AutoCloner

Multiple sequence alignment - TraesCS7D01G041400

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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	TraesCS7D01G041400	chr7D	100.000	3431	0	0	1	3431	20613859	20617289	0.000000e+00	6336.0
1	TraesCS7D01G041400	chr7D	97.386	880	21	2	2552	3431	111061346	111060469	0.000000e+00	1496.0
2	TraesCS7D01G041400	chr7A	95.521	1652	59	6	571	2220	20991679	20993317	0.000000e+00	2627.0
3	TraesCS7D01G041400	chr7A	83.569	992	134	19	1446	2414	20772680	20771695	0.000000e+00	902.0
4	TraesCS7D01G041400	chr7A	98.137	161	3	0	2216	2376	20998270	20998430	7.250000e-72	281.0
5	TraesCS7D01G041400	chr7A	95.035	141	7	0	2405	2545	20998431	20998571	4.460000e-54	222.0
6	TraesCS7D01G041400	chrUn	86.755	1578	155	19	974	2545	296649816	296651345	0.000000e+00	1707.0
7	TraesCS7D01G041400	chrUn	92.157	51	4	0	2490	2540	284571075	284571125	4.750000e-09	73.1
8	TraesCS7D01G041400	chr4A	86.755	1578	155	19	974	2545	669458375	669456846	0.000000e+00	1707.0
9	TraesCS7D01G041400	chr4A	89.703	573	54	4	2	573	589914683	589915251	0.000000e+00	726.0
10	TraesCS7D01G041400	chr2D	97.858	887	17	1	2545	3431	61306453	61305569	0.000000e+00	1531.0
11	TraesCS7D01G041400	chr2D	97.966	885	15	1	2547	3431	381187511	381188392	0.000000e+00	1531.0
12	TraesCS7D01G041400	chr6D	97.514	885	20	2	2547	3431	104483931	104483049	0.000000e+00	1511.0
13	TraesCS7D01G041400	chr6D	97.188	889	25	0	2543	3431	439411392	439412280	0.000000e+00	1504.0
14	TraesCS7D01G041400	chr4D	97.407	887	21	2	2545	3431	96493409	96494293	0.000000e+00	1509.0
15	TraesCS7D01G041400	chr3D	97.194	891	24	1	2541	3431	582832259	582831370	0.000000e+00	1506.0
16	TraesCS7D01G041400	chr3D	97.175	885	23	2	2547	3431	22101887	22101005	0.000000e+00	1495.0
17	TraesCS7D01G041400	chr3D	80.952	1386	222	33	1042	2402	1663754	1665122	0.000000e+00	1059.0
18	TraesCS7D01G041400	chr3D	80.391	1331	222	29	1089	2397	544781508	544782821	0.000000e+00	976.0
19	TraesCS7D01G041400	chr3D	77.794	1342	234	46	1084	2399	1650919	1652222	0.000000e+00	769.0
20	TraesCS7D01G041400	chr3D	89.878	573	54	2	1	573	23170616	23171184	0.000000e+00	734.0
21	TraesCS7D01G041400	chr3D	89.878	573	52	4	1	573	552628474	552629040	0.000000e+00	732.0
22	TraesCS7D01G041400	chr3D	89.703	573	55	2	1	573	85392744	85392176	0.000000e+00	728.0
23	TraesCS7D01G041400	chr3D	89.703	573	55	2	1	573	281091318	281091886	0.000000e+00	728.0
24	TraesCS7D01G041400	chr3D	77.913	987	198	13	1398	2374	1666308	1667284	6.340000e-167	597.0
25	TraesCS7D01G041400	chr5D	96.756	894	27	2	2538	3431	286954010	286954901	0.000000e+00	1489.0
26	TraesCS7D01G041400	chr5D	90.510	569	50	2	5	573	4360971	4361535	0.000000e+00	749.0
27	TraesCS7D01G041400	chr3A	80.708	1384	232	28	1042	2402	7307421	7306050	0.000000e+00	1044.0
28	TraesCS7D01G041400	chr3A	80.150	1330	222	29	1091	2397	681459029	681460339	0.000000e+00	955.0
29	TraesCS7D01G041400	chr3A	77.615	1300	235	42	1084	2364	7357873	7356611	0.000000e+00	737.0
30	TraesCS7D01G041400	chr3A	80.201	596	99	13	1136	1727	7407186	7407766	2.450000e-116	429.0
31	TraesCS7D01G041400	chr3B	77.913	1399	253	33	1019	2377	3769231	3770613	0.000000e+00	821.0
32	TraesCS7D01G041400	chr3B	77.754	1398	257	30	1019	2377	4669761	4671143	0.000000e+00	809.0
33	TraesCS7D01G041400	chr3B	78.830	1214	209	33	1089	2271	720957171	720958367	0.000000e+00	774.0
34	TraesCS7D01G041400	chr3B	77.846	1300	250	27	1087	2364	4642366	4641083	0.000000e+00	771.0
35	TraesCS7D01G041400	chr3B	89.474	57	6	0	2489	2545	3737410	3737354	4.750000e-09	73.1
36	TraesCS7D01G041400	chr3B	92.157	51	4	0	2490	2540	4630002	4629952	4.750000e-09	73.1
37	TraesCS7D01G041400	chr3B	89.474	57	6	0	2489	2545	4636174	4636118	4.750000e-09	73.1
38	TraesCS7D01G041400	chr3B	89.474	57	6	0	2489	2545	5144484	5144540	4.750000e-09	73.1
39	TraesCS7D01G041400	chr3B	89.474	57	6	0	2489	2545	5166402	5166458	4.750000e-09	73.1
40	TraesCS7D01G041400	chr5A	90.368	571	51	2	1	571	618481565	618482131	0.000000e+00	747.0
41	TraesCS7D01G041400	chr7B	90.052	573	53	3	1	573	462246157	462245589	0.000000e+00	739.0
42	TraesCS7D01G041400	chr1D	89.703	573	54	3	1	573	468047118	468047685	0.000000e+00	726.0

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	TraesCS7D01G041400	chr7D	20613859	20617289	3430	False	6336	6336	100.0000	1	3431	1	chr7D.!!$F1	3430
1	TraesCS7D01G041400	chr7D	111060469	111061346	877	True	1496	1496	97.3860	2552	3431	1	chr7D.!!$R1	879
2	TraesCS7D01G041400	chr7A	20991679	20993317	1638	False	2627	2627	95.5210	571	2220	1	chr7A.!!$F1	1649
3	TraesCS7D01G041400	chr7A	20771695	20772680	985	True	902	902	83.5690	1446	2414	1	chr7A.!!$R1	968
4	TraesCS7D01G041400	chrUn	296649816	296651345	1529	False	1707	1707	86.7550	974	2545	1	chrUn.!!$F2	1571
5	TraesCS7D01G041400	chr4A	669456846	669458375	1529	True	1707	1707	86.7550	974	2545	1	chr4A.!!$R1	1571
6	TraesCS7D01G041400	chr4A	589914683	589915251	568	False	726	726	89.7030	2	573	1	chr4A.!!$F1	571
7	TraesCS7D01G041400	chr2D	61305569	61306453	884	True	1531	1531	97.8580	2545	3431	1	chr2D.!!$R1	886
8	TraesCS7D01G041400	chr2D	381187511	381188392	881	False	1531	1531	97.9660	2547	3431	1	chr2D.!!$F1	884
9	TraesCS7D01G041400	chr6D	104483049	104483931	882	True	1511	1511	97.5140	2547	3431	1	chr6D.!!$R1	884
10	TraesCS7D01G041400	chr6D	439411392	439412280	888	False	1504	1504	97.1880	2543	3431	1	chr6D.!!$F1	888
11	TraesCS7D01G041400	chr4D	96493409	96494293	884	False	1509	1509	97.4070	2545	3431	1	chr4D.!!$F1	886
12	TraesCS7D01G041400	chr3D	582831370	582832259	889	True	1506	1506	97.1940	2541	3431	1	chr3D.!!$R3	890
13	TraesCS7D01G041400	chr3D	22101005	22101887	882	True	1495	1495	97.1750	2547	3431	1	chr3D.!!$R1	884
14	TraesCS7D01G041400	chr3D	544781508	544782821	1313	False	976	976	80.3910	1089	2397	1	chr3D.!!$F4	1308
15	TraesCS7D01G041400	chr3D	1663754	1667284	3530	False	828	1059	79.4325	1042	2402	2	chr3D.!!$F6	1360
16	TraesCS7D01G041400	chr3D	1650919	1652222	1303	False	769	769	77.7940	1084	2399	1	chr3D.!!$F1	1315
17	TraesCS7D01G041400	chr3D	23170616	23171184	568	False	734	734	89.8780	1	573	1	chr3D.!!$F2	572
18	TraesCS7D01G041400	chr3D	552628474	552629040	566	False	732	732	89.8780	1	573	1	chr3D.!!$F5	572
19	TraesCS7D01G041400	chr3D	85392176	85392744	568	True	728	728	89.7030	1	573	1	chr3D.!!$R2	572
20	TraesCS7D01G041400	chr3D	281091318	281091886	568	False	728	728	89.7030	1	573	1	chr3D.!!$F3	572
21	TraesCS7D01G041400	chr5D	286954010	286954901	891	False	1489	1489	96.7560	2538	3431	1	chr5D.!!$F2	893
22	TraesCS7D01G041400	chr5D	4360971	4361535	564	False	749	749	90.5100	5	573	1	chr5D.!!$F1	568
23	TraesCS7D01G041400	chr3A	7306050	7307421	1371	True	1044	1044	80.7080	1042	2402	1	chr3A.!!$R1	1360
24	TraesCS7D01G041400	chr3A	681459029	681460339	1310	False	955	955	80.1500	1091	2397	1	chr3A.!!$F2	1306
25	TraesCS7D01G041400	chr3A	7356611	7357873	1262	True	737	737	77.6150	1084	2364	1	chr3A.!!$R2	1280
26	TraesCS7D01G041400	chr3A	7407186	7407766	580	False	429	429	80.2010	1136	1727	1	chr3A.!!$F1	591
27	TraesCS7D01G041400	chr3B	3769231	3770613	1382	False	821	821	77.9130	1019	2377	1	chr3B.!!$F1	1358
28	TraesCS7D01G041400	chr3B	4669761	4671143	1382	False	809	809	77.7540	1019	2377	1	chr3B.!!$F2	1358
29	TraesCS7D01G041400	chr3B	720957171	720958367	1196	False	774	774	78.8300	1089	2271	1	chr3B.!!$F5	1182
30	TraesCS7D01G041400	chr3B	4641083	4642366	1283	True	771	771	77.8460	1087	2364	1	chr3B.!!$R4	1277
31	TraesCS7D01G041400	chr5A	618481565	618482131	566	False	747	747	90.3680	1	571	1	chr5A.!!$F1	570
32	TraesCS7D01G041400	chr7B	462245589	462246157	568	True	739	739	90.0520	1	573	1	chr7B.!!$R1	572
33	TraesCS7D01G041400	chr1D	468047118	468047685	567	False	726	726	89.7030	1	573	1	chr1D.!!$F1	572

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
609	613	0.176910	GCTGGACTGGAGGACTAAGC	59.823	60.0	0.0	0.0	0.0	3.09	F
2121	2214	0.321671	TTGCGGAGGAGGAGAAACTG	59.678	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2309	2408	0.458716	GTAGACGAGCAACAGCCCTC	60.459	60.0	0.00	0.0	0.0	4.30	R
3125	3234	1.712018	CCGTCTGATCTACCGCGTCA	61.712	60.0	4.92	0.0	0.0	4.35	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
76	78	2.042686	TGACACAAAAGAGTGCTGCT	57.957	45.000	0.00	0.00	43.23	4.24
103	105	1.523758	GTCTTGGCATCAAACCGAGT	58.476	50.000	0.00	0.00	39.42	4.18
152	154	3.726607	AGAATCTCCATCAAGCATCGTC	58.273	45.455	0.00	0.00	0.00	4.20
168	170	3.071837	TCTACATGGGTCGCCGCA	61.072	61.111	0.00	0.00	37.98	5.69
267	269	2.615465	CCAATCACCAGGCCCTCCA	61.615	63.158	0.00	0.00	33.74	3.86
268	270	1.616921	CAATCACCAGGCCCTCCAT	59.383	57.895	0.00	0.00	33.74	3.41
309	311	2.678580	TCAGATGGTCCGTCGCCA	60.679	61.111	5.40	0.00	40.68	5.69
519	523	0.541998	TGACGCAGGAGAGAGGGAAA	60.542	55.000	0.00	0.00	0.00	3.13
607	611	0.970937	CCGCTGGACTGGAGGACTAA	60.971	60.000	0.00	0.00	0.00	2.24
608	612	0.457851	CGCTGGACTGGAGGACTAAG	59.542	60.000	0.00	0.00	0.00	2.18
609	613	0.176910	GCTGGACTGGAGGACTAAGC	59.823	60.000	0.00	0.00	0.00	3.09
611	615	0.970937	TGGACTGGAGGACTAAGCGG	60.971	60.000	0.00	0.00	0.00	5.52
612	616	0.971447	GGACTGGAGGACTAAGCGGT	60.971	60.000	0.00	0.00	0.00	5.68
613	617	1.684248	GGACTGGAGGACTAAGCGGTA	60.684	57.143	0.00	0.00	0.00	4.02
614	618	1.677052	GACTGGAGGACTAAGCGGTAG	59.323	57.143	0.00	0.00	35.75	3.18
629	635	8.906867	ACTAAGCGGTAGTGTTATCTGTTTATA	58.093	33.333	2.68	0.00	41.75	0.98
632	638	7.424001	AGCGGTAGTGTTATCTGTTTATAGTC	58.576	38.462	0.00	0.00	0.00	2.59
650	656	4.028490	ACGGGCGGGCAGAATCAA	62.028	61.111	8.94	0.00	0.00	2.57
654	660	1.377202	GGCGGGCAGAATCAACAGA	60.377	57.895	0.00	0.00	0.00	3.41
744	750	1.336131	TACTTTTGCATGGCCAAGCA	58.664	45.000	30.72	30.72	39.32	3.91
803	809	4.625972	AATCGGATAACGCGGAAAATTT	57.374	36.364	12.47	0.00	43.86	1.82
804	810	3.392769	TCGGATAACGCGGAAAATTTG	57.607	42.857	12.47	0.00	43.86	2.32
805	811	2.743126	TCGGATAACGCGGAAAATTTGT	59.257	40.909	12.47	0.00	43.86	2.83
806	812	2.843643	CGGATAACGCGGAAAATTTGTG	59.156	45.455	12.47	0.00	34.82	3.33
863	869	7.253905	ACTAGTAGGAAATAGACCAGCAAAA	57.746	36.000	1.45	0.00	0.00	2.44
915	921	6.090129	GCTATCTAGCTATCGTGGAGAAAAG	58.910	44.000	0.00	0.00	45.62	2.27
918	924	9.168451	CTATCTAGCTATCGTGGAGAAAAGATA	57.832	37.037	0.00	0.00	0.00	1.98
922	928	9.729023	CTAGCTATCGTGGAGAAAAGATATATG	57.271	37.037	0.00	0.00	0.00	1.78
923	929	8.128322	AGCTATCGTGGAGAAAAGATATATGT	57.872	34.615	0.00	0.00	0.00	2.29
924	930	8.589338	AGCTATCGTGGAGAAAAGATATATGTT	58.411	33.333	0.00	0.00	0.00	2.71
925	931	9.856488	GCTATCGTGGAGAAAAGATATATGTTA	57.144	33.333	0.00	0.00	0.00	2.41
928	934	9.877178	ATCGTGGAGAAAAGATATATGTTATCC	57.123	33.333	6.94	6.94	0.00	2.59
929	935	8.027189	TCGTGGAGAAAAGATATATGTTATCCG	58.973	37.037	8.94	0.00	0.00	4.18
930	936	8.027189	CGTGGAGAAAAGATATATGTTATCCGA	58.973	37.037	8.94	0.00	0.00	4.55
931	937	9.877178	GTGGAGAAAAGATATATGTTATCCGAT	57.123	33.333	8.94	0.00	0.00	4.18
932	938	9.875691	TGGAGAAAAGATATATGTTATCCGATG	57.124	33.333	8.94	0.00	0.00	3.84
933	939	9.877178	GGAGAAAAGATATATGTTATCCGATGT	57.123	33.333	0.00	0.00	0.00	3.06
1032	1038	1.000771	CCACCTCCTCTCCGTCTCA	60.001	63.158	0.00	0.00	0.00	3.27
1501	1534	2.356135	ACGACAGCAACAACTTGAACT	58.644	42.857	0.00	0.00	0.00	3.01
1863	1930	4.646945	TGGTCATTTAGCTCCACTCTAGAG	59.353	45.833	18.49	18.49	0.00	2.43
2121	2214	0.321671	TTGCGGAGGAGGAGAAACTG	59.678	55.000	0.00	0.00	0.00	3.16
2221	2320	2.517875	AATCATCAGCGCAGGGGC	60.518	61.111	11.47	0.00	0.00	5.80
2292	2391	3.290948	AACCTTGTGCACTTGTTAGGA	57.709	42.857	19.41	0.00	0.00	2.94
2298	2397	1.732259	GTGCACTTGTTAGGATGGTCG	59.268	52.381	10.32	0.00	0.00	4.79
2307	2406	0.784495	TAGGATGGTCGGATAGCCCT	59.216	55.000	0.00	0.00	0.00	5.19
2309	2408	1.187087	GGATGGTCGGATAGCCCTAG	58.813	60.000	0.00	0.00	0.00	3.02
2386	2491	0.394192	CACCAGCTGTCTCACTTGGA	59.606	55.000	13.81	0.00	0.00	3.53
2399	2505	1.611977	CACTTGGACACAGAGGTACGA	59.388	52.381	0.00	0.00	0.00	3.43
2401	2507	2.296471	ACTTGGACACAGAGGTACGAAG	59.704	50.000	0.00	0.00	0.00	3.79
2411	2517	6.073222	ACACAGAGGTACGAAGCAAAATTAAG	60.073	38.462	0.00	0.00	0.00	1.85
2417	2523	6.708949	AGGTACGAAGCAAAATTAAGTTCTCA	59.291	34.615	0.00	0.00	0.00	3.27
2418	2524	7.015877	GGTACGAAGCAAAATTAAGTTCTCAG	58.984	38.462	0.00	0.00	0.00	3.35
2428	2534	9.971922	CAAAATTAAGTTCTCAGTTTCATTCCT	57.028	29.630	0.00	0.00	0.00	3.36
2433	2539	9.621629	TTAAGTTCTCAGTTTCATTCCTAAACA	57.378	29.630	0.00	0.00	38.92	2.83
2434	2540	7.736447	AGTTCTCAGTTTCATTCCTAAACAG	57.264	36.000	0.00	0.00	38.92	3.16
2435	2541	7.283329	AGTTCTCAGTTTCATTCCTAAACAGT	58.717	34.615	0.00	0.00	38.92	3.55
2436	2542	7.442666	AGTTCTCAGTTTCATTCCTAAACAGTC	59.557	37.037	0.00	0.00	38.92	3.51
2437	2543	6.826668	TCTCAGTTTCATTCCTAAACAGTCA	58.173	36.000	0.00	0.00	38.92	3.41
2438	2544	6.706270	TCTCAGTTTCATTCCTAAACAGTCAC	59.294	38.462	0.00	0.00	38.92	3.67
2439	2545	6.591935	TCAGTTTCATTCCTAAACAGTCACT	58.408	36.000	0.00	0.00	38.92	3.41
2440	2546	7.732025	TCAGTTTCATTCCTAAACAGTCACTA	58.268	34.615	0.00	0.00	38.92	2.74
2441	2547	7.872993	TCAGTTTCATTCCTAAACAGTCACTAG	59.127	37.037	0.00	0.00	38.92	2.57
2442	2548	6.651225	AGTTTCATTCCTAAACAGTCACTAGC	59.349	38.462	0.00	0.00	38.92	3.42
2443	2549	5.086104	TCATTCCTAAACAGTCACTAGCC	57.914	43.478	0.00	0.00	0.00	3.93
2444	2550	4.530553	TCATTCCTAAACAGTCACTAGCCA	59.469	41.667	0.00	0.00	0.00	4.75
2445	2551	4.967084	TTCCTAAACAGTCACTAGCCAA	57.033	40.909	0.00	0.00	0.00	4.52
2446	2552	5.499004	TTCCTAAACAGTCACTAGCCAAT	57.501	39.130	0.00	0.00	0.00	3.16
2447	2553	6.614694	TTCCTAAACAGTCACTAGCCAATA	57.385	37.500	0.00	0.00	0.00	1.90
2448	2554	5.974108	TCCTAAACAGTCACTAGCCAATAC	58.026	41.667	0.00	0.00	0.00	1.89
2449	2555	5.482526	TCCTAAACAGTCACTAGCCAATACA	59.517	40.000	0.00	0.00	0.00	2.29
2450	2556	6.014070	TCCTAAACAGTCACTAGCCAATACAA	60.014	38.462	0.00	0.00	0.00	2.41
2451	2557	6.313905	CCTAAACAGTCACTAGCCAATACAAG	59.686	42.308	0.00	0.00	0.00	3.16
2455	2561	6.476378	ACAGTCACTAGCCAATACAAGATTT	58.524	36.000	0.00	0.00	0.00	2.17
2730	2839	1.700042	GCTAGCTGGGCCACATACCT	61.700	60.000	7.70	0.00	0.00	3.08
3125	3234	1.810606	CGAGATATGCCCGGAGCTGT	61.811	60.000	0.73	0.85	44.23	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	99	2.486013	GGGTGAAAACCTTGTACTCGGT	60.486	50.000	0.00	0.00	34.27	4.69
103	105	2.290450	GGATCCGGGTGAAAACCTTGTA	60.290	50.000	0.00	0.00	0.00	2.41
152	154	2.369257	ATCTGCGGCGACCCATGTAG	62.369	60.000	12.98	0.00	0.00	2.74
253	255	1.708993	GCATATGGAGGGCCTGGTGA	61.709	60.000	12.95	0.00	34.31	4.02
379	381	3.303135	CCTAGGGCCGCGATGCTA	61.303	66.667	8.23	0.00	0.00	3.49
550	554	2.050623	GACGTCGCCGGCCTATAC	60.051	66.667	23.46	13.14	35.50	1.47
607	611	7.067859	TGACTATAAACAGATAACACTACCGCT	59.932	37.037	0.00	0.00	0.00	5.52
608	612	7.167136	GTGACTATAAACAGATAACACTACCGC	59.833	40.741	0.00	0.00	0.00	5.68
609	613	7.375280	CGTGACTATAAACAGATAACACTACCG	59.625	40.741	0.00	0.00	0.00	4.02
611	615	7.646922	CCCGTGACTATAAACAGATAACACTAC	59.353	40.741	0.00	0.00	0.00	2.73
612	616	7.682741	GCCCGTGACTATAAACAGATAACACTA	60.683	40.741	0.00	0.00	0.00	2.74
613	617	6.570692	CCCGTGACTATAAACAGATAACACT	58.429	40.000	0.00	0.00	0.00	3.55
614	618	5.233689	GCCCGTGACTATAAACAGATAACAC	59.766	44.000	0.00	0.00	0.00	3.32
632	638	4.776322	TGATTCTGCCCGCCCGTG	62.776	66.667	0.00	0.00	0.00	4.94
654	660	4.706842	AAACAGATTACACCACAGGTCT	57.293	40.909	0.00	0.00	31.02	3.85
744	750	4.515944	TGATCCCGTTAATCGTGTTTGTTT	59.484	37.500	0.00	0.00	37.94	2.83
765	771	3.308595	CCGATTATTACGCTGCAAACTGA	59.691	43.478	0.00	0.00	0.00	3.41
803	809	1.339247	ACTGACGTGTTTGGTTCCACA	60.339	47.619	0.00	0.00	0.00	4.17
804	810	1.375551	ACTGACGTGTTTGGTTCCAC	58.624	50.000	0.00	0.00	0.00	4.02
805	811	1.740585	CAACTGACGTGTTTGGTTCCA	59.259	47.619	0.00	0.00	0.00	3.53
806	812	2.011222	TCAACTGACGTGTTTGGTTCC	58.989	47.619	0.00	0.00	0.00	3.62
863	869	9.466497	TTGAATTCTCTTTTGCTTCTATATGGT	57.534	29.630	7.05	0.00	0.00	3.55
929	935	8.972349	CCACGCAAGATGTGATATATATACATC	58.028	37.037	22.89	22.89	46.83	3.06
930	936	8.478066	ACCACGCAAGATGTGATATATATACAT	58.522	33.333	12.50	12.50	39.73	2.29
931	937	7.759433	CACCACGCAAGATGTGATATATATACA	59.241	37.037	0.00	5.13	42.17	2.29
932	938	7.222805	CCACCACGCAAGATGTGATATATATAC	59.777	40.741	0.00	0.00	42.17	1.47
933	939	7.093509	ACCACCACGCAAGATGTGATATATATA	60.094	37.037	0.00	0.00	42.17	0.86
1032	1038	5.157940	AGCAGAGACAAATGATGTACACT	57.842	39.130	0.00	0.00	44.12	3.55
1501	1534	2.994995	ACGGTCATCGCCAGTGGA	60.995	61.111	15.20	0.00	43.89	4.02
1863	1930	2.101082	GGTAGCTAGTACAGTGGCTTCC	59.899	54.545	0.00	1.64	35.72	3.46
2176	2275	2.238646	AGAACATCTTTATGGCCACCGA	59.761	45.455	8.16	2.00	37.43	4.69
2221	2320	2.433868	TCCGACTCAAACTCTTTCCG	57.566	50.000	0.00	0.00	0.00	4.30
2292	2391	1.272760	CCTCTAGGGCTATCCGACCAT	60.273	57.143	0.00	0.00	46.64	3.55
2307	2406	0.612174	AGACGAGCAACAGCCCTCTA	60.612	55.000	0.00	0.00	0.00	2.43
2309	2408	0.458716	GTAGACGAGCAACAGCCCTC	60.459	60.000	0.00	0.00	0.00	4.30
2386	2491	2.902705	TTTGCTTCGTACCTCTGTGT	57.097	45.000	0.00	0.00	0.00	3.72
2399	2505	9.822185	AATGAAACTGAGAACTTAATTTTGCTT	57.178	25.926	0.00	0.00	0.00	3.91
2401	2507	8.703336	GGAATGAAACTGAGAACTTAATTTTGC	58.297	33.333	0.00	0.00	0.00	3.68
2411	2517	7.226720	TGACTGTTTAGGAATGAAACTGAGAAC	59.773	37.037	10.77	0.00	37.62	3.01
2417	2523	6.651225	GCTAGTGACTGTTTAGGAATGAAACT	59.349	38.462	0.00	0.00	37.62	2.66
2418	2524	6.128254	GGCTAGTGACTGTTTAGGAATGAAAC	60.128	42.308	0.00	0.00	37.32	2.78
2428	2534	6.999950	TCTTGTATTGGCTAGTGACTGTTTA	58.000	36.000	0.00	0.00	0.00	2.01
2429	2535	5.865085	TCTTGTATTGGCTAGTGACTGTTT	58.135	37.500	0.00	0.00	0.00	2.83
2430	2536	5.483685	TCTTGTATTGGCTAGTGACTGTT	57.516	39.130	0.00	0.00	0.00	3.16
2431	2537	5.683876	ATCTTGTATTGGCTAGTGACTGT	57.316	39.130	0.00	0.00	0.00	3.55
2432	2538	6.992063	AAATCTTGTATTGGCTAGTGACTG	57.008	37.500	0.00	0.00	0.00	3.51
2433	2539	9.686683	ATAAAAATCTTGTATTGGCTAGTGACT	57.313	29.630	0.00	0.00	0.00	3.41
2495	2604	6.013379	CAGATCCCAGGCCAAGTATAATTCTA	60.013	42.308	5.01	0.00	0.00	2.10
2497	2606	5.006386	CAGATCCCAGGCCAAGTATAATTC	58.994	45.833	5.01	0.00	0.00	2.17
2504	2613	2.233566	TGCAGATCCCAGGCCAAGT	61.234	57.895	5.01	0.00	0.00	3.16
2730	2839	8.598916	TGATGTTAGGTTTAGATGAGTGGTTTA	58.401	33.333	0.00	0.00	0.00	2.01
3039	3148	2.224793	GCCCTTCCTCACCTTGTACTTT	60.225	50.000	0.00	0.00	0.00	2.66
3125	3234	1.712018	CCGTCTGATCTACCGCGTCA	61.712	60.000	4.92	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.