AutoCloner

Multiple sequence alignment - TraesCS2D01G364500

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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	TraesCS2D01G364500	chr2D	100.000	4024	0	0	1	4024	470045501	470041478	0.000000e+00	7432.0
1	TraesCS2D01G364500	chr2D	92.560	1035	52	12	2118	3129	470057211	470056179	0.000000e+00	1461.0
2	TraesCS2D01G364500	chr2D	87.808	689	67	11	1396	2069	470057896	470057210	0.000000e+00	791.0
3	TraesCS2D01G364500	chr2D	88.363	507	38	12	454	953	470058960	470058468	1.250000e-164	590.0
4	TraesCS2D01G364500	chr2D	83.948	461	35	18	951	1377	470058415	470057960	4.840000e-109	405.0
5	TraesCS2D01G364500	chr2D	85.870	368	41	9	999	1363	470140016	470139657	8.160000e-102	381.0
6	TraesCS2D01G364500	chr2D	84.831	356	33	8	2334	2674	470138004	470137655	4.980000e-89	339.0
7	TraesCS2D01G364500	chr2D	80.729	384	56	11	16	387	21927575	21927198	2.370000e-72	283.0
8	TraesCS2D01G364500	chr2D	90.196	204	19	1	2825	3027	470137588	470137385	8.580000e-67	265.0
9	TraesCS2D01G364500	chr2D	79.581	191	27	8	2127	2314	470139590	470139409	4.220000e-25	126.0
10	TraesCS2D01G364500	chr2D	88.000	75	9	0	379	453	470060448	470060374	5.540000e-14	89.8
11	TraesCS2D01G364500	chr2A	92.379	1732	83	28	564	2256	611317735	611316014	0.000000e+00	2422.0
12	TraesCS2D01G364500	chr2A	88.357	773	53	23	3278	4024	611315062	611314301	0.000000e+00	894.0
13	TraesCS2D01G364500	chr2A	90.104	576	41	9	1	564	611334069	611333498	0.000000e+00	734.0
14	TraesCS2D01G364500	chr2A	89.200	500	37	7	2797	3280	611315586	611315088	3.440000e-170	608.0
15	TraesCS2D01G364500	chr2A	93.659	410	16	5	2294	2694	611316014	611315606	4.450000e-169	604.0
16	TraesCS2D01G364500	chr2A	83.596	634	72	18	1371	1989	612003360	612003976	2.100000e-157	566.0
17	TraesCS2D01G364500	chr2A	81.733	427	42	16	2276	2674	611746294	611745876	1.390000e-84	324.0
18	TraesCS2D01G364500	chr2A	90.686	204	17	2	2825	3027	611745799	611745597	1.840000e-68	270.0
19	TraesCS2D01G364500	chr2A	79.245	371	60	12	1001	1363	631795508	631795869	4.020000e-60	243.0
20	TraesCS2D01G364500	chr2A	89.286	140	15	0	999	1138	611746951	611746812	4.130000e-40	176.0
21	TraesCS2D01G364500	chr2A	83.333	132	17	5	2118	2246	611746483	611746354	2.540000e-22	117.0
22	TraesCS2D01G364500	chr2B	91.772	632	39	7	2074	2694	548662242	548661613	0.000000e+00	867.0
23	TraesCS2D01G364500	chr2B	92.841	433	21	7	951	1375	548663128	548662698	1.590000e-173	619.0
24	TraesCS2D01G364500	chr2B	88.386	508	43	6	453	958	548663662	548663169	7.440000e-167	597.0
25	TraesCS2D01G364500	chr2B	90.351	456	33	6	1	446	548667894	548667440	4.480000e-164	588.0
26	TraesCS2D01G364500	chr2B	89.059	393	29	6	2797	3182	548661593	548661208	3.640000e-130	475.0
27	TraesCS2D01G364500	chr2B	81.105	561	71	17	2126	2674	548911796	548911259	2.240000e-112	416.0
28	TraesCS2D01G364500	chr2B	76.284	818	84	59	634	1363	548912678	548911883	6.440000e-88	335.0
29	TraesCS2D01G364500	chr2B	80.270	370	55	13	1001	1363	571252421	571252779	3.080000e-66	263.0
30	TraesCS2D01G364500	chr7B	87.626	396	30	14	2	382	480698274	480697883	3.690000e-120	442.0
31	TraesCS2D01G364500	chr7B	78.680	394	66	14	8	388	6933283	6932895	3.110000e-61	246.0
32	TraesCS2D01G364500	chr3D	87.268	377	33	9	2	366	42399504	42399131	2.240000e-112	416.0
33	TraesCS2D01G364500	chr3D	100.000	28	0	0	3237	3264	114669061	114669034	7.000000e-03	52.8
34	TraesCS2D01G364500	chr7D	86.189	391	36	10	2	382	458728293	458727911	1.350000e-109	407.0
35	TraesCS2D01G364500	chr7D	79.648	398	60	14	2	387	45566542	45566930	2.380000e-67	267.0
36	TraesCS2D01G364500	chr3B	84.635	384	38	13	2	367	65332764	65333144	2.960000e-96	363.0
37	TraesCS2D01G364500	chr3B	81.224	245	29	10	2	231	421093736	421093494	8.880000e-42	182.0
38	TraesCS2D01G364500	chr3A	81.047	401	52	12	2	387	712197247	712196856	8.450000e-77	298.0
39	TraesCS2D01G364500	chr5D	85.000	220	28	5	172	389	300954315	300954099	6.770000e-53	219.0
40	TraesCS2D01G364500	chr5A	84.404	218	28	6	172	387	44802613	44802826	4.080000e-50	209.0
41	TraesCS2D01G364500	chr5B	84.018	219	30	5	172	388	556531629	556531414	5.270000e-49	206.0
42	TraesCS2D01G364500	chr1A	81.818	264	30	13	2	251	11154354	11154613	5.270000e-49	206.0
43	TraesCS2D01G364500	chr6D	86.301	73	8	1	1610	1680	283813039	283813111	1.200000e-10	78.7
44	TraesCS2D01G364500	chr7A	100.000	35	0	0	1668	1702	730850238	730850272	9.340000e-07	65.8

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	TraesCS2D01G364500	chr2D	470041478	470045501	4023	True	7432.00	7432	100.00000	1	4024	1	chr2D.!!$R2	4023
1	TraesCS2D01G364500	chr2D	470056179	470060448	4269	True	667.36	1461	88.13580	379	3129	5	chr2D.!!$R3	2750
2	TraesCS2D01G364500	chr2D	470137385	470140016	2631	True	277.75	381	85.11950	999	3027	4	chr2D.!!$R4	2028
3	TraesCS2D01G364500	chr2A	611314301	611317735	3434	True	1132.00	2422	90.89875	564	4024	4	chr2A.!!$R2	3460
4	TraesCS2D01G364500	chr2A	611333498	611334069	571	True	734.00	734	90.10400	1	564	1	chr2A.!!$R1	563
5	TraesCS2D01G364500	chr2A	612003360	612003976	616	False	566.00	566	83.59600	1371	1989	1	chr2A.!!$F1	618
6	TraesCS2D01G364500	chr2A	611745597	611746951	1354	True	221.75	324	86.25950	999	3027	4	chr2A.!!$R3	2028
7	TraesCS2D01G364500	chr2B	548661208	548667894	6686	True	629.20	867	90.48180	1	3182	5	chr2B.!!$R1	3181
8	TraesCS2D01G364500	chr2B	548911259	548912678	1419	True	375.50	416	78.69450	634	2674	2	chr2B.!!$R2	2040

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
737	5962	0.104304	GATGGAACCGTACGGCTCAT	59.896	55.0	32.30	29.30	39.32	2.90	F
738	5963	0.179084	ATGGAACCGTACGGCTCATG	60.179	55.0	32.30	12.04	39.32	3.07	F
1154	6500	0.590682	TTCCGTTCGTAGTACGTGCA	59.409	50.0	21.38	5.37	43.14	4.57	F
2682	9679	0.248565	GATGGTGAGCAGAGCACTGA	59.751	55.0	15.88	0.00	46.03	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1937	7479	0.174845	CGTCGTGGCCAGAGGAATAA	59.825	55.000	5.11	0.00	0.00	1.40	R
1985	7527	2.231964	ACTAATTTCCGTCACCGTGCTA	59.768	45.455	0.00	0.00	0.00	3.49	R
2822	9832	0.179234	TGAGTGGAACAACGCTTCCA	59.821	50.000	1.16	1.16	46.27	3.53	R
3936	11015	3.878778	AGTTTTCTTCGCATAGGAGCAT	58.121	40.909	0.00	0.00	0.00	3.79	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	4.711355	TGCTTTGCTATTTCCAGCCTAATT	59.289	37.500	0.00	0.00	41.04	1.40
128	130	4.884164	GCTATTTCCAGCCTAATTCACTGT	59.116	41.667	0.00	0.00	35.40	3.55
251	263	7.883229	AAAAATCGTCCAACCATTTATGTTC	57.117	32.000	0.00	0.00	0.00	3.18
262	274	4.022416	ACCATTTATGTTCGTGCACAACAT	60.022	37.500	31.48	31.48	44.78	2.71
294	306	2.264005	TGTTTCTTGTATGGCACCGT	57.736	45.000	0.00	0.00	0.00	4.83
323	335	7.080099	AGATTTCAAGTGATTTGTTGATGTCG	58.920	34.615	0.00	0.00	38.01	4.35
343	355	2.476352	CGTCGAGTGTGTGTATGAGAGG	60.476	54.545	0.00	0.00	0.00	3.69
344	356	2.488545	GTCGAGTGTGTGTATGAGAGGT	59.511	50.000	0.00	0.00	0.00	3.85
346	359	2.488153	CGAGTGTGTGTATGAGAGGTGA	59.512	50.000	0.00	0.00	0.00	4.02
371	384	4.462508	TTTTCTTCCATTGCAACACACA	57.537	36.364	0.00	0.00	0.00	3.72
425	438	0.249489	CGTCCGACTCCCATGGATTC	60.249	60.000	15.22	5.20	33.63	2.52
433	446	1.694150	CTCCCATGGATTCTTCGGCTA	59.306	52.381	15.22	0.00	0.00	3.93
434	447	1.694150	TCCCATGGATTCTTCGGCTAG	59.306	52.381	15.22	0.00	0.00	3.42
449	462	1.896465	GGCTAGAGAGATGGCCGTATT	59.104	52.381	0.00	0.00	37.06	1.89
450	463	2.300437	GGCTAGAGAGATGGCCGTATTT	59.700	50.000	0.00	0.00	37.06	1.40
554	5754	1.219664	CGCGGGGACACCTTTATGA	59.780	57.895	0.00	0.00	36.97	2.15
696	5898	4.324402	GTCAAGCAGATTAACCGCAAAATG	59.676	41.667	0.00	0.00	0.00	2.32
723	5941	1.305297	ACAGCACGAGGGAGATGGA	60.305	57.895	0.00	0.00	0.00	3.41
737	5962	0.104304	GATGGAACCGTACGGCTCAT	59.896	55.000	32.30	29.30	39.32	2.90
738	5963	0.179084	ATGGAACCGTACGGCTCATG	60.179	55.000	32.30	12.04	39.32	3.07
739	5964	2.171725	GGAACCGTACGGCTCATGC	61.172	63.158	32.30	19.37	39.32	4.06
751	5976	1.688772	GCTCATGCCTCATGGACAAT	58.311	50.000	6.92	0.00	41.66	2.71
886	6134	3.038017	CAATCGTGCACACTTTCACTTG	58.962	45.455	18.64	4.30	0.00	3.16
1118	6438	2.036256	CCTCCCAAAGCCCTGTGG	59.964	66.667	0.00	0.00	34.44	4.17
1146	6466	1.343506	CCCGTTTCTTCCGTTCGTAG	58.656	55.000	0.00	0.00	0.00	3.51
1148	6468	2.095263	CCCGTTTCTTCCGTTCGTAGTA	60.095	50.000	0.00	0.00	0.00	1.82
1149	6469	2.911102	CCGTTTCTTCCGTTCGTAGTAC	59.089	50.000	0.00	0.00	0.00	2.73
1150	6470	2.585517	CGTTTCTTCCGTTCGTAGTACG	59.414	50.000	16.65	16.65	44.19	3.67
1154	6500	0.590682	TTCCGTTCGTAGTACGTGCA	59.409	50.000	21.38	5.37	43.14	4.57
1355	6716	4.553678	TCGTCTATCCCTGGGAAACTTAT	58.446	43.478	21.42	4.31	34.34	1.73
1473	6890	4.151883	TGGCCAGAAGCTATCAAAAACTT	58.848	39.130	0.00	0.00	43.05	2.66
1476	6893	6.437162	TGGCCAGAAGCTATCAAAAACTTAAT	59.563	34.615	0.00	0.00	43.05	1.40
1523	6954	9.250246	CCCCCTTAAAAATAGTACAGATTTCAA	57.750	33.333	6.30	4.29	0.00	2.69
1538	6970	5.745294	CAGATTTCAATGCGGATTAAAGTGG	59.255	40.000	0.40	0.00	0.00	4.00
1543	6975	4.816385	TCAATGCGGATTAAAGTGGAGATC	59.184	41.667	0.40	0.00	0.00	2.75
1582	7023	7.712797	TCAATCAAAAAGGGTAAAACAGTCTC	58.287	34.615	0.00	0.00	0.00	3.36
1783	7313	7.021790	GCATGCAATCAGACATCATATGTAAG	58.978	38.462	14.21	0.00	45.03	2.34
1816	7346	9.159364	CATATATTTGACATACACATCTCCAGG	57.841	37.037	0.00	0.00	0.00	4.45
1824	7354	6.186957	ACATACACATCTCCAGGCATTAAAA	58.813	36.000	0.00	0.00	0.00	1.52
1923	7465	4.965814	TGAGACAGATGGATGGCTTTATC	58.034	43.478	0.00	0.00	39.20	1.75
1937	7479	2.412089	GCTTTATCGAACTCACTTGCGT	59.588	45.455	0.00	0.00	0.00	5.24
1985	7527	4.384547	GCGGCGTGAAATAACTTCAAATTT	59.615	37.500	9.37	0.00	45.67	1.82
1989	7531	6.584563	GGCGTGAAATAACTTCAAATTTAGCA	59.415	34.615	0.00	0.00	45.67	3.49
1991	7533	7.644893	CGTGAAATAACTTCAAATTTAGCACG	58.355	34.615	0.00	0.00	45.67	5.34
2018	7560	8.928733	GTGACGGAAATTAGTGAGTTATTAACA	58.071	33.333	9.15	0.00	0.00	2.41
2371	9340	3.799432	ATAGAGCTGGATACCGTCTCT	57.201	47.619	0.00	13.13	37.78	3.10
2402	9371	5.551233	CCCGTATACATCAAGAACATCCAT	58.449	41.667	3.32	0.00	0.00	3.41
2681	9678	0.743701	GGATGGTGAGCAGAGCACTG	60.744	60.000	6.80	6.80	45.91	3.66
2682	9679	0.248565	GATGGTGAGCAGAGCACTGA	59.751	55.000	15.88	0.00	46.03	3.41
2693	9697	3.256558	CAGAGCACTGACGAATTCATCA	58.743	45.455	5.03	3.90	46.03	3.07
2770	9780	3.171528	TGAATTGGATGGCATCAAACCA	58.828	40.909	27.39	19.97	42.61	3.67
2778	9788	4.741321	ATGGCATCAAACCATTTCGATT	57.259	36.364	0.00	0.00	45.86	3.34
2795	9805	6.932901	TTCGATTGCATCTTTTGTTTCATC	57.067	33.333	0.00	0.00	0.00	2.92
2809	9819	3.181462	TGTTTCATCAGCAGTCAGTGACT	60.181	43.478	20.34	20.34	44.44	3.41
2810	9820	3.758755	TTCATCAGCAGTCAGTGACTT	57.241	42.857	23.33	7.38	41.37	3.01
2822	9832	5.295292	CAGTCAGTGACTTGAAATGAACTGT	59.705	40.000	23.33	0.00	41.37	3.55
2857	9871	3.499918	CCACTCATGTTTGGTCTGAACTC	59.500	47.826	7.07	0.00	0.00	3.01
2862	9876	5.863965	TCATGTTTGGTCTGAACTCATGTA	58.136	37.500	17.83	8.59	34.67	2.29
2863	9877	5.700832	TCATGTTTGGTCTGAACTCATGTAC	59.299	40.000	17.83	0.00	34.67	2.90
2864	9878	5.029807	TGTTTGGTCTGAACTCATGTACA	57.970	39.130	0.00	0.00	0.00	2.90
2927	9941	2.124507	TTGCCAAGGACGAGGAAGGG	62.125	60.000	0.00	0.00	0.00	3.95
2939	9953	2.302019	GGAAGGGTTCCTCTCCAGG	58.698	63.158	0.00	0.00	46.57	4.45
2994	10008	1.796796	GAGTTCATCGCCCAGCAAC	59.203	57.895	0.00	0.00	0.00	4.17
3051	10066	6.314648	TGCAATTCTGTCATCTTCATGAGTAC	59.685	38.462	0.00	0.00	39.86	2.73
3060	10082	4.902443	TCTTCATGAGTACGACCAGATC	57.098	45.455	0.00	0.00	0.00	2.75
3104	10135	6.829229	TGAAATAAGAGAGGAACGAGTACA	57.171	37.500	0.00	0.00	0.00	2.90
3107	10138	8.145767	TGAAATAAGAGAGGAACGAGTACAAAA	58.854	33.333	0.00	0.00	0.00	2.44
3163	10194	9.915629	CTAAACTTGAGAACATAAGTACTCTGT	57.084	33.333	0.00	0.04	36.19	3.41
3250	10281	6.913170	ACTACAGCTGTGACAATTAATTTGG	58.087	36.000	29.57	1.70	39.80	3.28
3253	10284	6.624423	ACAGCTGTGACAATTAATTTGGATC	58.376	36.000	20.97	0.00	39.80	3.36
3254	10285	6.209192	ACAGCTGTGACAATTAATTTGGATCA	59.791	34.615	20.97	0.00	39.80	2.92
3270	10301	8.602472	ATTTGGATCAGAGAGAGTACTAACTT	57.398	34.615	0.00	0.00	35.56	2.66
3337	10397	2.700773	GCTGCGGTGATTTCCCCAC	61.701	63.158	0.00	0.00	0.00	4.61
3344	10404	0.601057	GTGATTTCCCCACAAACGGG	59.399	55.000	0.00	0.00	46.94	5.28
3376	10436	7.254455	CCAGCTACTTAGACAAAAATATGGTCG	60.254	40.741	0.00	0.00	36.68	4.79
3400	10460	4.710324	TGTACACTCGGAAGGAAAAACAT	58.290	39.130	0.00	0.00	0.00	2.71
3418	10478	4.294416	ACATATCGAAGAAGACCACTCG	57.706	45.455	0.00	0.00	43.58	4.18
3431	10491	1.353804	CACTCGCTCCTCGCTCTAC	59.646	63.158	0.00	0.00	38.27	2.59
3513	10573	6.836577	TTTAAAGCGGTGGATTTCAAAAAG	57.163	33.333	0.00	0.00	33.15	2.27
3516	10576	5.523438	AAGCGGTGGATTTCAAAAAGTAA	57.477	34.783	0.00	0.00	0.00	2.24
3517	10577	4.866921	AGCGGTGGATTTCAAAAAGTAAC	58.133	39.130	0.00	0.00	0.00	2.50
3526	10604	8.081633	TGGATTTCAAAAAGTAACTGTGCATAG	58.918	33.333	9.17	9.17	0.00	2.23
3598	10676	8.375608	ACTGTGCATAATTTTAAAATGTGCAA	57.624	26.923	33.25	25.98	44.74	4.08
3934	11013	8.996651	AAAACAAGGGGAACTAATATCCTATG	57.003	34.615	0.00	0.00	37.14	2.23
3936	11015	8.808240	AACAAGGGGAACTAATATCCTATGTA	57.192	34.615	0.00	0.00	37.14	2.29
3962	11041	6.037172	TGCTCCTATGCGAAGAAAACTATTTC	59.963	38.462	0.00	0.00	39.48	2.17
4014	11103	8.861033	TGAAAATTGTCAATGAAGAAAGACAG	57.139	30.769	0.00	0.00	41.46	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
122	124	6.345298	TCAGTGATACTCAACAAAACAGTGA	58.655	36.000	0.00	0.00	35.06	3.41
128	130	5.306937	TCCTCCTCAGTGATACTCAACAAAA	59.693	40.000	0.00	0.00	0.00	2.44
251	263	4.142838	ACATGATAAGTGATGTTGTGCACG	60.143	41.667	13.13	0.00	39.88	5.34
262	274	8.729756	CCATACAAGAAACAACATGATAAGTGA	58.270	33.333	0.00	0.00	0.00	3.41
294	306	9.251792	CATCAACAAATCACTTGAAATCTTTCA	57.748	29.630	1.28	1.28	44.78	2.69
323	335	2.488545	ACCTCTCATACACACACTCGAC	59.511	50.000	0.00	0.00	0.00	4.20
359	372	1.042229	ACATGCCTGTGTGTTGCAAT	58.958	45.000	0.59	0.00	38.69	3.56
367	380	2.276732	ACTAGCAAACATGCCTGTGT	57.723	45.000	0.00	0.00	35.22	3.72
371	384	3.721087	ACCTAACTAGCAAACATGCCT	57.279	42.857	0.00	0.00	34.90	4.75
425	438	0.316841	GGCCATCTCTCTAGCCGAAG	59.683	60.000	0.00	0.00	35.30	3.79
696	5898	1.361668	CCTCGTGCTGTGCCACATAC	61.362	60.000	0.00	0.00	35.47	2.39
737	5962	2.026075	TCACATCATTGTCCATGAGGCA	60.026	45.455	0.00	0.00	45.97	4.75
738	5963	2.357009	GTCACATCATTGTCCATGAGGC	59.643	50.000	0.00	0.00	45.97	4.70
739	5964	3.613030	TGTCACATCATTGTCCATGAGG	58.387	45.455	0.00	0.00	45.52	3.86
740	5965	4.036380	CCATGTCACATCATTGTCCATGAG	59.964	45.833	13.07	0.00	45.52	2.90
741	5966	3.949113	CCATGTCACATCATTGTCCATGA	59.051	43.478	13.07	0.00	46.41	3.07
742	5967	3.949113	TCCATGTCACATCATTGTCCATG	59.051	43.478	0.00	7.70	39.60	3.66
751	5976	0.972883	TGTCCGTCCATGTCACATCA	59.027	50.000	0.00	0.00	0.00	3.07
996	6314	3.541632	CTTAGCTTCCTCCGCCATAAAA	58.458	45.455	0.00	0.00	0.00	1.52
997	6315	2.158813	CCTTAGCTTCCTCCGCCATAAA	60.159	50.000	0.00	0.00	0.00	1.40
1118	6438	4.660938	AGAAACGGGGCAGGCACC	62.661	66.667	1.43	1.43	35.80	5.01
1146	6466	2.476185	GCTGATGAAACCATGCACGTAC	60.476	50.000	0.00	0.00	0.00	3.67
1148	6468	0.523072	GCTGATGAAACCATGCACGT	59.477	50.000	0.00	0.00	0.00	4.49
1149	6469	0.522626	TGCTGATGAAACCATGCACG	59.477	50.000	0.00	0.00	0.00	5.34
1150	6470	2.602878	CTTGCTGATGAAACCATGCAC	58.397	47.619	0.00	0.00	0.00	4.57
1154	6500	1.822990	CTGCCTTGCTGATGAAACCAT	59.177	47.619	0.00	0.00	0.00	3.55
1355	6716	6.503924	AGGCCATATACAAATACATACCTCCA	59.496	38.462	5.01	0.00	0.00	3.86
1483	6900	3.732048	AAGGGGGTGTATCGAAACAAT	57.268	42.857	0.00	0.00	0.00	2.71
1492	6909	8.396619	TCTGTACTATTTTTAAGGGGGTGTAT	57.603	34.615	0.00	0.00	0.00	2.29
1523	6954	4.422073	TGATCTCCACTTTAATCCGCAT	57.578	40.909	0.00	0.00	0.00	4.73
1527	6958	8.787852	GGTAAATGATGATCTCCACTTTAATCC	58.212	37.037	0.00	0.00	0.00	3.01
1538	6970	7.000472	TGATTGAAGGGGTAAATGATGATCTC	59.000	38.462	0.00	0.00	0.00	2.75
1543	6975	7.550196	CCTTTTTGATTGAAGGGGTAAATGATG	59.450	37.037	0.00	0.00	38.98	3.07
1751	7279	6.500910	TGATGTCTGATTGCATGCTTATTTC	58.499	36.000	20.33	8.82	0.00	2.17
1762	7292	8.783833	ATACCTTACATATGATGTCTGATTGC	57.216	34.615	10.38	0.00	43.67	3.56
1842	7379	6.157904	TGATGCAACACTTGGTTATTGAATG	58.842	36.000	0.00	0.00	37.72	2.67
1937	7479	0.174845	CGTCGTGGCCAGAGGAATAA	59.825	55.000	5.11	0.00	0.00	1.40
1968	7510	7.593273	CACCGTGCTAAATTTGAAGTTATTTCA	59.407	33.333	0.00	0.00	43.92	2.69
1969	7511	7.806014	TCACCGTGCTAAATTTGAAGTTATTTC	59.194	33.333	0.00	0.00	36.29	2.17
1985	7527	2.231964	ACTAATTTCCGTCACCGTGCTA	59.768	45.455	0.00	0.00	0.00	3.49
1989	7531	2.298163	ACTCACTAATTTCCGTCACCGT	59.702	45.455	0.00	0.00	0.00	4.83
1991	7533	6.980051	AATAACTCACTAATTTCCGTCACC	57.020	37.500	0.00	0.00	0.00	4.02
2102	7644	2.429478	ACATAAACTACGGCAACCACC	58.571	47.619	0.00	0.00	0.00	4.61
2371	9340	3.897141	TGATGTATACGGGCAACAAGA	57.103	42.857	0.00	0.00	39.74	3.02
2402	9371	2.884320	TCGCTACCATGCTTATCCCTA	58.116	47.619	0.00	0.00	0.00	3.53
2646	9643	4.935205	CACCATCCAATGAAGTCGAAGTTA	59.065	41.667	0.00	0.00	0.00	2.24
2681	9678	5.786401	AGTAAACTGCTGATGAATTCGTC	57.214	39.130	18.99	18.99	0.00	4.20
2682	9679	5.700832	TCAAGTAAACTGCTGATGAATTCGT	59.299	36.000	0.00	0.00	0.00	3.85
2755	9765	2.426738	TCGAAATGGTTTGATGCCATCC	59.573	45.455	1.49	0.00	45.21	3.51
2778	9788	4.038282	ACTGCTGATGAAACAAAAGATGCA	59.962	37.500	0.00	0.00	0.00	3.96
2795	9805	3.811497	TCATTTCAAGTCACTGACTGCTG	59.189	43.478	12.59	8.31	42.59	4.41
2809	9819	2.948979	ACGCTTCCACAGTTCATTTCAA	59.051	40.909	0.00	0.00	0.00	2.69
2810	9820	2.571212	ACGCTTCCACAGTTCATTTCA	58.429	42.857	0.00	0.00	0.00	2.69
2822	9832	0.179234	TGAGTGGAACAACGCTTCCA	59.821	50.000	1.16	1.16	46.27	3.53
2857	9871	4.637091	TGCTCACAATCCTGAATGTACATG	59.363	41.667	9.63	0.00	0.00	3.21
2862	9876	3.087031	CCTTGCTCACAATCCTGAATGT	58.913	45.455	0.00	0.00	34.61	2.71
2863	9877	2.426024	CCCTTGCTCACAATCCTGAATG	59.574	50.000	0.00	0.00	34.61	2.67
2864	9878	2.309755	TCCCTTGCTCACAATCCTGAAT	59.690	45.455	0.00	0.00	34.61	2.57
2927	9941	0.251634	CAGCTTCCCTGGAGAGGAAC	59.748	60.000	0.00	0.00	42.93	3.62
2994	10008	4.148825	CTCGTGGGCTTCCCTCCG	62.149	72.222	3.27	5.92	45.70	4.63
3031	10046	5.393135	GGTCGTACTCATGAAGATGACAGAA	60.393	44.000	21.67	0.00	34.71	3.02
3032	10047	4.096532	GGTCGTACTCATGAAGATGACAGA	59.903	45.833	21.67	3.82	34.71	3.41
3060	10082	1.888215	AGGCATACATGAGGCAATCG	58.112	50.000	0.00	0.00	36.23	3.34
3065	10087	6.881065	TCTTATTTCATAGGCATACATGAGGC	59.119	38.462	0.00	0.99	32.96	4.70
3163	10194	6.824196	TCACAGTAAATTCAACAACCACAGTA	59.176	34.615	0.00	0.00	0.00	2.74
3218	10249	5.977489	TGTCACAGCTGTAGTACAACTAT	57.023	39.130	21.20	0.00	32.65	2.12
3344	10404	2.109181	CTAAGTAGCTGGGCCGGC	59.891	66.667	30.23	30.23	35.73	6.13
3357	10417	9.093970	TGTACATCGACCATATTTTTGTCTAAG	57.906	33.333	0.00	0.00	0.00	2.18
3359	10419	8.255206	AGTGTACATCGACCATATTTTTGTCTA	58.745	33.333	0.00	0.00	0.00	2.59
3376	10436	4.753107	TGTTTTTCCTTCCGAGTGTACATC	59.247	41.667	0.00	0.00	0.00	3.06
3400	10460	2.355132	GAGCGAGTGGTCTTCTTCGATA	59.645	50.000	0.00	0.00	39.53	2.92
3418	10478	7.006405	AAAAACATTTTTGTAGAGCGAGGAGC	61.006	38.462	1.58	0.00	41.49	4.70
3445	10505	4.790718	AATTCCTTATTTAGACCCGGCT	57.209	40.909	0.00	0.00	0.00	5.52
3497	10557	5.685511	CACAGTTACTTTTTGAAATCCACCG	59.314	40.000	0.00	0.00	0.00	4.94
3631	10709	9.605955	GCACATATTAAATGACGCACAATTATA	57.394	29.630	5.11	0.00	0.00	0.98
3638	10716	6.624710	TTTTGCACATATTAAATGACGCAC	57.375	33.333	13.30	0.00	33.38	5.34
3929	11008	4.158579	TCTTCGCATAGGAGCATACATAGG	59.841	45.833	0.00	0.00	0.00	2.57
3934	11013	4.811557	AGTTTTCTTCGCATAGGAGCATAC	59.188	41.667	0.00	0.00	0.00	2.39
3936	11015	3.878778	AGTTTTCTTCGCATAGGAGCAT	58.121	40.909	0.00	0.00	0.00	3.79
3970	11049	9.836864	AATTTTCAGTTTTAAGATGCCTTTTCT	57.163	25.926	0.00	0.00	33.94	2.52
3971	11050	9.868389	CAATTTTCAGTTTTAAGATGCCTTTTC	57.132	29.630	0.00	0.00	33.94	2.29
3992	11081	8.078596	GCTACTGTCTTTCTTCATTGACAATTT	58.921	33.333	0.00	0.00	38.69	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.