AutoCloner

Multiple sequence alignment - TraesCS7A01G468500

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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	TraesCS7A01G468500	chr7A	100.000	2543	0	0	1	2543	664602102	664604644	0.000000e+00	4697.0
1	TraesCS7A01G468500	chr7A	84.488	967	84	23	887	1832	664699189	664700110	0.000000e+00	894.0
2	TraesCS7A01G468500	chr7A	93.659	552	34	1	1993	2543	131011292	131010741	0.000000e+00	824.0
3	TraesCS7A01G468500	chr7A	82.748	939	94	29	1038	1955	664781165	664780274	0.000000e+00	774.0
4	TraesCS7A01G468500	chr7A	84.218	697	72	19	1070	1758	664873622	664872956	0.000000e+00	643.0
5	TraesCS7A01G468500	chr7A	89.617	183	10	6	1813	1992	664700127	664700303	9.160000e-55	224.0
6	TraesCS7A01G468500	chr7A	97.500	80	2	0	934	1013	664781447	664781368	1.230000e-28	137.0
7	TraesCS7A01G468500	chr7A	93.478	46	3	0	496	541	105360787	105360832	4.540000e-08	69.4
8	TraesCS7A01G468500	chr7D	85.790	2062	182	47	1	1992	574926428	574924408	0.000000e+00	2082.0
9	TraesCS7A01G468500	chr7D	84.808	1119	88	29	886	1992	575074493	575073445	0.000000e+00	1050.0
10	TraesCS7A01G468500	chr7D	85.018	1088	95	37	886	1955	575149723	575148686	0.000000e+00	1044.0
11	TraesCS7A01G468500	chr7D	82.838	1177	121	37	843	1992	574874682	574875804	0.000000e+00	979.0
12	TraesCS7A01G468500	chr7D	84.086	886	94	21	886	1746	575218185	575217322	0.000000e+00	811.0
13	TraesCS7A01G468500	chr7D	87.861	173	11	4	1820	1992	575217314	575217152	7.180000e-46	195.0
14	TraesCS7A01G468500	chr7B	85.009	1134	97	30	886	1992	636433345	636432258	0.000000e+00	1085.0
15	TraesCS7A01G468500	chr7B	84.238	1142	108	31	881	1992	635300851	635301950	0.000000e+00	1046.0
16	TraesCS7A01G468500	chr7B	85.242	908	98	11	1092	1992	635749106	635748228	0.000000e+00	902.0
17	TraesCS7A01G468500	chr7B	86.866	670	49	16	938	1588	635064924	635065573	0.000000e+00	713.0
18	TraesCS7A01G468500	chr7B	88.931	533	45	8	1067	1588	635170650	635171179	0.000000e+00	645.0
19	TraesCS7A01G468500	chr7B	85.714	294	24	7	1657	1944	635065582	635065863	6.880000e-76	294.0
20	TraesCS7A01G468500	chr7B	83.813	278	19	5	1717	1992	635935518	635935265	9.090000e-60	241.0
21	TraesCS7A01G468500	chr7B	87.255	102	7	2	902	1003	635941659	635941564	7.440000e-21	111.0
22	TraesCS7A01G468500	chr7B	76.667	120	20	6	733	851	608725932	608726044	2.730000e-05	60.2
23	TraesCS7A01G468500	chr5A	93.852	553	33	1	1992	2543	376150437	376149885	0.000000e+00	832.0
24	TraesCS7A01G468500	chr5A	92.844	559	39	1	1986	2543	454275480	454276038	0.000000e+00	809.0
25	TraesCS7A01G468500	chr3A	93.478	552	35	1	1993	2543	58157316	58157867	0.000000e+00	819.0
26	TraesCS7A01G468500	chr3A	93.466	551	36	0	1993	2543	278884337	278883787	0.000000e+00	819.0
27	TraesCS7A01G468500	chr6A	93.297	552	36	1	1993	2543	456618581	456619132	0.000000e+00	813.0
28	TraesCS7A01G468500	chr6A	92.857	560	39	1	1985	2543	55101430	55100871	0.000000e+00	811.0
29	TraesCS7A01G468500	chr4A	93.297	552	35	2	1993	2543	102215592	102215042	0.000000e+00	813.0
30	TraesCS7A01G468500	chr4A	92.566	565	40	2	1980	2543	182940322	182940885	0.000000e+00	809.0
31	TraesCS7A01G468500	chr4D	95.652	46	2	0	496	541	397682294	397682339	9.760000e-10	75.0
32	TraesCS7A01G468500	chr6B	100.000	28	0	0	514	541	555959156	555959183	5.000000e-03	52.8

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	TraesCS7A01G468500	chr7A	664602102	664604644	2542	False	4697.0	4697	100.0000	1	2543	1	chr7A.!!$F2	2542
1	TraesCS7A01G468500	chr7A	131010741	131011292	551	True	824.0	824	93.6590	1993	2543	1	chr7A.!!$R1	550
2	TraesCS7A01G468500	chr7A	664872956	664873622	666	True	643.0	643	84.2180	1070	1758	1	chr7A.!!$R2	688
3	TraesCS7A01G468500	chr7A	664699189	664700303	1114	False	559.0	894	87.0525	887	1992	2	chr7A.!!$F3	1105
4	TraesCS7A01G468500	chr7A	664780274	664781447	1173	True	455.5	774	90.1240	934	1955	2	chr7A.!!$R3	1021
5	TraesCS7A01G468500	chr7D	574924408	574926428	2020	True	2082.0	2082	85.7900	1	1992	1	chr7D.!!$R1	1991
6	TraesCS7A01G468500	chr7D	575073445	575074493	1048	True	1050.0	1050	84.8080	886	1992	1	chr7D.!!$R2	1106
7	TraesCS7A01G468500	chr7D	575148686	575149723	1037	True	1044.0	1044	85.0180	886	1955	1	chr7D.!!$R3	1069
8	TraesCS7A01G468500	chr7D	574874682	574875804	1122	False	979.0	979	82.8380	843	1992	1	chr7D.!!$F1	1149
9	TraesCS7A01G468500	chr7D	575217152	575218185	1033	True	503.0	811	85.9735	886	1992	2	chr7D.!!$R4	1106
10	TraesCS7A01G468500	chr7B	636432258	636433345	1087	True	1085.0	1085	85.0090	886	1992	1	chr7B.!!$R4	1106
11	TraesCS7A01G468500	chr7B	635300851	635301950	1099	False	1046.0	1046	84.2380	881	1992	1	chr7B.!!$F3	1111
12	TraesCS7A01G468500	chr7B	635748228	635749106	878	True	902.0	902	85.2420	1092	1992	1	chr7B.!!$R1	900
13	TraesCS7A01G468500	chr7B	635170650	635171179	529	False	645.0	645	88.9310	1067	1588	1	chr7B.!!$F2	521
14	TraesCS7A01G468500	chr7B	635064924	635065863	939	False	503.5	713	86.2900	938	1944	2	chr7B.!!$F4	1006
15	TraesCS7A01G468500	chr5A	376149885	376150437	552	True	832.0	832	93.8520	1992	2543	1	chr5A.!!$R1	551
16	TraesCS7A01G468500	chr5A	454275480	454276038	558	False	809.0	809	92.8440	1986	2543	1	chr5A.!!$F1	557
17	TraesCS7A01G468500	chr3A	58157316	58157867	551	False	819.0	819	93.4780	1993	2543	1	chr3A.!!$F1	550
18	TraesCS7A01G468500	chr3A	278883787	278884337	550	True	819.0	819	93.4660	1993	2543	1	chr3A.!!$R1	550
19	TraesCS7A01G468500	chr6A	456618581	456619132	551	False	813.0	813	93.2970	1993	2543	1	chr6A.!!$F1	550
20	TraesCS7A01G468500	chr6A	55100871	55101430	559	True	811.0	811	92.8570	1985	2543	1	chr6A.!!$R1	558
21	TraesCS7A01G468500	chr4A	102215042	102215592	550	True	813.0	813	93.2970	1993	2543	1	chr4A.!!$R1	550
22	TraesCS7A01G468500	chr4A	182940322	182940885	563	False	809.0	809	92.5660	1980	2543	1	chr4A.!!$F1	563

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
553	591	0.109342	AGGGAGTGCACCTGTTTGAG	59.891	55.0	14.63	0.00	36.85	3.02	F
1132	1408	0.039798	CAGCAACAACATGAAGCGCT	60.040	50.0	2.64	2.64	0.00	5.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1539	1845	0.616679	ACGGGGAAGTGCTAGGCTAA	60.617	55.000	0.00	0.0	0.0	3.09	R
2037	2428	1.228124	CCAACAGTCCGGCCAAAGA	60.228	57.895	2.24	0.0	0.0	2.52	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	0.177604	CTCCATCCCAGCTCTCACAC	59.822	60.000	0.00	0.00	0.00	3.82
42	43	0.537188	CCCAGCTCTCACACGGTAAT	59.463	55.000	0.00	0.00	0.00	1.89
133	165	9.899661	ATATGTAGTTAAAATAGTGCCAGTGAA	57.100	29.630	0.00	0.00	0.00	3.18
134	166	8.807948	ATGTAGTTAAAATAGTGCCAGTGAAT	57.192	30.769	0.00	0.00	0.00	2.57
135	167	8.630054	TGTAGTTAAAATAGTGCCAGTGAATT	57.370	30.769	0.00	0.00	0.00	2.17
197	230	7.169645	GGCATGCCACTAATATTGTACAAAATG	59.830	37.037	32.08	5.00	35.81	2.32
230	263	2.109181	GCCAGATACGAGGGTGCC	59.891	66.667	0.00	0.00	0.00	5.01
238	271	3.322254	AGATACGAGGGTGCCTGATAAAG	59.678	47.826	0.00	0.00	31.76	1.85
246	279	1.143183	GCCTGATAAAGCCGGACGA	59.857	57.895	5.05	0.00	0.00	4.20
249	282	1.136305	CCTGATAAAGCCGGACGAAGA	59.864	52.381	5.05	0.00	0.00	2.87
258	291	0.443869	CCGGACGAAGAAAGTGCATG	59.556	55.000	0.00	0.00	0.00	4.06
260	293	1.531149	CGGACGAAGAAAGTGCATGTT	59.469	47.619	0.00	0.00	0.00	2.71
261	294	2.734606	CGGACGAAGAAAGTGCATGTTA	59.265	45.455	0.00	0.00	0.00	2.41
262	295	3.185594	CGGACGAAGAAAGTGCATGTTAA	59.814	43.478	0.00	0.00	0.00	2.01
263	296	4.666655	CGGACGAAGAAAGTGCATGTTAAG	60.667	45.833	0.00	0.00	0.00	1.85
264	297	4.213482	GGACGAAGAAAGTGCATGTTAAGT	59.787	41.667	0.00	0.00	0.00	2.24
265	298	5.407387	GGACGAAGAAAGTGCATGTTAAGTA	59.593	40.000	0.00	0.00	0.00	2.24
266	299	6.224420	ACGAAGAAAGTGCATGTTAAGTAC	57.776	37.500	0.00	0.00	0.00	2.73
267	300	5.756347	ACGAAGAAAGTGCATGTTAAGTACA	59.244	36.000	0.00	0.00	41.97	2.90
320	353	8.095937	ACTGTACTTCTACAAAATTAACAGCC	57.904	34.615	0.00	0.00	32.24	4.85
339	372	4.941263	CAGCCTAGTTTATTTAGTGGCACA	59.059	41.667	21.41	2.83	41.12	4.57
387	420	1.173913	GTTGTGGGGTGCCAAGTATC	58.826	55.000	0.00	0.00	0.00	2.24
396	429	2.492088	GGTGCCAAGTATCCTCCAAAAC	59.508	50.000	0.00	0.00	0.00	2.43
440	478	6.151817	CCTCTGATCCATATTATCTGACGACA	59.848	42.308	0.00	0.00	30.84	4.35
456	494	7.706159	TCTGACGACAGTTTAGTACAACTTTA	58.294	34.615	14.38	0.00	43.81	1.85
458	496	6.418819	TGACGACAGTTTAGTACAACTTTAGC	59.581	38.462	0.00	0.00	34.60	3.09
465	503	9.730420	CAGTTTAGTACAACTTTAGCACAAAAT	57.270	29.630	0.00	0.00	34.60	1.82
482	520	6.561350	GCACAAAATTTGTACTAAAGTTGCGG	60.561	38.462	11.33	0.00	43.23	5.69
485	523	4.839668	ATTTGTACTAAAGTTGCGGCAA	57.160	36.364	12.11	12.11	0.00	4.52
486	524	3.612472	TTGTACTAAAGTTGCGGCAAC	57.388	42.857	32.68	32.68	43.83	4.17
494	532	0.817013	AGTTGCGGCAACAATATGGG	59.183	50.000	38.11	0.00	45.66	4.00
524	562	7.551617	AGTTATACTAAAACTGCGGCAAGTAAT	59.448	33.333	13.61	7.05	35.87	1.89
534	572	2.611971	GCGGCAAGTAATATGGATCGGA	60.612	50.000	0.00	0.00	0.00	4.55
553	591	0.109342	AGGGAGTGCACCTGTTTGAG	59.891	55.000	14.63	0.00	36.85	3.02
562	600	3.318839	TGCACCTGTTTGAGAAATGAAGG	59.681	43.478	0.00	0.00	0.00	3.46
563	601	3.569701	GCACCTGTTTGAGAAATGAAGGA	59.430	43.478	0.00	0.00	0.00	3.36
564	602	4.320788	GCACCTGTTTGAGAAATGAAGGAG	60.321	45.833	0.00	0.00	0.00	3.69
565	603	3.823304	ACCTGTTTGAGAAATGAAGGAGC	59.177	43.478	0.00	0.00	0.00	4.70
566	604	3.120060	CCTGTTTGAGAAATGAAGGAGCG	60.120	47.826	0.00	0.00	0.00	5.03
567	605	3.738982	TGTTTGAGAAATGAAGGAGCGA	58.261	40.909	0.00	0.00	0.00	4.93
568	606	4.133820	TGTTTGAGAAATGAAGGAGCGAA	58.866	39.130	0.00	0.00	0.00	4.70
569	607	4.024048	TGTTTGAGAAATGAAGGAGCGAAC	60.024	41.667	0.00	0.00	0.00	3.95
570	608	2.337583	TGAGAAATGAAGGAGCGAACG	58.662	47.619	0.00	0.00	0.00	3.95
580	618	1.814169	GAGCGAACGATCCCCAACC	60.814	63.158	0.89	0.00	0.00	3.77
593	631	5.278463	CGATCCCCAACCATTTGTCATAATC	60.278	44.000	0.00	0.00	0.00	1.75
661	699	6.861065	TGTTGCGAAGTTCTCTAGATTTTT	57.139	33.333	0.56	0.00	0.00	1.94
690	728	6.684897	AATGGGTCCAAATCTTGAAATGAA	57.315	33.333	0.00	0.00	0.00	2.57
692	730	4.527816	TGGGTCCAAATCTTGAAATGAAGG	59.472	41.667	0.00	0.00	0.00	3.46
703	741	3.476552	TGAAATGAAGGAAGCAACGTCT	58.523	40.909	0.00	0.00	0.00	4.18
710	748	0.796927	GGAAGCAACGTCTTGTAGCC	59.203	55.000	0.00	0.00	0.00	3.93
715	753	0.438830	CAACGTCTTGTAGCCGAAGC	59.561	55.000	0.00	0.00	40.32	3.86
740	778	7.201732	GCAGGCTTGCTAAATAAATTCTACTCA	60.202	37.037	14.45	0.00	46.95	3.41
743	781	8.338986	GGCTTGCTAAATAAATTCTACTCACTC	58.661	37.037	0.00	0.00	0.00	3.51
800	841	8.848474	TCTGAATCAGATGTATATAGACGTGA	57.152	34.615	9.18	0.00	35.39	4.35
817	858	5.924825	AGACGTGATTTACTGTGTTTAGTCC	59.075	40.000	0.00	0.00	32.19	3.85
904	948	5.069516	GGTGATACATTCCATTCCAAGCAAT	59.930	40.000	0.00	0.00	0.00	3.56
923	970	5.120519	AGCAATGAATTTGTAAATGCCAACG	59.879	36.000	0.00	0.00	37.65	4.10
987	1039	4.087182	CCTCCAGCTCTCCCGTTATATAA	58.913	47.826	0.00	0.00	0.00	0.98
988	1040	4.158764	CCTCCAGCTCTCCCGTTATATAAG	59.841	50.000	0.00	0.00	0.00	1.73
989	1041	4.087182	TCCAGCTCTCCCGTTATATAAGG	58.913	47.826	7.99	7.99	0.00	2.69
1027	1265	2.218603	CCTCAGTACAAACGCCTTGTT	58.781	47.619	8.60	0.00	46.49	2.83
1036	1279	1.594331	AACGCCTTGTTTCCTCTCAC	58.406	50.000	0.00	0.00	37.59	3.51
1048	1298	3.637911	TCCTCTCACTCACCTCTAGTC	57.362	52.381	0.00	0.00	0.00	2.59
1051	1301	3.054728	CCTCTCACTCACCTCTAGTCTCA	60.055	52.174	0.00	0.00	0.00	3.27
1072	1322	4.394712	CTCGCCAAGAACCCGCCT	62.395	66.667	0.00	0.00	0.00	5.52
1100	1376	1.027792	AAGAGTCTCGAGGTCTCCGC	61.028	60.000	24.17	9.72	0.00	5.54
1118	1394	2.733218	CGTCGACCGAAGCAGCAA	60.733	61.111	10.58	0.00	39.56	3.91
1132	1408	0.039798	CAGCAACAACATGAAGCGCT	60.040	50.000	2.64	2.64	0.00	5.92
1396	1702	2.348998	CGTTCAAGGCCCTGCTCT	59.651	61.111	0.00	0.00	0.00	4.09
1425	1731	2.413142	GCAGGAGTACGGCTACGGT	61.413	63.158	0.00	0.00	46.48	4.83
1434	1740	2.682494	GGCTACGGTCACCCAGGA	60.682	66.667	0.00	0.00	0.00	3.86
1539	1845	1.210413	CGATGCCGCGCTCTACTAT	59.790	57.895	5.56	0.00	0.00	2.12
1666	2002	3.277211	AATTGCCAGCTGCTGCGTG	62.277	57.895	23.86	11.74	45.42	5.34
1685	2022	0.912486	GCTGACCAATCTACCCCTGT	59.088	55.000	0.00	0.00	0.00	4.00
1702	2039	3.370421	CCCTGTGTGGATGCTGTACATAA	60.370	47.826	0.00	0.00	39.84	1.90
1707	2045	3.134458	GTGGATGCTGTACATAAGAGGC	58.866	50.000	0.00	0.00	39.84	4.70
1746	2085	1.975680	GGTAGAATAGGGATTCCGCCA	59.024	52.381	0.00	0.00	42.25	5.69
1781	2121	4.379918	GCAGCTCAACAATTTTAGGACCTC	60.380	45.833	0.00	0.00	0.00	3.85
1872	2254	4.541705	AGCTCTAGATCAAGCTCTGGTAA	58.458	43.478	10.48	0.00	45.57	2.85
1877	2259	2.568956	AGATCAAGCTCTGGTAACTGCA	59.431	45.455	0.00	0.00	35.12	4.41
1878	2260	2.928801	TCAAGCTCTGGTAACTGCAA	57.071	45.000	0.00	0.00	35.12	4.08
1879	2261	3.423539	TCAAGCTCTGGTAACTGCAAT	57.576	42.857	0.00	0.00	35.12	3.56
1880	2262	3.754965	TCAAGCTCTGGTAACTGCAATT	58.245	40.909	0.00	0.00	35.12	2.32
2005	2396	1.203187	TGCTACTTGAGGGAGTCCTGT	60.203	52.381	9.58	0.00	45.05	4.00
2026	2417	2.500269	TTAGGGGGTATCCGGACATT	57.500	50.000	6.12	0.00	36.01	2.71
2112	2503	3.280295	GTCCGGATGAGACTCTACTTGA	58.720	50.000	7.81	0.00	0.00	3.02
2167	2558	5.684030	GCATATCTCCTCCTTTGTAACCGAA	60.684	44.000	0.00	0.00	0.00	4.30
2171	2562	4.102054	TCTCCTCCTTTGTAACCGAACTTT	59.898	41.667	0.00	0.00	0.00	2.66
2178	2569	6.598850	TCCTTTGTAACCGAACTTTTGTAACT	59.401	34.615	0.00	0.00	0.00	2.24
2182	2573	8.715191	TTGTAACCGAACTTTTGTAACTCTAA	57.285	30.769	0.00	0.00	0.00	2.10
2184	2575	7.981225	TGTAACCGAACTTTTGTAACTCTAACT	59.019	33.333	0.00	0.00	0.00	2.24
2302	2693	3.128764	CGTGGTAGATCAGCTCTTGTACA	59.871	47.826	0.00	0.00	35.28	2.90
2343	2734	1.927487	TCAAGCAGGACGTAGGGTTA	58.073	50.000	0.00	0.00	0.00	2.85
2445	2837	0.693430	GGGACCCCTACCCGAAATCT	60.693	60.000	0.00	0.00	37.85	2.40
2455	2847	1.271488	ACCCGAAATCTGCCGGTTTTA	60.271	47.619	1.90	0.00	43.93	1.52
2504	2896	1.812922	CCTCTGTGCCATCGCTGTC	60.813	63.158	0.00	0.00	35.36	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	3.120338	AGCACGTGTTCATTCAATTACCG	60.120	43.478	18.38	0.00	0.00	4.02
42	43	2.548057	GAGGAAGCACGTGTTCATTCAA	59.452	45.455	18.38	0.00	0.00	2.69
107	139	9.899661	TTCACTGGCACTATTTTAACTACATAT	57.100	29.630	0.00	0.00	0.00	1.78
188	221	6.435428	CCTGGCCGTATATTTCATTTTGTAC	58.565	40.000	0.00	0.00	0.00	2.90
208	241	2.511452	CCCTCGTATCTGGCCCTGG	61.511	68.421	0.00	0.00	0.00	4.45
230	263	2.579207	TCTTCGTCCGGCTTTATCAG	57.421	50.000	0.00	0.00	0.00	2.90
238	271	1.298859	ATGCACTTTCTTCGTCCGGC	61.299	55.000	0.00	0.00	0.00	6.13
294	327	8.565416	GGCTGTTAATTTTGTAGAAGTACAGTT	58.435	33.333	0.00	0.00	40.33	3.16
298	331	9.433153	ACTAGGCTGTTAATTTTGTAGAAGTAC	57.567	33.333	0.00	0.00	0.00	2.73
312	345	7.120138	GTGCCACTAAATAAACTAGGCTGTTAA	59.880	37.037	0.00	0.00	41.12	2.01
320	353	9.691362	ACAAAATTGTGCCACTAAATAAACTAG	57.309	29.630	0.00	0.00	40.49	2.57
334	367	7.585936	GCAATTTAGTAACAACAAAATTGTGCC	59.414	33.333	16.35	2.33	44.97	5.01
339	372	9.108284	AGCTTGCAATTTAGTAACAACAAAATT	57.892	25.926	0.00	0.00	33.07	1.82
410	443	9.206690	GTCAGATAATATGGATCAGAGGGAATA	57.793	37.037	0.00	0.00	0.00	1.75
412	445	6.153510	CGTCAGATAATATGGATCAGAGGGAA	59.846	42.308	0.00	0.00	0.00	3.97
431	469	5.762825	AGTTGTACTAAACTGTCGTCAGA	57.237	39.130	16.64	0.00	43.76	3.27
432	470	6.823678	AAAGTTGTACTAAACTGTCGTCAG	57.176	37.500	8.17	8.17	46.18	3.51
458	496	6.561350	GCCGCAACTTTAGTACAAATTTTGTG	60.561	38.462	22.04	8.79	45.03	3.33
465	503	3.377485	TGTTGCCGCAACTTTAGTACAAA	59.623	39.130	30.89	9.21	43.85	2.83
477	515	2.130272	TACCCATATTGTTGCCGCAA	57.870	45.000	0.38	0.38	0.00	4.85
494	532	7.064060	TGCCGCAGTTTTAGTATAACTTTAC	57.936	36.000	3.51	0.00	33.73	2.01
508	546	3.616219	TCCATATTACTTGCCGCAGTTT	58.384	40.909	0.00	0.00	0.00	2.66
524	562	0.105709	TGCACTCCCTCCGATCCATA	60.106	55.000	0.00	0.00	0.00	2.74
534	572	0.109342	CTCAAACAGGTGCACTCCCT	59.891	55.000	17.98	2.00	0.00	4.20
553	591	2.285488	GGATCGTTCGCTCCTTCATTTC	59.715	50.000	7.68	0.00	0.00	2.17
562	600	1.814169	GGTTGGGGATCGTTCGCTC	60.814	63.158	10.01	2.31	35.26	5.03
563	601	1.910580	ATGGTTGGGGATCGTTCGCT	61.911	55.000	10.01	0.00	35.26	4.93
564	602	1.029947	AATGGTTGGGGATCGTTCGC	61.030	55.000	2.08	2.08	0.00	4.70
565	603	1.132262	CAAATGGTTGGGGATCGTTCG	59.868	52.381	0.00	0.00	0.00	3.95
566	604	2.163613	GACAAATGGTTGGGGATCGTTC	59.836	50.000	0.00	0.00	39.22	3.95
567	605	2.167662	GACAAATGGTTGGGGATCGTT	58.832	47.619	0.00	0.00	39.22	3.85
568	606	1.074727	TGACAAATGGTTGGGGATCGT	59.925	47.619	0.00	0.00	39.22	3.73
569	607	1.832883	TGACAAATGGTTGGGGATCG	58.167	50.000	0.00	0.00	39.22	3.69
570	608	5.835280	AGATTATGACAAATGGTTGGGGATC	59.165	40.000	0.00	0.00	39.22	3.36
622	660	3.420576	CGCAACAACGAAACTGTAATTGG	59.579	43.478	0.00	0.00	34.06	3.16
637	675	6.861065	AAAATCTAGAGAACTTCGCAACAA	57.139	33.333	0.00	0.00	0.00	2.83
661	699	7.789202	TTCAAGATTTGGACCCATTTCATAA	57.211	32.000	0.00	0.00	0.00	1.90
680	718	4.023707	AGACGTTGCTTCCTTCATTTCAAG	60.024	41.667	0.00	0.00	0.00	3.02
690	728	1.608283	GGCTACAAGACGTTGCTTCCT	60.608	52.381	0.00	0.00	44.60	3.36
692	730	0.438830	CGGCTACAAGACGTTGCTTC	59.561	55.000	0.00	0.00	42.99	3.86
715	753	8.125448	GTGAGTAGAATTTATTTAGCAAGCCTG	58.875	37.037	0.00	0.00	0.00	4.85
721	759	7.553334	ACCGAGTGAGTAGAATTTATTTAGCA	58.447	34.615	0.00	0.00	0.00	3.49
740	778	8.848182	AGAATATCTTATAGTTCGAAACCGAGT	58.152	33.333	0.00	0.00	37.37	4.18
904	948	4.520874	TCTCCGTTGGCATTTACAAATTCA	59.479	37.500	0.00	0.00	0.00	2.57
923	970	5.163509	GGTCCTCTTGCCATTATTTTTCTCC	60.164	44.000	0.00	0.00	0.00	3.71
1027	1265	3.589735	AGACTAGAGGTGAGTGAGAGGAA	59.410	47.826	0.00	0.00	0.00	3.36
1033	1276	3.372133	GGGATGAGACTAGAGGTGAGTGA	60.372	52.174	0.00	0.00	0.00	3.41
1034	1277	2.955660	GGGATGAGACTAGAGGTGAGTG	59.044	54.545	0.00	0.00	0.00	3.51
1035	1278	2.856231	AGGGATGAGACTAGAGGTGAGT	59.144	50.000	0.00	0.00	0.00	3.41
1036	1279	3.486383	GAGGGATGAGACTAGAGGTGAG	58.514	54.545	0.00	0.00	0.00	3.51
1048	1298	0.462759	GGTTCTTGGCGAGGGATGAG	60.463	60.000	0.97	0.00	0.00	2.90
1051	1301	2.998949	GGGTTCTTGGCGAGGGAT	59.001	61.111	0.97	0.00	0.00	3.85
1072	1322	0.608308	TCGAGACTCTTGGAAGCGGA	60.608	55.000	0.03	0.00	0.00	5.54
1100	1376	4.717629	TGCTGCTTCGGTCGACGG	62.718	66.667	16.37	16.37	44.45	4.79
1118	1394	4.950744	GCAAGCGCTTCATGTTGT	57.049	50.000	22.21	0.00	34.30	3.32
1402	1708	4.129737	GCCGTACTCCTGCGCAGA	62.130	66.667	38.06	22.07	0.00	4.26
1404	1710	2.752640	TAGCCGTACTCCTGCGCA	60.753	61.111	10.98	10.98	0.00	6.09
1504	1810	4.353437	GTCGTCGTCGGTGGCCTT	62.353	66.667	3.32	0.00	37.69	4.35
1539	1845	0.616679	ACGGGGAAGTGCTAGGCTAA	60.617	55.000	0.00	0.00	0.00	3.09
1666	2002	0.912486	ACAGGGGTAGATTGGTCAGC	59.088	55.000	0.00	0.00	0.00	4.26
1685	2022	3.432186	GCCTCTTATGTACAGCATCCACA	60.432	47.826	0.33	0.00	38.94	4.17
1714	2052	3.521937	CCTATTCTACCTTCCACCAACCA	59.478	47.826	0.00	0.00	0.00	3.67
1725	2064	2.258109	GGCGGAATCCCTATTCTACCT	58.742	52.381	0.00	0.00	41.18	3.08
1746	2085	7.636150	ATTGTTGAGCTGCAGTAGAAAATAT	57.364	32.000	16.64	0.00	0.00	1.28
1781	2121	1.279271	CCCTACTTCCCACAAGACAGG	59.721	57.143	0.00	0.00	0.00	4.00
1832	2208	4.347000	AGAGCTACCTACAAGAACACCAAA	59.653	41.667	0.00	0.00	0.00	3.28
1835	2211	4.948621	TCTAGAGCTACCTACAAGAACACC	59.051	45.833	0.00	0.00	0.00	4.16
1872	2254	5.259632	AGAAGAAGCTCCATTAATTGCAGT	58.740	37.500	0.00	0.00	0.00	4.40
1877	2259	6.967897	AGAGGAAGAAGAAGCTCCATTAATT	58.032	36.000	0.00	0.00	0.00	1.40
1878	2260	6.573712	AGAGGAAGAAGAAGCTCCATTAAT	57.426	37.500	0.00	0.00	0.00	1.40
1879	2261	6.214412	AGAAGAGGAAGAAGAAGCTCCATTAA	59.786	38.462	0.00	0.00	0.00	1.40
1880	2262	5.723887	AGAAGAGGAAGAAGAAGCTCCATTA	59.276	40.000	0.00	0.00	0.00	1.90
2005	2396	3.858696	ATGTCCGGATACCCCCTAATA	57.141	47.619	7.81	0.00	0.00	0.98
2026	2417	3.325425	TCCGGCCAAAGAATATAATCCGA	59.675	43.478	2.24	0.00	38.02	4.55
2037	2428	1.228124	CCAACAGTCCGGCCAAAGA	60.228	57.895	2.24	0.00	0.00	2.52
2100	2491	2.820787	CCTTCCACGTCAAGTAGAGTCT	59.179	50.000	0.00	0.00	0.00	3.24
2112	2503	1.296715	CCTAGCTTGCCTTCCACGT	59.703	57.895	0.00	0.00	0.00	4.49
2167	2558	5.605488	TGGAGGGAGTTAGAGTTACAAAAGT	59.395	40.000	0.00	0.00	0.00	2.66
2171	2562	4.527038	CACTGGAGGGAGTTAGAGTTACAA	59.473	45.833	0.00	0.00	0.00	2.41
2178	2569	4.883021	ATAGACACTGGAGGGAGTTAGA	57.117	45.455	0.00	0.00	0.00	2.10
2182	2573	5.839606	GGTTTATATAGACACTGGAGGGAGT	59.160	44.000	5.83	0.00	0.00	3.85
2184	2575	4.831155	CGGTTTATATAGACACTGGAGGGA	59.169	45.833	5.83	0.00	0.00	4.20
2218	2609	3.306502	GGATTGTCTGTTGTCCTACGGAA	60.307	47.826	0.00	0.00	35.31	4.30
2240	2631	4.020543	CCCTAGAAGCTAGCCTATGGTAG	58.979	52.174	12.13	4.35	43.84	3.18
2314	2705	6.984474	CCTACGTCCTGCTTGATTTATTCTTA	59.016	38.462	0.00	0.00	0.00	2.10
2504	2896	1.270199	CGAGATGAGGCATCCTTCCTG	60.270	57.143	0.00	0.00	41.36	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.