AutoCloner

Multiple sequence alignment - TraesCS1B01G432800

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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	TraesCS1B01G432800	chr1B	100.000	2420	0	0	1	2420	657315933	657318352	0.000000e+00	4470.0
1	TraesCS1B01G432800	chr1B	86.018	658	76	12	749	1404	278741649	278742292	0.000000e+00	691.0
2	TraesCS1B01G432800	chr5B	87.365	926	91	14	1434	2343	284002999	284002084	0.000000e+00	1038.0
3	TraesCS1B01G432800	chr5B	89.019	683	55	12	728	1403	255416139	255416808	0.000000e+00	828.0
4	TraesCS1B01G432800	chr5B	82.353	714	68	24	26	727	255415421	255416088	3.490000e-158	568.0
5	TraesCS1B01G432800	chr5B	79.012	648	98	24	760	1403	280181557	280180944	2.240000e-110	409.0
6	TraesCS1B01G432800	chr5B	81.905	210	28	6	1776	1985	411094252	411094451	4.140000e-38	169.0
7	TraesCS1B01G432800	chr1A	93.960	596	27	6	1429	2024	566595361	566595947	0.000000e+00	893.0
8	TraesCS1B01G432800	chr1A	90.278	216	18	3	2028	2242	566596857	566597070	1.830000e-71	279.0
9	TraesCS1B01G432800	chr1A	87.817	197	16	5	2224	2420	566597087	566597275	8.710000e-55	224.0
10	TraesCS1B01G432800	chr6B	93.266	594	30	7	728	1316	118849626	118849038	0.000000e+00	867.0
11	TraesCS1B01G432800	chr6B	88.073	654	45	15	88	730	118850302	118849671	0.000000e+00	745.0
12	TraesCS1B01G432800	chr6B	82.879	257	30	11	1775	2026	693072654	693072407	4.050000e-53	219.0
13	TraesCS1B01G432800	chr3B	89.660	677	56	11	728	1404	796252702	796252040	0.000000e+00	850.0
14	TraesCS1B01G432800	chr3B	84.414	725	73	18	8	727	796253439	796252750	0.000000e+00	676.0
15	TraesCS1B01G432800	chr3B	90.625	448	36	2	940	1384	785636654	785637098	7.450000e-165	590.0
16	TraesCS1B01G432800	chr5D	87.026	686	72	9	728	1404	14709647	14708970	0.000000e+00	758.0
17	TraesCS1B01G432800	chr5D	80.687	932	125	37	1432	2343	251957427	251956531	0.000000e+00	673.0
18	TraesCS1B01G432800	chr5D	80.714	280	41	11	1775	2047	453783014	453782741	3.150000e-49	206.0
19	TraesCS1B01G432800	chr7D	86.754	687	72	11	728	1404	53671467	53670790	0.000000e+00	747.0
20	TraesCS1B01G432800	chr7D	78.322	286	46	14	1775	2048	39960459	39960740	1.150000e-38	171.0
21	TraesCS1B01G432800	chr2A	86.618	680	69	13	730	1404	621688875	621689537	0.000000e+00	732.0
22	TraesCS1B01G432800	chr2A	77.755	481	53	40	258	727	621688386	621688823	1.860000e-61	246.0
23	TraesCS1B01G432800	chr2A	79.909	219	30	11	1775	1992	19032677	19032882	5.390000e-32	148.0
24	TraesCS1B01G432800	chr5A	81.310	931	130	31	1432	2343	334747434	334746529	0.000000e+00	715.0
25	TraesCS1B01G432800	chr5A	80.443	271	34	12	1776	2043	450883616	450883870	3.180000e-44	189.0
26	TraesCS1B01G432800	chr5A	80.128	156	26	5	1854	2009	29779550	29779700	7.070000e-21	111.0
27	TraesCS1B01G432800	chr2B	85.745	463	42	13	730	1188	658480797	658480355	3.640000e-128	468.0
28	TraesCS1B01G432800	chr6A	82.490	257	30	12	1775	2026	602635515	602635269	6.780000e-51	211.0
29	TraesCS1B01G432800	chr2D	79.638	221	29	13	1775	1992	17610466	17610673	6.970000e-31	145.0
30	TraesCS1B01G432800	chr3D	74.394	289	53	17	1775	2048	11779959	11780241	1.180000e-18	104.0
31	TraesCS1B01G432800	chr7B	86.047	86	6	6	1655	1735	379416900	379416984	1.190000e-13	87.9
32	TraesCS1B01G432800	chr4B	100.000	30	0	0	1402	1431	547569310	547569281	3.360000e-04	56.5

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	TraesCS1B01G432800	chr1B	657315933	657318352	2419	False	4470.000000	4470	100.0000	1	2420	1	chr1B.!!$F2	2419
1	TraesCS1B01G432800	chr1B	278741649	278742292	643	False	691.000000	691	86.0180	749	1404	1	chr1B.!!$F1	655
2	TraesCS1B01G432800	chr5B	284002084	284002999	915	True	1038.000000	1038	87.3650	1434	2343	1	chr5B.!!$R2	909
3	TraesCS1B01G432800	chr5B	255415421	255416808	1387	False	698.000000	828	85.6860	26	1403	2	chr5B.!!$F2	1377
4	TraesCS1B01G432800	chr5B	280180944	280181557	613	True	409.000000	409	79.0120	760	1403	1	chr5B.!!$R1	643
5	TraesCS1B01G432800	chr1A	566595361	566597275	1914	False	465.333333	893	90.6850	1429	2420	3	chr1A.!!$F1	991
6	TraesCS1B01G432800	chr6B	118849038	118850302	1264	True	806.000000	867	90.6695	88	1316	2	chr6B.!!$R2	1228
7	TraesCS1B01G432800	chr3B	796252040	796253439	1399	True	763.000000	850	87.0370	8	1404	2	chr3B.!!$R1	1396
8	TraesCS1B01G432800	chr5D	14708970	14709647	677	True	758.000000	758	87.0260	728	1404	1	chr5D.!!$R1	676
9	TraesCS1B01G432800	chr5D	251956531	251957427	896	True	673.000000	673	80.6870	1432	2343	1	chr5D.!!$R2	911
10	TraesCS1B01G432800	chr7D	53670790	53671467	677	True	747.000000	747	86.7540	728	1404	1	chr7D.!!$R1	676
11	TraesCS1B01G432800	chr2A	621688386	621689537	1151	False	489.000000	732	82.1865	258	1404	2	chr2A.!!$F2	1146
12	TraesCS1B01G432800	chr5A	334746529	334747434	905	True	715.000000	715	81.3100	1432	2343	1	chr5A.!!$R1	911

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
706	744	0.10576	TGTGCATTTTCCCCCACTGT	60.106	50.0	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2386	3467	0.537371	CGCTGGGAAGTTGGGAGTTT	60.537	55.0	0.0	0.0	0.0	2.66	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
42	43	3.753787	CTTTCCAAGCAACTCCCCT	57.246	52.632	0.00	0.00	0.00	4.79
51	52	3.121929	AGCAACTCCCCTCTCTCATAA	57.878	47.619	0.00	0.00	0.00	1.90
72	73	7.865385	TCATAAGGTTTACAGATGTTTGCAAAC	59.135	33.333	30.95	30.95	39.33	2.93
90	91	5.401972	TGCAAACAAGATAAAATGAGCAACG	59.598	36.000	0.00	0.00	0.00	4.10
144	145	6.127479	TGTTCCTTTAACAACTGCAGAACATT	60.127	34.615	23.35	11.21	45.11	2.71
145	146	5.830912	TCCTTTAACAACTGCAGAACATTG	58.169	37.500	23.35	16.58	0.00	2.82
146	147	5.359576	TCCTTTAACAACTGCAGAACATTGT	59.640	36.000	23.35	17.28	33.93	2.71
147	148	5.459762	CCTTTAACAACTGCAGAACATTGTG	59.540	40.000	23.35	8.15	33.29	3.33
148	149	5.574891	TTAACAACTGCAGAACATTGTGT	57.425	34.783	23.35	12.64	33.29	3.72
149	150	3.425577	ACAACTGCAGAACATTGTGTG	57.574	42.857	23.35	6.20	32.40	3.82
150	151	2.754552	ACAACTGCAGAACATTGTGTGT	59.245	40.909	23.35	6.80	44.84	3.72
151	152	3.110358	CAACTGCAGAACATTGTGTGTG	58.890	45.455	23.35	0.00	41.14	3.82
152	153	2.368439	ACTGCAGAACATTGTGTGTGT	58.632	42.857	23.35	0.00	41.14	3.72
153	154	2.097954	ACTGCAGAACATTGTGTGTGTG	59.902	45.455	23.35	0.00	41.14	3.82
154	155	2.090760	TGCAGAACATTGTGTGTGTGT	58.909	42.857	0.00	0.00	41.14	3.72
155	156	2.159407	TGCAGAACATTGTGTGTGTGTG	60.159	45.455	0.00	0.00	41.14	3.82
156	157	2.159393	GCAGAACATTGTGTGTGTGTGT	60.159	45.455	0.00	0.00	41.14	3.72
157	158	3.428163	CAGAACATTGTGTGTGTGTGTG	58.572	45.455	0.00	0.00	41.14	3.82
158	159	2.423185	AGAACATTGTGTGTGTGTGTGG	59.577	45.455	0.00	0.00	41.14	4.17
159	160	1.102154	ACATTGTGTGTGTGTGTGGG	58.898	50.000	0.00	0.00	40.28	4.61
160	161	0.385029	CATTGTGTGTGTGTGTGGGG	59.615	55.000	0.00	0.00	0.00	4.96
242	244	5.290643	TGTTCTTTTCCTGATTTGCAAAACG	59.709	36.000	17.19	9.70	0.00	3.60
243	245	5.255710	TCTTTTCCTGATTTGCAAAACGA	57.744	34.783	17.19	4.50	0.00	3.85
297	299	6.643388	AGAAACAATTTCCAAGCAAACTTCT	58.357	32.000	0.00	0.00	40.54	2.85
469	486	5.420725	TCAAACTGCCAGTGTCTACATAT	57.579	39.130	0.00	0.00	0.00	1.78
494	521	7.893124	AGTTCTCAATGATCCATAAAAGCAT	57.107	32.000	0.00	0.00	0.00	3.79
548	578	6.756542	ACAAAAGCATTCAAACCTAGTTCAAC	59.243	34.615	0.00	0.00	0.00	3.18
627	664	4.521146	AGATCTGCCTTATCCACACAAAG	58.479	43.478	0.00	0.00	0.00	2.77
636	673	6.407202	CCTTATCCACACAAAGCTACTACTT	58.593	40.000	0.00	0.00	0.00	2.24
637	674	6.879458	CCTTATCCACACAAAGCTACTACTTT	59.121	38.462	0.00	0.00	40.49	2.66
706	744	0.105760	TGTGCATTTTCCCCCACTGT	60.106	50.000	0.00	0.00	0.00	3.55
707	745	0.318120	GTGCATTTTCCCCCACTGTG	59.682	55.000	0.00	0.00	0.00	3.66
716	755	0.675633	CCCCCACTGTGAAAAAGCAG	59.324	55.000	9.86	0.00	38.58	4.24
735	824	1.891919	TTGTCGCCTCTTGTGTGCC	60.892	57.895	0.00	0.00	0.00	5.01
834	932	9.612620	CTGTTTATCTTTACAGTTGCCTAAAAG	57.387	33.333	0.00	0.00	37.56	2.27
936	1038	6.989759	TCTTTACTGCACTGTTATTGACAAGA	59.010	34.615	0.00	0.00	37.93	3.02
972	1078	3.084039	TGCAGGGTCAGCTGATAAAAAG	58.916	45.455	21.47	9.34	0.00	2.27
1019	1134	8.591114	AAAAGGATGATTGATCTCAATGAACT	57.409	30.769	10.04	2.90	45.72	3.01
1036	1151	0.807496	ACTACCGGTTGACGTAGAGC	59.193	55.000	23.12	0.00	42.24	4.09
1065	1180	2.999739	TTTCGGTTGAGTCGGGTGCC	63.000	60.000	0.00	0.00	0.00	5.01
1087	1202	5.511888	GCCCCGTTCTTAAATACAGCCTATA	60.512	44.000	0.00	0.00	0.00	1.31
1156	1271	4.141251	ACCCCGACATTGGCTCTAATAATT	60.141	41.667	0.00	0.00	0.00	1.40
1165	1280	9.193806	ACATTGGCTCTAATAATTCTCATGTTT	57.806	29.630	0.00	0.00	0.00	2.83
1265	1381	0.533032	GAAGAAGTAGGGTCGCAGCT	59.467	55.000	0.00	0.00	0.00	4.24
1290	1406	0.833949	TGCCCTATGTTGGTATGCGA	59.166	50.000	0.00	0.00	0.00	5.10
1328	1444	3.559171	GGGGCAAGAGAACACTACAATCA	60.559	47.826	0.00	0.00	0.00	2.57
1359	1475	2.432510	AGCGGTGGGTTTTTCAATCAAA	59.567	40.909	0.00	0.00	0.00	2.69
1376	1492	3.017442	TCAAATCAAACACGTCCCACAA	58.983	40.909	0.00	0.00	0.00	3.33
1404	1520	1.146930	CACAGGTGTGCTGGACAGT	59.853	57.895	0.98	0.00	39.39	3.55
1405	1521	0.464373	CACAGGTGTGCTGGACAGTT	60.464	55.000	0.98	0.00	39.39	3.16
1406	1522	0.179045	ACAGGTGTGCTGGACAGTTC	60.179	55.000	0.98	0.00	34.28	3.01
1407	1523	0.179048	CAGGTGTGCTGGACAGTTCA	60.179	55.000	0.98	0.00	34.28	3.18
1408	1524	0.546122	AGGTGTGCTGGACAGTTCAA	59.454	50.000	0.98	0.00	34.28	2.69
1409	1525	1.143684	AGGTGTGCTGGACAGTTCAAT	59.856	47.619	0.98	0.00	34.28	2.57
1410	1526	1.537202	GGTGTGCTGGACAGTTCAATC	59.463	52.381	0.98	0.00	34.28	2.67
1411	1527	1.195448	GTGTGCTGGACAGTTCAATCG	59.805	52.381	0.98	0.00	34.28	3.34
1412	1528	0.798776	GTGCTGGACAGTTCAATCGG	59.201	55.000	0.82	0.00	0.00	4.18
1413	1529	0.396435	TGCTGGACAGTTCAATCGGT	59.604	50.000	0.82	0.00	0.00	4.69
1414	1530	0.798776	GCTGGACAGTTCAATCGGTG	59.201	55.000	0.82	0.00	0.00	4.94
1415	1531	0.798776	CTGGACAGTTCAATCGGTGC	59.201	55.000	0.00	0.00	0.00	5.01
1416	1532	0.107643	TGGACAGTTCAATCGGTGCA	59.892	50.000	0.00	0.00	32.77	4.57
1417	1533	1.271325	TGGACAGTTCAATCGGTGCAT	60.271	47.619	0.00	0.00	30.79	3.96
1418	1534	2.027653	TGGACAGTTCAATCGGTGCATA	60.028	45.455	0.00	0.00	30.79	3.14
1419	1535	2.609459	GGACAGTTCAATCGGTGCATAG	59.391	50.000	0.00	0.00	0.00	2.23
1420	1536	2.609459	GACAGTTCAATCGGTGCATAGG	59.391	50.000	0.00	0.00	0.00	2.57
1421	1537	2.236146	ACAGTTCAATCGGTGCATAGGA	59.764	45.455	0.00	0.00	0.00	2.94
1422	1538	3.118261	ACAGTTCAATCGGTGCATAGGAT	60.118	43.478	0.00	0.00	0.00	3.24
1423	1539	4.100963	ACAGTTCAATCGGTGCATAGGATA	59.899	41.667	0.00	0.00	0.00	2.59
1424	1540	4.449068	CAGTTCAATCGGTGCATAGGATAC	59.551	45.833	0.00	0.00	0.00	2.24
1425	1541	3.297830	TCAATCGGTGCATAGGATACG	57.702	47.619	0.00	0.00	46.39	3.06
1426	1542	2.626266	TCAATCGGTGCATAGGATACGT	59.374	45.455	0.00	0.00	46.39	3.57
1427	1543	3.069016	TCAATCGGTGCATAGGATACGTT	59.931	43.478	0.00	0.00	46.39	3.99
1428	1544	2.787601	TCGGTGCATAGGATACGTTC	57.212	50.000	0.00	0.00	46.39	3.95
1429	1545	2.304092	TCGGTGCATAGGATACGTTCT	58.696	47.619	0.00	0.00	46.39	3.01
1430	1546	2.292569	TCGGTGCATAGGATACGTTCTC	59.707	50.000	0.00	0.00	46.39	2.87
1529	1645	9.950496	AGAAGTAACAAATGACAGTAAGATCAT	57.050	29.630	0.00	0.00	37.14	2.45
1567	1684	6.420306	CCATCGATGTTTGTTTTTCATGTTCA	59.580	34.615	23.27	0.00	0.00	3.18
1692	1811	7.432148	AAAATGGTCCCTTAACTTCAAAACT	57.568	32.000	0.00	0.00	0.00	2.66
1735	1854	5.367945	TGAAACCAGACAAGTTTAGTCCT	57.632	39.130	0.00	0.00	37.55	3.85
1839	1958	1.968704	TCATCCGACGAGCTCTACAT	58.031	50.000	12.85	0.00	0.00	2.29
1901	2022	6.774354	TGAGCAATGAAATCTTTTTCTTGC	57.226	33.333	17.83	17.83	44.86	4.01
1948	2069	1.392168	CAGCATGAAATTTGGCAAGCG	59.608	47.619	0.00	0.00	39.69	4.68
1988	2109	9.661563	AGCATATTTGATGTCACAAAATTTCAT	57.338	25.926	0.00	0.00	41.88	2.57
2033	3061	6.715718	TGAATTTACGGTTCATGAGGGTTTAA	59.284	34.615	0.00	0.00	31.07	1.52
2062	3090	0.618680	AGAGCAGACATGGCCACCTA	60.619	55.000	8.16	0.00	0.00	3.08
2087	3117	0.834612	TACCTAGGTTTCGGCCCATG	59.165	55.000	22.11	0.00	0.00	3.66
2197	3230	2.034066	CGTGGTCAGGCCCATGTT	59.966	61.111	0.00	0.00	36.85	2.71
2207	3240	2.993471	GCCCATGTTCCGGCACAAG	61.993	63.158	11.91	6.77	45.01	3.16
2260	3328	8.602472	TTATATAGGTCAAAACAGCCCAAATT	57.398	30.769	0.00	0.00	0.00	1.82
2337	3418	0.465097	CTAATGTGCTGGGCCTGGAG	60.465	60.000	12.70	0.00	0.00	3.86
2368	3449	7.554835	ACGAGATCACTAATTGAGAAGTACTCT	59.445	37.037	0.00	0.00	45.13	3.24
2372	3453	9.646427	GATCACTAATTGAGAAGTACTCTTTGT	57.354	33.333	0.00	0.00	45.13	2.83
2384	3465	9.877178	AGAAGTACTCTTTGTAATACAAGATGG	57.123	33.333	5.94	1.98	39.53	3.51
2385	3466	9.099454	GAAGTACTCTTTGTAATACAAGATGGG	57.901	37.037	5.94	4.08	39.53	4.00
2386	3467	8.375493	AGTACTCTTTGTAATACAAGATGGGA	57.625	34.615	5.94	1.70	39.53	4.37
2387	3468	8.822805	AGTACTCTTTGTAATACAAGATGGGAA	58.177	33.333	5.94	0.00	39.53	3.97
2405	3486	0.537371	AAACTCCCAACTTCCCAGCG	60.537	55.000	0.00	0.00	0.00	5.18
2411	3492	1.371183	CAACTTCCCAGCGGTGAGA	59.629	57.895	17.83	5.16	0.00	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.282838	CCCCCTCCCCCACTTTTT	58.717	61.111	0.00	0.00	0.00	1.94
38	39	4.962995	TCTGTAAACCTTATGAGAGAGGGG	59.037	45.833	0.00	0.00	37.36	4.79
42	43	7.334421	GCAAACATCTGTAAACCTTATGAGAGA	59.666	37.037	0.00	0.00	0.00	3.10
51	52	5.590530	TGTTTGCAAACATCTGTAAACCT	57.409	34.783	35.10	0.00	45.71	3.50
72	73	5.297776	AGGATCCGTTGCTCATTTTATCTTG	59.702	40.000	5.98	0.00	0.00	3.02
75	76	5.349824	GAGGATCCGTTGCTCATTTTATC	57.650	43.478	5.98	0.00	42.11	1.75
144	145	2.273776	CCCCCACACACACACACA	59.726	61.111	0.00	0.00	0.00	3.72
197	198	3.197927	ACCCCTCTTCATCTCTCAAGT	57.802	47.619	0.00	0.00	0.00	3.16
253	255	9.023962	TGTTTCTCCTTTTCTTACATAATGCAT	57.976	29.630	0.00	0.00	0.00	3.96
469	486	8.985315	ATGCTTTTATGGATCATTGAGAACTA	57.015	30.769	0.00	0.00	0.00	2.24
548	578	4.332428	TGTGAGAGGAGATGCATATGTG	57.668	45.455	0.00	0.00	0.00	3.21
580	610	6.611381	TCTATGCAATGCTGTTACTTTTCAC	58.389	36.000	6.82	0.00	0.00	3.18
595	632	6.179040	GGATAAGGCAGATCTTCTATGCAAT	58.821	40.000	6.27	0.00	41.78	3.56
641	678	4.383661	GGGCAGAAGACCCTTTTTCAAAAA	60.384	41.667	0.00	0.00	44.68	1.94
643	680	2.698274	GGGCAGAAGACCCTTTTTCAAA	59.302	45.455	0.00	0.00	44.68	2.69
644	681	2.316108	GGGCAGAAGACCCTTTTTCAA	58.684	47.619	0.00	0.00	44.68	2.69
645	682	1.216678	TGGGCAGAAGACCCTTTTTCA	59.783	47.619	0.00	0.00	45.14	2.69
646	683	1.613925	GTGGGCAGAAGACCCTTTTTC	59.386	52.381	0.00	0.00	45.14	2.29
647	684	1.704641	GTGGGCAGAAGACCCTTTTT	58.295	50.000	0.00	0.00	45.14	1.94
652	689	2.180159	TAAGCGTGGGCAGAAGACCC	62.180	60.000	0.00	0.00	45.14	4.46
706	744	1.333619	GAGGCGACAACTGCTTTTTCA	59.666	47.619	0.00	0.00	0.00	2.69
707	745	1.604278	AGAGGCGACAACTGCTTTTTC	59.396	47.619	0.00	0.00	0.00	2.29
716	755	1.279840	GCACACAAGAGGCGACAAC	59.720	57.895	0.00	0.00	0.00	3.32
735	824	4.358494	TTTGTTGTTTCTGTTACCACCG	57.642	40.909	0.00	0.00	0.00	4.94
912	1013	7.189693	TCTTGTCAATAACAGTGCAGTAAAG	57.810	36.000	0.00	0.00	39.58	1.85
915	1016	7.561021	TTTTCTTGTCAATAACAGTGCAGTA	57.439	32.000	0.00	0.00	39.58	2.74
916	1017	6.449635	TTTTCTTGTCAATAACAGTGCAGT	57.550	33.333	0.00	0.00	39.58	4.40
972	1078	2.833631	TTTCTTGTCCCTCTCCGTTC	57.166	50.000	0.00	0.00	0.00	3.95
1019	1134	0.322816	AGGCTCTACGTCAACCGGTA	60.323	55.000	8.00	0.00	42.24	4.02
1065	1180	7.876068	TGATTATAGGCTGTATTTAAGAACGGG	59.124	37.037	0.00	0.00	0.00	5.28
1087	1202	5.329191	TCCAAATGGATATCCTGCTGATT	57.671	39.130	22.35	10.44	39.78	2.57
1156	1271	1.052617	TGGGTGGTCGAAACATGAGA	58.947	50.000	0.00	0.00	0.00	3.27
1265	1381	0.112218	ACCAACATAGGGCAGTTGCA	59.888	50.000	6.43	0.00	42.77	4.08
1290	1406	0.035439	CCCCCACTAGCGTGTCAAAT	60.035	55.000	0.00	0.00	39.55	2.32
1328	1444	0.397254	ACCCACCGCTAGAGCATAGT	60.397	55.000	1.89	0.00	42.21	2.12
1359	1475	2.218603	GACTTGTGGGACGTGTTTGAT	58.781	47.619	0.00	0.00	0.00	2.57
1376	1492	0.037326	CACACCTGTGTATGCCGACT	60.037	55.000	2.05	0.00	42.83	4.18
1404	1520	3.069016	ACGTATCCTATGCACCGATTGAA	59.931	43.478	0.00	0.00	0.00	2.69
1405	1521	2.626266	ACGTATCCTATGCACCGATTGA	59.374	45.455	0.00	0.00	0.00	2.57
1406	1522	3.026630	ACGTATCCTATGCACCGATTG	57.973	47.619	0.00	0.00	0.00	2.67
1407	1523	3.321111	AGAACGTATCCTATGCACCGATT	59.679	43.478	0.00	0.00	0.00	3.34
1408	1524	2.891580	AGAACGTATCCTATGCACCGAT	59.108	45.455	0.00	0.00	0.00	4.18
1409	1525	2.292569	GAGAACGTATCCTATGCACCGA	59.707	50.000	0.00	0.00	0.00	4.69
1410	1526	2.293677	AGAGAACGTATCCTATGCACCG	59.706	50.000	0.00	0.00	0.00	4.94
1411	1527	3.553096	CCAGAGAACGTATCCTATGCACC	60.553	52.174	0.00	0.00	0.00	5.01
1412	1528	3.318275	TCCAGAGAACGTATCCTATGCAC	59.682	47.826	0.00	0.00	0.00	4.57
1413	1529	3.562182	TCCAGAGAACGTATCCTATGCA	58.438	45.455	0.00	0.00	0.00	3.96
1414	1530	4.299978	GTTCCAGAGAACGTATCCTATGC	58.700	47.826	0.00	0.00	42.85	3.14
1426	1542	1.621814	CCGGTAACTGGTTCCAGAGAA	59.378	52.381	23.45	7.06	37.49	2.87
1427	1543	1.263356	CCGGTAACTGGTTCCAGAGA	58.737	55.000	23.45	9.12	37.49	3.10
1428	1544	0.974383	ACCGGTAACTGGTTCCAGAG	59.026	55.000	23.45	9.84	39.88	3.35
1429	1545	0.682852	CACCGGTAACTGGTTCCAGA	59.317	55.000	23.45	1.21	40.68	3.86
1430	1546	0.321298	CCACCGGTAACTGGTTCCAG	60.321	60.000	6.87	16.25	40.68	3.86
1526	1642	6.434340	ACATCGATGGCACTATCTTACTATGA	59.566	38.462	28.09	0.00	0.00	2.15
1529	1645	6.650427	AACATCGATGGCACTATCTTACTA	57.350	37.500	28.09	0.00	0.00	1.82
1735	1854	1.374947	CCACCCGAAGAAGCAGGAA	59.625	57.895	0.00	0.00	0.00	3.36
1839	1958	3.523606	AGCATTGTTTTGTTGCTCACA	57.476	38.095	0.00	0.00	42.88	3.58
1845	1964	5.023286	GCACTTTTGAGCATTGTTTTGTTG	58.977	37.500	0.00	0.00	36.05	3.33
1884	2005	6.150140	AGCTCTACGCAAGAAAAAGATTTCAT	59.850	34.615	4.34	0.00	43.42	2.57
1901	2022	1.819288	TGTTTGAGGAGGAGCTCTACG	59.181	52.381	14.64	0.00	0.00	3.51
1948	2069	6.620678	TCAAATATGCTCAAACTTTGTAGGC	58.379	36.000	1.44	5.88	0.00	3.93
2033	3061	1.979693	GTCTGCTCTCGGGTGTCCT	60.980	63.158	0.00	0.00	0.00	3.85
2087	3117	1.154073	GTGTCGGGTACGTGAGCTC	60.154	63.158	6.82	6.82	41.85	4.09
2193	3226	3.055719	CGCCTTGTGCCGGAACAT	61.056	61.111	18.31	0.00	36.24	2.71
2194	3227	4.243008	TCGCCTTGTGCCGGAACA	62.243	61.111	12.64	12.64	36.24	3.18
2197	3230	4.980805	GTGTCGCCTTGTGCCGGA	62.981	66.667	5.05	0.00	36.24	5.14
2207	3240	5.803020	ATTCTAGAAAGAAATGTGTCGCC	57.197	39.130	9.71	0.00	44.75	5.54
2260	3328	4.342427	GCACATGATTCTGGGCCA	57.658	55.556	5.85	5.85	39.74	5.36
2267	3348	4.090761	TCCCTTATGGAGCACATGATTC	57.909	45.455	0.00	0.00	40.82	2.52
2337	3418	4.046938	TCAATTAGTGATCTCGTCCTGC	57.953	45.455	0.00	0.00	0.00	4.85
2346	3427	9.646427	ACAAAGAGTACTTCTCAATTAGTGATC	57.354	33.333	0.00	0.00	44.98	2.92
2368	3449	7.696992	GGAGTTTCCCATCTTGTATTACAAA	57.303	36.000	10.32	3.11	37.69	2.83
2384	3465	1.911057	CTGGGAAGTTGGGAGTTTCC	58.089	55.000	0.00	0.00	39.69	3.13
2385	3466	1.248486	GCTGGGAAGTTGGGAGTTTC	58.752	55.000	0.00	0.00	0.00	2.78
2386	3467	0.537371	CGCTGGGAAGTTGGGAGTTT	60.537	55.000	0.00	0.00	0.00	2.66
2387	3468	1.073199	CGCTGGGAAGTTGGGAGTT	59.927	57.895	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.