AutoCloner

Multiple sequence alignment - TraesCS5A01G288100

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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	TraesCS5A01G288100	chr5A	100.000	3161	0	0	1	3161	495842195	495839035	0.000000e+00	5838.0
1	TraesCS5A01G288100	chr5A	95.770	662	19	2	2508	3161	398693138	398693798	0.000000e+00	1059.0
2	TraesCS5A01G288100	chr5A	95.463	551	22	2	1948	2498	495602136	495601589	0.000000e+00	876.0
3	TraesCS5A01G288100	chr5A	93.663	505	28	1	1948	2452	495735552	495735052	0.000000e+00	752.0
4	TraesCS5A01G288100	chr5A	96.089	179	6	1	2509	2687	398720030	398720207	1.110000e-74	291.0
5	TraesCS5A01G288100	chr5A	95.506	178	7	1	2509	2686	495833660	495833484	1.860000e-72	283.0
6	TraesCS5A01G288100	chr5A	85.227	264	32	4	1501	1763	495339745	495339488	6.720000e-67	265.0
7	TraesCS5A01G288100	chr5A	84.815	270	32	6	1501	1770	495359387	495359127	2.420000e-66	263.0
8	TraesCS5A01G288100	chr5A	79.434	389	61	15	996	1380	495340117	495339744	1.120000e-64	257.0
9	TraesCS5A01G288100	chr5A	97.436	39	1	0	718	756	495841435	495841397	2.030000e-07	67.6
10	TraesCS5A01G288100	chr5A	97.436	39	1	0	761	799	495841478	495841440	2.030000e-07	67.6
11	TraesCS5A01G288100	chr5D	91.702	1398	77	19	1	1380	393754153	393752777	0.000000e+00	1903.0
12	TraesCS5A01G288100	chr5D	89.344	976	56	27	1501	2463	393752778	393751838	0.000000e+00	1182.0
13	TraesCS5A01G288100	chr5D	80.779	385	57	14	1003	1380	393570174	393569800	5.160000e-73	285.0
14	TraesCS5A01G288100	chr5D	85.660	265	31	5	1501	1764	393569801	393569543	4.020000e-69	272.0
15	TraesCS5A01G288100	chr5D	84.074	270	34	7	1501	1770	393608377	393608117	5.230000e-63	252.0
16	TraesCS5A01G288100	chr5D	95.455	44	2	0	756	799	393753441	393753398	1.570000e-08	71.3
17	TraesCS5A01G288100	chr5D	97.436	39	1	0	718	756	393753393	393753355	2.030000e-07	67.6
18	TraesCS5A01G288100	chr5B	90.371	1402	80	30	1	1380	473627077	473625709	0.000000e+00	1790.0
19	TraesCS5A01G288100	chr5B	86.593	1268	110	33	997	2235	473455426	473454190	0.000000e+00	1345.0
20	TraesCS5A01G288100	chr5B	89.867	750	57	13	1501	2235	473625710	473624965	0.000000e+00	946.0
21	TraesCS5A01G288100	chr5B	79.358	436	79	8	1795	2222	473291454	473291022	2.380000e-76	296.0
22	TraesCS5A01G288100	chr5B	86.415	265	29	5	1501	1764	473291806	473291548	1.860000e-72	283.0
23	TraesCS5A01G288100	chr5B	84.151	265	35	5	1501	1764	473467838	473467580	1.880000e-62	250.0
24	TraesCS5A01G288100	chr5B	80.278	360	43	16	1032	1380	473292147	473291805	2.440000e-61	246.0
25	TraesCS5A01G288100	chr5B	92.683	82	5	1	2418	2498	473453988	473453907	1.990000e-22	117.0
26	TraesCS5A01G288100	chr5B	95.455	44	2	0	756	799	473626379	473626336	1.570000e-08	71.3
27	TraesCS5A01G288100	chr5B	97.222	36	1	0	721	756	473626328	473626293	9.470000e-06	62.1
28	TraesCS5A01G288100	chr2A	92.496	653	21	12	2519	3161	123165954	123165320	0.000000e+00	909.0
29	TraesCS5A01G288100	chr2A	97.059	170	2	3	2519	2686	123137750	123137582	1.860000e-72	283.0
30	TraesCS5A01G288100	chrUn	96.537	462	16	0	2700	3161	48463267	48462806	0.000000e+00	765.0
31	TraesCS5A01G288100	chrUn	94.767	172	4	4	2519	2686	48439897	48439727	2.420000e-66	263.0
32	TraesCS5A01G288100	chr2B	92.231	502	30	2	2668	3161	43210013	43210513	0.000000e+00	702.0
33	TraesCS5A01G288100	chr2B	86.667	345	30	6	2808	3137	413867782	413868125	4.980000e-98	368.0
34	TraesCS5A01G288100	chr7D	85.249	461	46	9	2682	3123	567282285	567281828	3.720000e-124	455.0
35	TraesCS5A01G288100	chr7D	86.932	176	15	4	2972	3141	567274782	567274609	1.160000e-44	191.0
36	TraesCS5A01G288100	chr7D	84.906	106	16	0	2871	2976	537322993	537323098	1.200000e-19	108.0
37	TraesCS5A01G288100	chr4A	95.906	171	4	3	2519	2687	186686654	186686823	1.120000e-69	274.0
38	TraesCS5A01G288100	chr7A	94.904	157	4	3	2519	2671	77599444	77599288	3.150000e-60	243.0
39	TraesCS5A01G288100	chr7A	84.211	190	22	7	2519	2702	56015581	56015768	9.010000e-41	178.0
40	TraesCS5A01G288100	chr1A	86.061	165	18	4	2524	2684	59856437	59856600	4.190000e-39	172.0

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	TraesCS5A01G288100	chr5A	495839035	495842195	3160	True	1991.066667	5838	98.290667	1	3161	3	chr5A.!!$R6	3160
1	TraesCS5A01G288100	chr5A	398693138	398693798	660	False	1059.000000	1059	95.770000	2508	3161	1	chr5A.!!$F1	653
2	TraesCS5A01G288100	chr5A	495601589	495602136	547	True	876.000000	876	95.463000	1948	2498	1	chr5A.!!$R2	550
3	TraesCS5A01G288100	chr5A	495735052	495735552	500	True	752.000000	752	93.663000	1948	2452	1	chr5A.!!$R3	504
4	TraesCS5A01G288100	chr5A	495339488	495340117	629	True	261.000000	265	82.330500	996	1763	2	chr5A.!!$R5	767
5	TraesCS5A01G288100	chr5D	393751838	393754153	2315	True	805.975000	1903	93.484250	1	2463	4	chr5D.!!$R3	2462
6	TraesCS5A01G288100	chr5D	393569543	393570174	631	True	278.500000	285	83.219500	1003	1764	2	chr5D.!!$R2	761
7	TraesCS5A01G288100	chr5B	473453907	473455426	1519	True	731.000000	1345	89.638000	997	2498	2	chr5B.!!$R3	1501
8	TraesCS5A01G288100	chr5B	473624965	473627077	2112	True	717.350000	1790	93.228750	1	2235	4	chr5B.!!$R4	2234
9	TraesCS5A01G288100	chr5B	473291022	473292147	1125	True	275.000000	296	82.017000	1032	2222	3	chr5B.!!$R2	1190
10	TraesCS5A01G288100	chr2A	123165320	123165954	634	True	909.000000	909	92.496000	2519	3161	1	chr2A.!!$R2	642
11	TraesCS5A01G288100	chr2B	43210013	43210513	500	False	702.000000	702	92.231000	2668	3161	1	chr2B.!!$F1	493

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
929	950	0.030101	CTTGGAGATCCGTCGAGAGC	59.970	60.0	0.0	0.0	39.43	4.09	F
1388	1450	0.107993	GGACAACCCGGTAAGTAGGC	60.108	60.0	0.0	0.0	0.00	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1944	2082	1.966451	GAAGTGTGTGAAGCCCCGG	60.966	63.158	0.0	0.0	0.00	5.73	R
2677	2910	3.846744	GCGTGCTGATAACGTGTTGAAAA	60.847	43.478	0.0	0.0	42.93	2.29	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
122	124	2.742589	GGTTCTAGTTTTGAAGCCCTCG	59.257	50.000	0.00	0.00	36.33	4.63
311	313	0.394899	GGAAGGAAGCATGTCCCCTG	60.395	60.000	0.00	0.00	38.59	4.45
345	347	4.132336	TCACAATCATGGATCAAGCTAGC	58.868	43.478	6.62	6.62	0.00	3.42
379	381	0.470456	TACCGGTGGACACAAGGAGT	60.470	55.000	19.93	5.60	35.53	3.85
469	477	0.955428	ATGTGCCGCAGATCAACGTT	60.955	50.000	0.00	0.00	0.00	3.99
543	554	6.363577	TGATTGAATGGCGAATTAGAGAAC	57.636	37.500	0.00	0.00	0.00	3.01
550	561	3.055819	TGGCGAATTAGAGAACTTGAGCT	60.056	43.478	0.00	0.00	0.00	4.09
715	726	2.046314	CGCCAAGGTTGACGGGAT	60.046	61.111	0.00	0.00	30.17	3.85
716	727	1.674322	CGCCAAGGTTGACGGGATT	60.674	57.895	0.00	0.00	30.17	3.01
717	728	1.241315	CGCCAAGGTTGACGGGATTT	61.241	55.000	0.00	0.00	30.17	2.17
719	730	0.887933	CCAAGGTTGACGGGATTTGG	59.112	55.000	0.00	0.00	0.00	3.28
823	838	4.899239	CCGTGATCCAGGCCGAGC	62.899	72.222	0.00	0.00	0.00	5.03
845	860	1.181098	GGTTGCACATGTTCCCTGCT	61.181	55.000	0.00	0.00	0.00	4.24
885	902	4.412933	CGTACCCACGGTATGCTG	57.587	61.111	0.00	0.00	44.59	4.41
893	910	1.270305	CCACGGTATGCTGGACCATAG	60.270	57.143	0.00	0.00	36.72	2.23
929	950	0.030101	CTTGGAGATCCGTCGAGAGC	59.970	60.000	0.00	0.00	39.43	4.09
947	968	0.592754	GCTGCGACGACTTAGGCTAG	60.593	60.000	0.00	0.00	0.00	3.42
950	971	1.667724	TGCGACGACTTAGGCTAGTAC	59.332	52.381	0.00	0.00	0.00	2.73
951	972	1.667724	GCGACGACTTAGGCTAGTACA	59.332	52.381	0.00	0.00	0.00	2.90
952	973	2.286301	GCGACGACTTAGGCTAGTACAG	60.286	54.545	0.00	0.00	0.00	2.74
953	974	2.935201	CGACGACTTAGGCTAGTACAGT	59.065	50.000	0.00	0.00	0.00	3.55
977	998	2.489275	CCAGCTCTCGAGAGGCTCC	61.489	68.421	36.65	23.08	42.29	4.70
981	1002	1.747367	CTCTCGAGAGGCTCCACGT	60.747	63.158	31.01	2.93	38.48	4.49
983	1004	0.743701	TCTCGAGAGGCTCCACGTAC	60.744	60.000	23.57	5.76	0.00	3.67
984	1005	2.037913	CTCGAGAGGCTCCACGTACG	62.038	65.000	23.57	15.01	0.00	3.67
985	1006	2.799371	GAGAGGCTCCACGTACGG	59.201	66.667	21.06	8.46	0.00	4.02
986	1007	2.754658	AGAGGCTCCACGTACGGG	60.755	66.667	21.06	16.64	0.00	5.28
1210	1234	1.280206	GCGCACCGAAGAGTACGTTT	61.280	55.000	0.30	0.00	0.00	3.60
1248	1272	2.185310	ATCCGGCCGTCTTCTTGCTT	62.185	55.000	26.12	0.00	0.00	3.91
1249	1273	1.079405	CCGGCCGTCTTCTTGCTTA	60.079	57.895	26.12	0.00	0.00	3.09
1250	1274	1.359459	CCGGCCGTCTTCTTGCTTAC	61.359	60.000	26.12	0.00	0.00	2.34
1251	1275	1.359459	CGGCCGTCTTCTTGCTTACC	61.359	60.000	19.50	0.00	0.00	2.85
1254	1278	1.337823	GCCGTCTTCTTGCTTACCTGA	60.338	52.381	0.00	0.00	0.00	3.86
1274	1324	0.809385	TTAGCTCTTCGAGTCCACCG	59.191	55.000	0.00	0.00	31.39	4.94
1288	1349	4.220724	AGTCCACCGACCTATTGCTAATA	58.779	43.478	0.00	0.00	40.12	0.98
1301	1362	6.870965	CCTATTGCTAATAGTGATGTCTGGAC	59.129	42.308	12.12	0.00	39.36	4.02
1308	1370	6.479972	AATAGTGATGTCTGGACCGATTTA	57.520	37.500	0.00	0.00	0.00	1.40
1388	1450	0.107993	GGACAACCCGGTAAGTAGGC	60.108	60.000	0.00	0.00	0.00	3.93
1401	1471	4.081420	GGTAAGTAGGCCATCATCGATCAT	60.081	45.833	5.01	0.00	0.00	2.45
1402	1472	3.883830	AGTAGGCCATCATCGATCATC	57.116	47.619	5.01	0.00	0.00	2.92
1403	1473	2.165234	AGTAGGCCATCATCGATCATCG	59.835	50.000	5.01	0.00	42.10	3.84
1418	1488	5.316488	GATCATCGATCGAACAAAATCGT	57.684	39.130	23.50	0.00	43.91	3.73
1419	1489	6.434181	GATCATCGATCGAACAAAATCGTA	57.566	37.500	23.50	0.00	43.91	3.43
1420	1490	5.615495	TCATCGATCGAACAAAATCGTAC	57.385	39.130	23.50	0.00	43.91	3.67
1434	1504	1.456296	TCGTACTACATGTCCGTGCT	58.544	50.000	0.00	0.00	29.86	4.40
1435	1505	1.814394	TCGTACTACATGTCCGTGCTT	59.186	47.619	0.00	0.00	29.86	3.91
1443	1513	2.226437	ACATGTCCGTGCTTTGTTGATC	59.774	45.455	0.00	0.00	0.00	2.92
1484	1554	7.849804	ATTTATACTGACAGAACATGTGGAC	57.150	36.000	10.08	0.00	44.17	4.02
1485	1555	2.154854	ACTGACAGAACATGTGGACG	57.845	50.000	10.08	0.00	44.17	4.79
1486	1556	0.792640	CTGACAGAACATGTGGACGC	59.207	55.000	0.00	0.00	44.17	5.19
1487	1557	0.943835	TGACAGAACATGTGGACGCG	60.944	55.000	3.53	3.53	44.17	6.01
1488	1558	0.944311	GACAGAACATGTGGACGCGT	60.944	55.000	13.85	13.85	44.17	6.01
1489	1559	1.221466	ACAGAACATGTGGACGCGTG	61.221	55.000	20.70	2.79	41.91	5.34
1490	1560	1.069090	AGAACATGTGGACGCGTGT	59.931	52.632	20.70	3.62	40.00	4.49
1491	1561	0.315886	AGAACATGTGGACGCGTGTA	59.684	50.000	20.70	1.01	37.60	2.90
1492	1562	1.141645	GAACATGTGGACGCGTGTAA	58.858	50.000	20.70	0.00	37.60	2.41
1493	1563	1.730064	GAACATGTGGACGCGTGTAAT	59.270	47.619	20.70	1.32	37.60	1.89
1630	1700	1.147600	AAACGGAGGCGGAACACTT	59.852	52.632	0.00	0.00	0.00	3.16
1748	1820	2.594592	GCAGCGACCACCACCTTT	60.595	61.111	0.00	0.00	0.00	3.11
1766	1838	3.506067	CCTTTAACCGCCATGAGAAAACT	59.494	43.478	0.00	0.00	0.00	2.66
1771	1843	1.261619	CCGCCATGAGAAAACTATCGC	59.738	52.381	0.00	0.00	0.00	4.58
1944	2082	3.509184	AGAAGAGCCAAGAAAATGAAGGC	59.491	43.478	0.00	0.00	45.54	4.35
2189	2343	2.516923	CGGATCTACACGACAAGTCAC	58.483	52.381	0.72	0.00	0.00	3.67
2234	2388	8.353423	ACTCAATGAAAAGTATATGCCACTTT	57.647	30.769	0.00	0.00	45.73	2.66
2345	2526	5.115480	CCTATTCTCCAGAAGCTCTTCAAC	58.885	45.833	11.69	0.00	41.84	3.18
2354	2535	3.117888	AGAAGCTCTTCAACTTTGGGTCA	60.118	43.478	11.69	0.00	41.84	4.02
2375	2556	8.041323	GGGTCAAACATCATCTCTAAGTTAGAA	58.959	37.037	13.51	5.81	33.75	2.10
2606	2839	1.298713	CTCCGGATGCGTCTCTTCG	60.299	63.158	3.57	0.48	0.00	3.79
2677	2910	9.877178	AATACTATCAATTGTCTCTCGTTTTCT	57.123	29.630	5.13	0.00	0.00	2.52
3048	3289	4.021925	GGTCAGCACGCCCTCCTT	62.022	66.667	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	9.546428	TTAATGATACACATGATTGTAGGTGAG	57.454	33.333	0.00	0.00	39.39	3.51
91	92	7.504924	TTCAAAACTAGAACCTATGTTGGTG	57.495	36.000	0.00	0.00	40.73	4.17
292	294	0.394899	CAGGGGACATGCTTCCTTCC	60.395	60.000	2.63	0.00	35.76	3.46
293	295	0.329596	ACAGGGGACATGCTTCCTTC	59.670	55.000	2.63	0.00	35.76	3.46
294	296	1.668826	TACAGGGGACATGCTTCCTT	58.331	50.000	2.63	0.00	35.76	3.36
295	297	1.898863	ATACAGGGGACATGCTTCCT	58.101	50.000	2.63	0.00	35.76	3.36
311	313	8.728337	ATCCATGATTGTGATACAGCATATAC	57.272	34.615	0.00	0.00	0.00	1.47
345	347	1.068741	CCGGTAAGTAGCTAGGCAAGG	59.931	57.143	0.00	0.00	0.00	3.61
379	381	0.895530	CCGTCCTTGTCCTTCTGCTA	59.104	55.000	0.00	0.00	0.00	3.49
469	477	0.609957	CATTGCAGGCTCAAGGACCA	60.610	55.000	0.00	0.00	30.08	4.02
550	561	2.930040	GCTAGCAACACGAGCTAAATCA	59.070	45.455	10.63	0.00	43.39	2.57
627	638	4.448732	CGGCCGGGTTTATTTATAGTACAC	59.551	45.833	20.10	0.00	0.00	2.90
715	726	2.796500	GGACACCCGAACAACCAAA	58.204	52.632	0.00	0.00	0.00	3.28
716	727	4.563404	GGACACCCGAACAACCAA	57.437	55.556	0.00	0.00	0.00	3.67
823	838	2.635443	GGGAACATGTGCAACCCGG	61.635	63.158	6.08	0.00	34.36	5.73
845	860	6.376299	ACGTGCGTATATATTAGGGATCAGAA	59.624	38.462	0.00	0.00	0.00	3.02
881	898	1.153369	GCTTCGCTATGGTCCAGCA	60.153	57.895	0.00	0.00	39.04	4.41
882	899	1.153369	TGCTTCGCTATGGTCCAGC	60.153	57.895	0.00	0.00	35.61	4.85
885	902	0.747255	TCTCTGCTTCGCTATGGTCC	59.253	55.000	0.00	0.00	0.00	4.46
893	910	1.991965	CAAGAAGTCTCTCTGCTTCGC	59.008	52.381	0.00	0.00	39.87	4.70
929	950	0.733729	ACTAGCCTAAGTCGTCGCAG	59.266	55.000	0.00	0.00	0.00	5.18
977	998	3.243336	CTCTTCTTTTCTCCCGTACGTG	58.757	50.000	15.21	2.17	0.00	4.49
981	1002	3.118738	GCATCCTCTTCTTTTCTCCCGTA	60.119	47.826	0.00	0.00	0.00	4.02
983	1004	2.093235	AGCATCCTCTTCTTTTCTCCCG	60.093	50.000	0.00	0.00	0.00	5.14
984	1005	3.540617	GAGCATCCTCTTCTTTTCTCCC	58.459	50.000	0.00	0.00	35.16	4.30
985	1006	3.194062	CGAGCATCCTCTTCTTTTCTCC	58.806	50.000	0.00	0.00	35.90	3.71
986	1007	2.607180	GCGAGCATCCTCTTCTTTTCTC	59.393	50.000	0.00	0.00	35.90	2.87
1188	1212	1.080705	GTACTCTTCGGTGCGCTGT	60.081	57.895	9.73	0.00	0.00	4.40
1210	1234	1.227586	CGGAGTCGGAGATCGGAGA	60.228	63.158	0.00	0.00	40.67	3.71
1241	1265	5.665459	GAAGAGCTAATCAGGTAAGCAAGA	58.335	41.667	0.00	0.00	38.75	3.02
1274	1324	6.870965	CCAGACATCACTATTAGCAATAGGTC	59.129	42.308	15.67	13.11	44.10	3.85
1288	1349	3.513912	TGTAAATCGGTCCAGACATCACT	59.486	43.478	0.00	0.00	0.00	3.41
1301	1362	2.237751	CGCGCTCCCTGTAAATCGG	61.238	63.158	5.56	0.00	0.00	4.18
1351	1413	4.789075	GCGTTGTAGCGGCGGAGA	62.789	66.667	9.78	0.00	0.00	3.71
1369	1431	0.107993	GCCTACTTACCGGGTTGTCC	60.108	60.000	4.31	0.00	0.00	4.02
1382	1444	2.165234	CGATGATCGATGATGGCCTACT	59.835	50.000	9.62	0.00	43.74	2.57
1401	1471	5.630061	TGTAGTACGATTTTGTTCGATCGA	58.370	37.500	15.15	15.15	45.90	3.59
1403	1473	7.218145	ACATGTAGTACGATTTTGTTCGATC	57.782	36.000	0.00	0.00	41.62	3.69
1404	1474	6.255020	GGACATGTAGTACGATTTTGTTCGAT	59.745	38.462	0.00	0.00	41.62	3.59
1405	1475	5.574055	GGACATGTAGTACGATTTTGTTCGA	59.426	40.000	0.00	0.00	41.62	3.71
1406	1476	5.782255	GGACATGTAGTACGATTTTGTTCG	58.218	41.667	0.00	0.00	44.56	3.95
1417	1487	3.323243	ACAAAGCACGGACATGTAGTAC	58.677	45.455	0.00	0.00	0.00	2.73
1418	1488	3.671008	ACAAAGCACGGACATGTAGTA	57.329	42.857	0.00	0.00	0.00	1.82
1419	1489	2.543777	ACAAAGCACGGACATGTAGT	57.456	45.000	0.00	0.00	0.00	2.73
1420	1490	2.805671	TCAACAAAGCACGGACATGTAG	59.194	45.455	0.00	0.00	0.00	2.74
1461	1531	5.867174	CGTCCACATGTTCTGTCAGTATAAA	59.133	40.000	0.00	0.00	35.29	1.40
1462	1532	5.407502	CGTCCACATGTTCTGTCAGTATAA	58.592	41.667	0.00	0.00	35.29	0.98
1463	1533	4.676986	GCGTCCACATGTTCTGTCAGTATA	60.677	45.833	0.00	0.00	35.29	1.47
1464	1534	3.849911	CGTCCACATGTTCTGTCAGTAT	58.150	45.455	0.00	0.00	35.29	2.12
1465	1535	2.609491	GCGTCCACATGTTCTGTCAGTA	60.609	50.000	0.00	0.00	35.29	2.74
1466	1536	1.873903	GCGTCCACATGTTCTGTCAGT	60.874	52.381	0.00	0.00	35.29	3.41
1478	1548	1.527736	GAAACATTACACGCGTCCACA	59.472	47.619	9.86	0.00	0.00	4.17
1479	1549	1.527736	TGAAACATTACACGCGTCCAC	59.472	47.619	9.86	0.00	0.00	4.02
1480	1550	1.795872	CTGAAACATTACACGCGTCCA	59.204	47.619	9.86	0.00	0.00	4.02
1482	1552	1.127951	CCCTGAAACATTACACGCGTC	59.872	52.381	9.86	0.00	0.00	5.19
1483	1553	1.153353	CCCTGAAACATTACACGCGT	58.847	50.000	5.58	5.58	0.00	6.01
1484	1554	0.179200	GCCCTGAAACATTACACGCG	60.179	55.000	3.53	3.53	0.00	6.01
1485	1555	1.130561	GAGCCCTGAAACATTACACGC	59.869	52.381	0.00	0.00	0.00	5.34
1486	1556	1.393539	CGAGCCCTGAAACATTACACG	59.606	52.381	0.00	0.00	0.00	4.49
1487	1557	1.737793	CCGAGCCCTGAAACATTACAC	59.262	52.381	0.00	0.00	0.00	2.90
1488	1558	1.626321	TCCGAGCCCTGAAACATTACA	59.374	47.619	0.00	0.00	0.00	2.41
1489	1559	2.280628	CTCCGAGCCCTGAAACATTAC	58.719	52.381	0.00	0.00	0.00	1.89
1490	1560	1.906574	ACTCCGAGCCCTGAAACATTA	59.093	47.619	0.00	0.00	0.00	1.90
1491	1561	0.693049	ACTCCGAGCCCTGAAACATT	59.307	50.000	0.00	0.00	0.00	2.71
1492	1562	0.693049	AACTCCGAGCCCTGAAACAT	59.307	50.000	0.00	0.00	0.00	2.71
1493	1563	0.034896	GAACTCCGAGCCCTGAAACA	59.965	55.000	0.00	0.00	0.00	2.83
1551	1621	1.077429	GACCCAGATGTGGCCTTCC	60.077	63.158	3.32	0.00	43.44	3.46
1630	1700	2.028484	GGTGACGGTGTCGCTGAA	59.972	61.111	10.00	0.00	42.03	3.02
1701	1771	0.816018	TGGTGCATGTTTCGACGGTT	60.816	50.000	0.00	0.00	0.00	4.44
1748	1820	4.116961	CGATAGTTTTCTCATGGCGGTTA	58.883	43.478	0.00	0.00	0.00	2.85
1766	1838	2.293677	GTGAGAATCCGAAGAGGCGATA	59.706	50.000	0.00	0.00	40.77	2.92
1771	1843	4.039730	ACATATGGTGAGAATCCGAAGAGG	59.960	45.833	7.80	0.00	42.97	3.69
1944	2082	1.966451	GAAGTGTGTGAAGCCCCGG	60.966	63.158	0.00	0.00	0.00	5.73
2049	2202	2.630580	GCTACTATGTTCCTCCTCCTGG	59.369	54.545	0.00	0.00	0.00	4.45
2189	2343	8.763049	TTGAGTCTAACATGAACTCATTACAG	57.237	34.615	18.46	0.00	37.31	2.74
2345	2526	6.656693	ACTTAGAGATGATGTTTGACCCAAAG	59.343	38.462	0.00	0.00	33.82	2.77
2542	2775	5.994235	CGTCTATTTATATGACGGTCAGC	57.006	43.478	16.84	0.00	46.45	4.26
2660	2893	7.484959	GTGTTGAAAAGAAAACGAGAGACAATT	59.515	33.333	0.00	0.00	0.00	2.32
2677	2910	3.846744	GCGTGCTGATAACGTGTTGAAAA	60.847	43.478	0.00	0.00	42.93	2.29
3033	3274	4.020617	CCAAGGAGGGCGTGCTGA	62.021	66.667	0.92	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.