2.27
523	526	7.288852	TGAAGCTAGAGAGTTTATATTGAGCCT	59.711	37.037	0.00	0.00	0.00	4.58
524	527	7.437748	TGAAGCTAGAGAGTTTATATTGAGCC	58.562	38.462	0.00	0.00	0.00	4.70
525	528	8.924691	CATGAAGCTAGAGAGTTTATATTGAGC	58.075	37.037	0.00	0.00	0.00	4.26
526	529	9.421806	CCATGAAGCTAGAGAGTTTATATTGAG	57.578	37.037	0.00	0.00	0.00	3.02
527	530	9.147732	TCCATGAAGCTAGAGAGTTTATATTGA	57.852	33.333	0.00	0.00	0.00	2.57
528	531	9.770097	TTCCATGAAGCTAGAGAGTTTATATTG	57.230	33.333	0.00	0.00	0.00	1.90
530	533	8.371699	GGTTCCATGAAGCTAGAGAGTTTATAT	58.628	37.037	0.00	0.00	37.13	0.86
531	534	7.344612	TGGTTCCATGAAGCTAGAGAGTTTATA	59.655	37.037	0.00	0.00	40.24	0.98
532	535	6.156949	TGGTTCCATGAAGCTAGAGAGTTTAT	59.843	38.462	0.00	0.00	40.24	1.40
533	536	5.483937	TGGTTCCATGAAGCTAGAGAGTTTA	59.516	40.000	0.00	0.00	40.24	2.01
572	732	9.186837	TCGGATCTTCAAGAGTAAACTACTATT	57.813	33.333	0.00	0.00	40.55	1.73
574	734	7.282675	CCTCGGATCTTCAAGAGTAAACTACTA	59.717	40.741	0.00	0.00	39.59	1.82
579	739	4.434520	CCCTCGGATCTTCAAGAGTAAAC	58.565	47.826	0.00	0.00	0.00	2.01
602	762	4.416738	GGCACTGAGAGGTGGGGC	62.417	72.222	0.00	0.00	37.65	5.80
646	806	2.315901	CATCGCCACGGAAACTTTTTC	58.684	47.619	0.00	0.00	0.00	2.29
662	822	4.181010	CTCCAGCCCCCACCATCG	62.181	72.222	0.00	0.00	0.00	3.84
679	839	5.220381	TGACCTAGATCGCATCGAAATAAC	58.780	41.667	0.00	0.00	39.99	1.89
688	848	8.902540	TTATTTTATGTTGACCTAGATCGCAT	57.097	30.769	0.00	0.00	0.00	4.73
707	867	8.880750	GGATTTAGAGCGACAGTTACTTATTTT	58.119	33.333	0.00	0.00	0.00	1.82
708	868	8.038944	TGGATTTAGAGCGACAGTTACTTATTT	58.961	33.333	0.00	0.00	0.00	1.40
709	869	7.553334	TGGATTTAGAGCGACAGTTACTTATT	58.447	34.615	0.00	0.00	0.00	1.40
710	870	7.108841	TGGATTTAGAGCGACAGTTACTTAT	57.891	36.000	0.00	0.00	0.00	1.73
711	871	6.519679	TGGATTTAGAGCGACAGTTACTTA	57.480	37.500	0.00	0.00	0.00	2.24
712	872	5.401531	TGGATTTAGAGCGACAGTTACTT	57.598	39.130	0.00	0.00	0.00	2.24
824	989	2.056223	GGCTGGGCTACGTACTCCA	61.056	63.158	10.60	10.60	0.00	3.86
1525	2846	4.257267	TGTGACCTTGATGGCGATATAG	57.743	45.455	0.00	0.00	40.22	1.31
1579	2900	2.069273	CGGAACTGTGATGTGACCTTC	58.931	52.381	0.00	0.00	0.00	3.46
1798	3121	9.847706	AATCAATAACTACTCTATGCGTATCAG	57.152	33.333	0.00	0.00	0.00	2.90
1844	3171	2.420628	TTCGTGTACGTACCTGTTGG	57.579	50.000	22.43	5.95	40.80	3.77
1859	3186	4.508662	GTCTCATTCTCTTCCCATTTCGT	58.491	43.478	0.00	0.00	0.00	3.85
1860	3187	3.553511	CGTCTCATTCTCTTCCCATTTCG	59.446	47.826	0.00	0.00	0.00	3.46
1882	4187	6.655078	AAGAAATGAATGTGCCCCATATAC	57.345	37.500	0.00	0.00	31.97	1.47
1952	4259	7.926018	ACTTGATGTTTAGTTGGTTTTCAATCC	59.074	33.333	0.00	0.00	37.73	3.01
2063	4370	2.366916	CAGTGGGATAGACATGGAGGAC	59.633	54.545	0.00	0.00	0.00	3.85
2113	5084	4.610945	ACTTTCATACTTGCTTGCACAAC	58.389	39.130	0.00	0.00	0.00	3.32
2217	5806	9.729023	TCATTCAATTGTACTTTTACACACTTG	57.271	29.630	5.13	0.00	37.97	3.16
2300	5891	4.742201	ATGCCACGAAGACGCGCT	62.742	61.111	5.73	0.50	43.96	5.92
2463	6059	0.411452	TCAGGGAGGAAGAGTGAGCT	59.589	55.000	0.00	0.00	0.00	4.09
2496	6092	2.268920	GTGGCCTCGCTCCATCAA	59.731	61.111	3.32	0.00	35.81	2.57
3134	6733	0.975040	AGAGCATCGTGAGGAAGGCT	60.975	55.000	4.69	4.69	42.67	4.58
3296	6895	1.616865	TCGTCATCTCCGACAAACCTT	59.383	47.619	0.00	0.00	35.54	3.50
3358	9247	9.330063	GTCATCTACAATGAGGTTTTCATGATA	57.670	33.333	0.00	0.00	45.82	2.15
3359	9248	7.830697	TGTCATCTACAATGAGGTTTTCATGAT	59.169	33.333	0.00	0.00	45.82	2.45
3360	9249	7.167535	TGTCATCTACAATGAGGTTTTCATGA	58.832	34.615	0.00	0.00	45.82	3.07
3361	9250	7.381766	TGTCATCTACAATGAGGTTTTCATG	57.618	36.000	0.00	0.00	45.82	3.07
3651	9629	6.267242	TCTGACCATCCAAGAGAGAATATCAG	59.733	42.308	0.00	0.00	0.00	2.90
3767	9745	2.830317	TTTTTCGCGGAGGGGTCA	59.170	55.556	6.13	0.00	42.39	4.02
3796	9774	3.953775	CCTTGGGCTGGGTGACGT	61.954	66.667	0.00	0.00	0.00	4.34
3910	9888	4.016790	TGGGAGAGAGCCTGGCCT	62.017	66.667	16.57	12.30	0.00	5.19
3929	9907	1.617947	CCTACAGGAAGGAAGCCGCT	61.618	60.000	0.00	0.00	39.15	5.52
3973	9955	2.283143	ATCCTAAGGCCCAATGCGCA	62.283	55.000	14.96	14.96	42.61	6.09
3979	9961	2.076184	CCGGGATCCTAAGGCCCAA	61.076	63.158	12.58	0.00	42.14	4.12
3984	9966	2.735237	GTCGCCGGGATCCTAAGG	59.265	66.667	12.58	13.72	0.00	2.69
4047	10029	3.055719	CCAAATGGCCACGACGCT	61.056	61.111	8.16	0.00	0.00	5.07
4067	10049	2.388890	GACATCCTCCCCCGATGCAG	62.389	65.000	0.00	0.00	40.70	4.41
4088	10070	0.457851	GATCTAGGCAGTGTCACGCT	59.542	55.000	15.86	0.00	0.00	5.07
4126	10108	4.760047	CAACCACCTCGGGGCTCG	62.760	72.222	0.00	0.00	40.22	5.03
4133	10115	0.974010	TAGTAGGGCCAACCACCTCG	60.974	60.000	6.18	0.00	43.89	4.63
4135	10117	1.844497	GAATAGTAGGGCCAACCACCT	59.156	52.381	6.18	0.00	43.89	4.00
4149	10131	6.758886	CGAAGTTATGGAGCTTGAAGAATAGT	59.241	38.462	0.00	0.00	0.00	2.12
4188	10170	1.144936	GTCCAGATCAAGGAGGCCG	59.855	63.158	7.13	0.00	35.42	6.13
4197	10179	1.538047	GCCAAAAGCTGTCCAGATCA	58.462	50.000	0.00	0.00	38.99	2.92
4206	10188	1.274596	GATGCAATCGCCAAAAGCTG	58.725	50.000	0.00	0.00	40.39	4.24
4285	10268	1.376609	GCGCCACACCCTCATAAAGG	61.377	60.000	0.00	0.00	45.77	3.11

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.