AutoCloner

Multiple sequence alignment - TraesCS2B01G257500

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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	TraesCS2B01G257500	chr2B	100.000	2708	0	0	1	2708	309472103	309469396	0.000000e+00	5001
1	TraesCS2B01G257500	chr2B	93.931	1137	59	8	1581	2708	206783898	206782763	0.000000e+00	1709
2	TraesCS2B01G257500	chr2B	93.717	1130	59	4	1581	2708	435051881	435053000	0.000000e+00	1683
3	TraesCS2B01G257500	chr2B	94.752	343	16	1	1	343	402398668	402398328	1.430000e-147	532
4	TraesCS2B01G257500	chr2B	93.983	349	19	1	1	349	329584548	329584202	6.640000e-146	527
5	TraesCS2B01G257500	chr3B	91.344	2403	143	42	343	2708	372313020	372315394	0.000000e+00	3225
6	TraesCS2B01G257500	chr3B	89.349	2366	214	24	351	2708	363522415	363524750	0.000000e+00	2939
7	TraesCS2B01G257500	chr3B	94.272	419	22	2	1644	2060	467038758	467038340	8.180000e-180	640
8	TraesCS2B01G257500	chrUn	88.963	2383	202	43	341	2706	106422937	106425275	0.000000e+00	2887
9	TraesCS2B01G257500	chrUn	88.376	2383	202	54	341	2706	105920189	105922513	0.000000e+00	2796
10	TraesCS2B01G257500	chrUn	94.955	337	15	2	1	337	108197122	108196788	6.640000e-146	527
11	TraesCS2B01G257500	chrUn	94.925	335	14	2	4	337	375419790	375420122	3.090000e-144	521
12	TraesCS2B01G257500	chrUn	94.328	335	16	2	4	337	210313606	210313938	6.690000e-141	510
13	TraesCS2B01G257500	chrUn	94.065	337	18	2	1	337	359858697	359859031	6.690000e-141	510
14	TraesCS2B01G257500	chrUn	94.328	335	16	2	4	337	404854010	404853678	6.690000e-141	510
15	TraesCS2B01G257500	chrUn	94.328	335	15	3	4	337	415852800	415852469	6.690000e-141	510
16	TraesCS2B01G257500	chrUn	94.328	335	16	2	4	337	444141277	444141609	6.690000e-141	510
17	TraesCS2B01G257500	chrUn	93.769	337	19	1	1	337	94484137	94483803	3.110000e-139	505
18	TraesCS2B01G257500	chr5D	88.460	2383	205	42	341	2706	187625917	187628246	0.000000e+00	2813
19	TraesCS2B01G257500	chr5D	85.680	1669	208	27	348	2002	160585747	160587398	0.000000e+00	1729
20	TraesCS2B01G257500	chr5D	95.224	335	13	2	4	337	201810771	201811103	6.640000e-146	527
21	TraesCS2B01G257500	chr6B	92.992	1698	110	8	341	2033	172841378	172839685	0.000000e+00	2468
22	TraesCS2B01G257500	chr6B	93.623	1129	65	5	1581	2707	449540745	449541868	0.000000e+00	1679
23	TraesCS2B01G257500	chr6B	93.363	1130	68	5	1581	2707	288877602	288876477	0.000000e+00	1664
24	TraesCS2B01G257500	chr6B	94.721	341	16	1	3	343	162098635	162098973	1.850000e-146	529
25	TraesCS2B01G257500	chr6B	94.461	343	17	1	1	343	169339368	169339028	6.640000e-146	527
26	TraesCS2B01G257500	chr7B	94.915	1239	61	2	348	1585	397304386	397303149	0.000000e+00	1938
27	TraesCS2B01G257500	chr7B	95.918	343	12	1	1	343	310782958	310783298	3.050000e-154	555
28	TraesCS2B01G257500	chr7B	95.549	337	13	1	1	337	628078322	628077988	3.070000e-149	538
29	TraesCS2B01G257500	chr7B	95.252	337	14	1	1	337	628086468	628086134	1.430000e-147	532
30	TraesCS2B01G257500	chr1A	87.380	1561	157	28	4	1547	80404305	80402768	0.000000e+00	1755
31	TraesCS2B01G257500	chr4B	94.607	1131	57	4	1581	2708	407897624	407898753	0.000000e+00	1748
32	TraesCS2B01G257500	chr4B	95.044	343	15	1	1	343	396412508	396412848	3.070000e-149	538
33	TraesCS2B01G257500	chr4B	94.461	343	17	1	1	343	131019073	131019413	6.640000e-146	527
34	TraesCS2B01G257500	chr4B	94.461	343	17	1	1	343	242655959	242655619	6.640000e-146	527
35	TraesCS2B01G257500	chr4B	94.444	342	17	1	2	343	327764079	327764418	2.390000e-145	525
36	TraesCS2B01G257500	chr5B	94.154	1129	54	4	1581	2707	593699545	593698427	0.000000e+00	1709
37	TraesCS2B01G257500	chr5B	94.066	1129	54	6	1581	2707	202281402	202282519	0.000000e+00	1701
38	TraesCS2B01G257500	chr7D	93.988	1131	58	7	1581	2707	418462	417338	0.000000e+00	1703
39	TraesCS2B01G257500	chr7D	94.955	337	15	2	1	337	169519258	169519592	6.640000e-146	527
40	TraesCS2B01G257500	chr7D	94.169	343	18	1	1	343	420692477	420692137	3.090000e-144	521
41	TraesCS2B01G257500	chr1B	93.286	1132	71	3	1581	2707	289340508	289341639	0.000000e+00	1664
42	TraesCS2B01G257500	chr1B	94.444	342	17	1	2	343	251120579	251120240	2.390000e-145	525
43	TraesCS2B01G257500	chr2D	95.044	343	15	1	1	343	597743161	597743501	3.070000e-149	538
44	TraesCS2B01G257500	chr2D	94.955	337	15	1	1	337	474023978	474023644	6.640000e-146	527
45	TraesCS2B01G257500	chr4D	95.266	338	12	3	1	337	23793858	23794192	1.430000e-147	532
46	TraesCS2B01G257500	chr4D	94.659	337	16	1	1	337	322093245	322093579	3.090000e-144	521
47	TraesCS2B01G257500	chr3D	95.252	337	14	1	1	337	419710431	419710097	1.430000e-147	532
48	TraesCS2B01G257500	chr6D	94.659	337	16	1	1	337	148548097	148547763	3.090000e-144	521
49	TraesCS2B01G257500	chr6D	94.659	337	16	1	1	337	463046240	463046574	3.090000e-144	521
50	TraesCS2B01G257500	chr6D	94.643	336	16	1	1	336	148539606	148539273	1.110000e-143	520
51	TraesCS2B01G257500	chr6D	94.643	336	16	1	2	337	198064397	198064064	1.110000e-143	520
52	TraesCS2B01G257500	chr6D	94.627	335	14	3	4	337	201052289	201052620	1.440000e-142	516
53	TraesCS2B01G257500	chr6D	94.362	337	17	1	1	337	268767716	268768050	1.440000e-142	516
54	TraesCS2B01G257500	chr6D	94.362	337	17	2	1	337	436867377	436867043	1.440000e-142	516
55	TraesCS2B01G257500	chr1D	94.925	335	13	3	4	337	309237269	309237600	3.090000e-144	521
56	TraesCS2B01G257500	chr1D	94.659	337	16	2	1	337	355324803	355325137	3.090000e-144	521

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	TraesCS2B01G257500	chr2B	309469396	309472103	2707	True	5001	5001	100.000	1	2708	1	chr2B.!!$R2	2707
1	TraesCS2B01G257500	chr2B	206782763	206783898	1135	True	1709	1709	93.931	1581	2708	1	chr2B.!!$R1	1127
2	TraesCS2B01G257500	chr2B	435051881	435053000	1119	False	1683	1683	93.717	1581	2708	1	chr2B.!!$F1	1127
3	TraesCS2B01G257500	chr3B	372313020	372315394	2374	False	3225	3225	91.344	343	2708	1	chr3B.!!$F2	2365
4	TraesCS2B01G257500	chr3B	363522415	363524750	2335	False	2939	2939	89.349	351	2708	1	chr3B.!!$F1	2357
5	TraesCS2B01G257500	chrUn	106422937	106425275	2338	False	2887	2887	88.963	341	2706	1	chrUn.!!$F2	2365
6	TraesCS2B01G257500	chrUn	105920189	105922513	2324	False	2796	2796	88.376	341	2706	1	chrUn.!!$F1	2365
7	TraesCS2B01G257500	chr5D	187625917	187628246	2329	False	2813	2813	88.460	341	2706	1	chr5D.!!$F2	2365
8	TraesCS2B01G257500	chr5D	160585747	160587398	1651	False	1729	1729	85.680	348	2002	1	chr5D.!!$F1	1654
9	TraesCS2B01G257500	chr6B	172839685	172841378	1693	True	2468	2468	92.992	341	2033	1	chr6B.!!$R2	1692
10	TraesCS2B01G257500	chr6B	449540745	449541868	1123	False	1679	1679	93.623	1581	2707	1	chr6B.!!$F2	1126
11	TraesCS2B01G257500	chr6B	288876477	288877602	1125	True	1664	1664	93.363	1581	2707	1	chr6B.!!$R3	1126
12	TraesCS2B01G257500	chr7B	397303149	397304386	1237	True	1938	1938	94.915	348	1585	1	chr7B.!!$R1	1237
13	TraesCS2B01G257500	chr1A	80402768	80404305	1537	True	1755	1755	87.380	4	1547	1	chr1A.!!$R1	1543
14	TraesCS2B01G257500	chr4B	407897624	407898753	1129	False	1748	1748	94.607	1581	2708	1	chr4B.!!$F4	1127
15	TraesCS2B01G257500	chr5B	593698427	593699545	1118	True	1709	1709	94.154	1581	2707	1	chr5B.!!$R1	1126
16	TraesCS2B01G257500	chr5B	202281402	202282519	1117	False	1701	1701	94.066	1581	2707	1	chr5B.!!$F1	1126
17	TraesCS2B01G257500	chr7D	417338	418462	1124	True	1703	1703	93.988	1581	2707	1	chr7D.!!$R1	1126
18	TraesCS2B01G257500	chr1B	289340508	289341639	1131	False	1664	1664	93.286	1581	2707	1	chr1B.!!$F1	1126

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
265	267	0.030101	CGGAGGAGATCGAGTCTTGC	59.970	60.0	0.00	0.00	37.29	4.01	F
338	340	0.531974	CGTGTCCCCGGTTATGGATG	60.532	60.0	0.00	0.00	32.20	3.51	F
1328	1353	0.540830	TACCAAATTTGTGGGCGCCT	60.541	50.0	28.56	0.85	43.56	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1308	1333	0.389296	GGCGCCCACAAATTTGGTAC	60.389	55.0	18.11	7.72	34.44	3.34	R
1431	1456	1.402787	TCAGATCTATCGTGCCTGCA	58.597	50.0	0.00	0.00	0.00	4.41	R
2353	2453	0.322975	ACTCACGCTTCTTCATGGCT	59.677	50.0	0.00	0.00	0.00	4.75	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
37	38	3.054576	AGGCTCAAAGGGATCATGAGAT	58.945	45.455	16.53	5.74	42.48	2.75
57	58	8.668510	TGAGATTATTCATGCTAGAAACTTCC	57.331	34.615	0.00	0.00	0.00	3.46
58	59	7.439356	TGAGATTATTCATGCTAGAAACTTCCG	59.561	37.037	0.00	0.00	0.00	4.30
59	60	7.275920	AGATTATTCATGCTAGAAACTTCCGT	58.724	34.615	0.00	0.00	0.00	4.69
60	61	6.662414	TTATTCATGCTAGAAACTTCCGTG	57.338	37.500	0.00	0.00	0.00	4.94
61	62	3.678056	TCATGCTAGAAACTTCCGTGT	57.322	42.857	0.00	0.00	0.00	4.49
62	63	3.325870	TCATGCTAGAAACTTCCGTGTG	58.674	45.455	0.00	0.00	0.00	3.82
63	64	1.508632	TGCTAGAAACTTCCGTGTGC	58.491	50.000	0.00	0.00	0.00	4.57
68	69	2.443957	GAAACTTCCGTGTGCAGCCG	62.444	60.000	0.00	0.00	0.00	5.52
127	128	4.557205	GTGTGAACTCTTACAGTGGTAGG	58.443	47.826	0.00	0.00	34.56	3.18
144	145	0.563173	AGGCTAGCAGATGTAGGGGA	59.437	55.000	18.24	0.00	0.00	4.81
145	146	1.062121	AGGCTAGCAGATGTAGGGGAA	60.062	52.381	18.24	0.00	0.00	3.97
146	147	1.768870	GGCTAGCAGATGTAGGGGAAA	59.231	52.381	18.24	0.00	0.00	3.13
154	155	3.775316	CAGATGTAGGGGAAAGTAGGTGT	59.225	47.826	0.00	0.00	0.00	4.16
155	156	4.960469	CAGATGTAGGGGAAAGTAGGTGTA	59.040	45.833	0.00	0.00	0.00	2.90
158	159	4.755437	TGTAGGGGAAAGTAGGTGTAACT	58.245	43.478	0.00	0.00	36.74	2.24
164	165	5.337089	GGGGAAAGTAGGTGTAACTGTCTAC	60.337	48.000	0.00	0.00	36.74	2.59
197	198	4.212214	GGTGCTAACACTTCTGAAAGACTG	59.788	45.833	0.00	0.00	43.28	3.51
224	226	4.503910	TCGATCATCCGTTTCTCAAACAT	58.496	39.130	0.00	0.00	41.44	2.71
241	243	5.643348	TCAAACATCATGTAGTGCGAGAAAT	59.357	36.000	0.00	0.00	0.00	2.17
242	244	6.149308	TCAAACATCATGTAGTGCGAGAAATT	59.851	34.615	0.00	0.00	0.00	1.82
243	245	5.725110	ACATCATGTAGTGCGAGAAATTC	57.275	39.130	0.00	0.00	0.00	2.17
245	247	5.292834	ACATCATGTAGTGCGAGAAATTCAG	59.707	40.000	0.00	0.00	0.00	3.02
252	254	0.460284	GCGAGAAATTCAGCGGAGGA	60.460	55.000	9.55	0.00	0.00	3.71
265	267	0.030101	CGGAGGAGATCGAGTCTTGC	59.970	60.000	0.00	0.00	37.29	4.01
269	271	1.590259	GAGATCGAGTCTTGCGGGC	60.590	63.158	0.00	0.00	37.29	6.13
288	290	2.650608	GCAAAAGTGCGTAAACCTCTG	58.349	47.619	0.00	0.00	41.93	3.35
291	293	1.961793	AAGTGCGTAAACCTCTGCAA	58.038	45.000	0.00	0.00	39.34	4.08
298	300	3.435671	GCGTAAACCTCTGCAAAGTGTAT	59.564	43.478	0.00	0.00	0.00	2.29
337	339	1.692173	CCGTGTCCCCGGTTATGGAT	61.692	60.000	0.00	0.00	43.07	3.41
338	340	0.531974	CGTGTCCCCGGTTATGGATG	60.532	60.000	0.00	0.00	32.20	3.51
340	342	1.064979	GTGTCCCCGGTTATGGATGTT	60.065	52.381	0.00	0.00	32.20	2.71
343	345	2.686405	GTCCCCGGTTATGGATGTTTTC	59.314	50.000	0.00	0.00	32.20	2.29
344	346	2.578940	TCCCCGGTTATGGATGTTTTCT	59.421	45.455	0.00	0.00	0.00	2.52
358	362	8.251383	TGGATGTTTTCTGTTTGGGTTTAATA	57.749	30.769	0.00	0.00	0.00	0.98
394	401	3.230976	GGATTGAGTTGGGTGAACCTTT	58.769	45.455	0.00	0.00	41.11	3.11
586	599	3.554934	TCCATGTGCTGACTTGTTTTCT	58.445	40.909	0.00	0.00	0.00	2.52
593	606	1.000938	CTGACTTGTTTTCTGGCTGCC	60.001	52.381	12.87	12.87	0.00	4.85
664	680	4.548451	TGATCTTTCACTCAGTGATGCT	57.452	40.909	8.74	0.00	42.40	3.79
687	704	4.137543	GTTGGAGTTGATGGACTCACTTT	58.862	43.478	7.27	0.00	46.21	2.66
705	722	3.009143	ACTTTATCTTCCAAGCCTTCCGT	59.991	43.478	0.00	0.00	0.00	4.69
715	732	3.255725	CAAGCCTTCCGTTGTTATCGTA	58.744	45.455	0.00	0.00	0.00	3.43
723	740	7.596248	GCCTTCCGTTGTTATCGTATTTAGATA	59.404	37.037	0.00	0.00	0.00	1.98
804	821	8.721478	AGTGTGTGATTGCTACTTTGTTATAAG	58.279	33.333	0.00	0.00	0.00	1.73
880	898	3.260380	ACAGAGATCAGACTGTTTGAGGG	59.740	47.826	7.14	0.00	43.52	4.30
1027	1051	1.082104	GCAAGGAACAAGTTCGCGG	60.082	57.895	6.13	0.00	40.37	6.46
1041	1065	1.878522	CGCGGAACCGGATGAAGAG	60.879	63.158	9.46	0.00	40.19	2.85
1056	1080	2.169769	TGAAGAGACACCTTTTGGACGT	59.830	45.455	0.00	0.00	44.07	4.34
1096	1120	6.431543	CACTAGATACCTGAACATCGGAGTAT	59.568	42.308	0.00	0.00	0.00	2.12
1175	1199	6.688073	TCAAGTTCAAGTTCTAGGAAGGAT	57.312	37.500	0.00	0.00	0.00	3.24
1182	1206	7.733773	TCAAGTTCTAGGAAGGATGTTCATA	57.266	36.000	0.00	0.00	0.00	2.15
1220	1245	5.416952	CCATAGAGTTTTCCTTTGATGCACT	59.583	40.000	0.00	0.00	0.00	4.40
1265	1290	1.303948	CAGCCCACATCACCATGGA	59.696	57.895	21.47	0.00	38.34	3.41
1308	1333	6.042552	ACCACAAGGATCTCAAGGATACTATG	59.957	42.308	0.00	0.00	44.42	2.23
1328	1353	0.540830	TACCAAATTTGTGGGCGCCT	60.541	50.000	28.56	0.85	43.56	5.52
1431	1456	0.326264	GCCAGGAGAACCAGATGTGT	59.674	55.000	0.00	0.00	38.94	3.72
1439	1464	1.174712	AACCAGATGTGTGCAGGCAC	61.175	55.000	17.11	17.11	46.33	5.01
1518	1543	1.686587	ACACGCGATGGATATGAGGAA	59.313	47.619	15.93	0.00	0.00	3.36
1552	1577	3.511540	ACTCGTGGAGAAGAATGATGACA	59.488	43.478	0.00	0.00	33.32	3.58
1621	1679	1.751351	ACATCATCATCGACGACACCT	59.249	47.619	0.00	0.00	0.00	4.00
1688	1746	4.657504	TGGAGCAGATATCATGGAGTCTTT	59.342	41.667	5.32	0.00	0.00	2.52
1690	1748	4.970711	AGCAGATATCATGGAGTCTTTGG	58.029	43.478	5.32	0.00	0.00	3.28
1861	1929	5.065218	GTGCATATGGGTAGTGTTTTCTCTG	59.935	44.000	4.56	0.00	0.00	3.35
2005	2081	6.496218	TGATGCAGATACTAGTCCAGAATCAT	59.504	38.462	0.00	0.00	0.00	2.45
2038	2120	6.293135	GGAACAACAACAACAACAACAACAAT	60.293	34.615	0.00	0.00	0.00	2.71
2303	2403	0.723414	CATCGACACTGTCACATGGC	59.277	55.000	9.84	0.00	32.09	4.40
2445	2545	7.710907	TGACTTTAGTAAGCTAGCATGTTATGG	59.289	37.037	18.83	3.95	34.60	2.74
2447	2547	4.696479	AGTAAGCTAGCATGTTATGGCT	57.304	40.909	18.83	0.00	43.94	4.75
2553	2653	2.884639	CAACCTTCAACAACTACCAGGG	59.115	50.000	0.00	0.00	0.00	4.45
2554	2654	2.414612	ACCTTCAACAACTACCAGGGA	58.585	47.619	0.00	0.00	0.00	4.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.505982	CTGGGTGGCGGTCCATAG	59.494	66.667	0.00	0.00	45.62	2.23
37	38	6.092122	CACACGGAAGTTTCTAGCATGAATAA	59.908	38.462	0.00	0.00	46.40	1.40
45	46	1.461127	CTGCACACGGAAGTTTCTAGC	59.539	52.381	0.00	0.00	46.40	3.42
47	48	1.508632	GCTGCACACGGAAGTTTCTA	58.491	50.000	0.00	0.00	46.40	2.10
48	49	1.166531	GGCTGCACACGGAAGTTTCT	61.167	55.000	0.50	0.00	46.40	2.52
49	50	1.282875	GGCTGCACACGGAAGTTTC	59.717	57.895	0.50	0.00	46.40	2.78
50	51	2.542907	CGGCTGCACACGGAAGTTT	61.543	57.895	0.50	0.00	46.40	2.66
51	52	2.972505	CGGCTGCACACGGAAGTT	60.973	61.111	0.50	0.00	46.40	2.66
68	69	2.611722	GCTAGAGCCCATAGTAGCTTGC	60.612	54.545	0.00	0.00	40.11	4.01
76	77	5.674052	ATCAACTATGCTAGAGCCCATAG	57.326	43.478	11.44	11.44	44.01	2.23
127	128	2.436173	ACTTTCCCCTACATCTGCTAGC	59.564	50.000	8.10	8.10	0.00	3.42
144	145	5.149976	TGGGTAGACAGTTACACCTACTTT	58.850	41.667	0.00	0.00	33.79	2.66
145	146	4.744237	TGGGTAGACAGTTACACCTACTT	58.256	43.478	0.00	0.00	33.79	2.24
146	147	4.393239	TGGGTAGACAGTTACACCTACT	57.607	45.455	0.00	0.00	33.79	2.57
154	155	4.400251	CACCTTACGATGGGTAGACAGTTA	59.600	45.833	0.00	0.00	34.07	2.24
155	156	3.194968	CACCTTACGATGGGTAGACAGTT	59.805	47.826	0.00	0.00	34.07	3.16
158	159	1.479323	GCACCTTACGATGGGTAGACA	59.521	52.381	0.00	0.00	34.07	3.41
164	165	2.093658	AGTGTTAGCACCTTACGATGGG	60.094	50.000	6.04	0.00	46.35	4.00
179	180	6.222038	AGACACAGTCTTTCAGAAGTGTTA	57.778	37.500	12.11	0.00	42.22	2.41
183	184	3.632604	TCGAGACACAGTCTTTCAGAAGT	59.367	43.478	0.70	0.00	43.53	3.01
197	198	3.109619	GAGAAACGGATGATCGAGACAC	58.890	50.000	0.00	0.00	0.00	3.67
205	206	5.649395	ACATGATGTTTGAGAAACGGATGAT	59.351	36.000	0.00	0.00	44.28	2.45
206	207	5.003160	ACATGATGTTTGAGAAACGGATGA	58.997	37.500	0.00	0.00	44.28	2.92
224	226	3.618594	GCTGAATTTCTCGCACTACATGA	59.381	43.478	0.00	0.00	0.00	3.07
241	243	0.394488	ACTCGATCTCCTCCGCTGAA	60.394	55.000	0.00	0.00	0.00	3.02
242	244	0.816018	GACTCGATCTCCTCCGCTGA	60.816	60.000	0.00	0.00	0.00	4.26
243	245	0.817634	AGACTCGATCTCCTCCGCTG	60.818	60.000	0.00	0.00	28.16	5.18
245	247	0.030101	CAAGACTCGATCTCCTCCGC	59.970	60.000	0.00	0.00	36.27	5.54
252	254	1.888436	TTGCCCGCAAGACTCGATCT	61.888	55.000	0.00	0.00	40.46	2.75
269	271	2.032799	TGCAGAGGTTTACGCACTTTTG	59.967	45.455	0.00	0.00	0.00	2.44
279	281	9.953565	AGTTTATATACACTTTGCAGAGGTTTA	57.046	29.630	9.34	4.34	0.00	2.01
298	300	7.502696	ACACGGCTAACCATGATTAGTTTATA	58.497	34.615	8.66	0.00	35.05	0.98
340	342	8.592809	AGCATCATTATTAAACCCAAACAGAAA	58.407	29.630	0.00	0.00	0.00	2.52
343	345	9.868277	TTAAGCATCATTATTAAACCCAAACAG	57.132	29.630	0.00	0.00	0.00	3.16
358	362	7.270047	CAACTCAATCCCAATTAAGCATCATT	58.730	34.615	0.00	0.00	0.00	2.57
394	401	6.471233	TCATGGTGGTTGTTAAACATTGAA	57.529	33.333	0.00	0.00	38.10	2.69
541	553	6.957920	ATATGCTGGCAATGTAACACATAA	57.042	33.333	0.00	0.00	37.97	1.90
578	590	1.034838	ACGTGGCAGCCAGAAAACAA	61.035	50.000	16.83	0.00	32.34	2.83
586	599	1.528076	AACATGAACGTGGCAGCCA	60.528	52.632	11.22	11.22	0.00	4.75
593	606	3.338818	AAAGTCTGCAACATGAACGTG	57.661	42.857	0.00	0.00	0.00	4.49
664	680	2.705658	AGTGAGTCCATCAACTCCAACA	59.294	45.455	1.88	0.00	44.17	3.33
687	704	2.304761	ACAACGGAAGGCTTGGAAGATA	59.695	45.455	3.46	0.00	0.00	1.98
804	821	1.792949	CACGCACAGTACTTGAAGGAC	59.207	52.381	0.00	0.00	0.00	3.85
834	852	4.202295	GCATCAGTGTCATCCCTAGATTGA	60.202	45.833	0.00	0.00	0.00	2.57
836	854	3.713248	TGCATCAGTGTCATCCCTAGATT	59.287	43.478	0.00	0.00	0.00	2.40
1027	1051	1.550976	AGGTGTCTCTTCATCCGGTTC	59.449	52.381	0.00	0.00	0.00	3.62
1041	1065	1.949465	AGTGACGTCCAAAAGGTGTC	58.051	50.000	14.12	0.00	0.00	3.67
1056	1080	6.153000	GGTATCTAGTGACTTCCTTCAAGTGA	59.847	42.308	0.00	0.00	46.10	3.41
1175	1199	2.028112	GGCTCAGTGACTGGTATGAACA	60.028	50.000	13.33	0.00	31.51	3.18
1182	1206	1.198713	CTATGGGCTCAGTGACTGGT	58.801	55.000	13.33	0.00	31.51	4.00
1220	1245	4.024670	GCTCTTTCCTAGACTCCAGGTTA	58.975	47.826	0.00	0.00	34.56	2.85
1265	1290	3.252458	GTGGTAAACTTCTCCAATGCGTT	59.748	43.478	0.00	0.00	32.82	4.84
1308	1333	0.389296	GGCGCCCACAAATTTGGTAC	60.389	55.000	18.11	7.72	34.44	3.34
1328	1353	4.842380	TGATCATCTCCCATTGCTCATCTA	59.158	41.667	0.00	0.00	0.00	1.98
1431	1456	1.402787	TCAGATCTATCGTGCCTGCA	58.597	50.000	0.00	0.00	0.00	4.41
1439	1464	5.404968	GTCATTGCCTTCTTCAGATCTATCG	59.595	44.000	0.00	0.00	0.00	2.92
1688	1746	5.575606	GTCGACTAGAAAAATTGATCGACCA	59.424	40.000	8.70	0.00	46.88	4.02
2005	2081	4.537751	TGTTGTTGTTGTTCCCCTGATTA	58.462	39.130	0.00	0.00	0.00	1.75
2038	2120	4.989168	GGGTTGTTGTTGTTGTTGTTGTTA	59.011	37.500	0.00	0.00	0.00	2.41
2303	2403	3.426695	CGGAAAGCCTGCTAAAACTGATG	60.427	47.826	0.00	0.00	0.00	3.07
2353	2453	0.322975	ACTCACGCTTCTTCATGGCT	59.677	50.000	0.00	0.00	0.00	4.75
2445	2545	0.917259	CGTAGCAACGTCATCTGAGC	59.083	55.000	0.00	0.00	44.21	4.26
2553	2653	6.832520	TCATGAGAGCTCTATCTACCAATC	57.167	41.667	18.25	0.35	0.00	2.67
2554	2654	7.454066	TCAATCATGAGAGCTCTATCTACCAAT	59.546	37.037	18.25	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.