AutoCloner

Multiple sequence alignment - TraesCS3B01G515200

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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	TraesCS3B01G515200	chr3B	100.000	3256	0	0	1	3256	757733151	757736406	0.000000e+00	6013.0
1	TraesCS3B01G515200	chr3B	83.133	1328	169	32	992	2308	757708078	757709361	0.000000e+00	1160.0
2	TraesCS3B01G515200	chr3B	83.306	1222	182	19	1048	2256	757739782	757738570	0.000000e+00	1107.0
3	TraesCS3B01G515200	chr3B	82.841	1218	192	16	1049	2257	757773386	757772177	0.000000e+00	1075.0
4	TraesCS3B01G515200	chr3B	82.320	1267	182	32	994	2243	685039270	685038029	0.000000e+00	1061.0
5	TraesCS3B01G515200	chr3B	81.038	1329	211	30	989	2292	757807616	757808928	0.000000e+00	1020.0
6	TraesCS3B01G515200	chr3A	92.854	2435	103	32	1	2421	703269325	703271702	0.000000e+00	3467.0
7	TraesCS3B01G515200	chr3A	84.781	1209	141	23	997	2198	703203822	703204994	0.000000e+00	1173.0
8	TraesCS3B01G515200	chr3A	82.444	1293	201	16	980	2262	703304315	703303039	0.000000e+00	1107.0
9	TraesCS3B01G515200	chr3A	88.739	666	63	4	2461	3126	703300172	703300825	0.000000e+00	804.0
10	TraesCS3B01G515200	chr3A	95.652	46	1	1	3209	3253	703300821	703300866	4.510000e-09	73.1
11	TraesCS3B01G515200	chr3D	92.677	2144	106	22	661	2773	570393327	570395450	0.000000e+00	3042.0
12	TraesCS3B01G515200	chr3D	84.345	1335	154	30	978	2302	570379564	570380853	0.000000e+00	1256.0
13	TraesCS3B01G515200	chr3D	84.401	1218	142	27	992	2198	570281032	570282212	0.000000e+00	1153.0
14	TraesCS3B01G515200	chr3D	83.488	1187	157	23	1094	2270	570311115	570312272	0.000000e+00	1070.0
15	TraesCS3B01G515200	chr3D	82.019	1268	184	32	994	2243	520191927	520190686	0.000000e+00	1038.0
16	TraesCS3B01G515200	chr3D	81.042	1324	213	26	993	2292	570559180	570560489	0.000000e+00	1020.0
17	TraesCS3B01G515200	chr3D	91.277	470	39	2	2784	3253	570396658	570397125	9.850000e-180	640.0
18	TraesCS3B01G515200	chr3D	85.242	393	37	9	1	374	570392442	570392832	5.100000e-103	385.0
19	TraesCS3B01G515200	chr1D	83.881	335	42	7	2923	3245	15418651	15418317	3.160000e-80	309.0
20	TraesCS3B01G515200	chr1A	78.297	364	46	21	2923	3253	16189861	16190224	1.530000e-48	204.0
21	TraesCS3B01G515200	chr6B	91.667	144	12	0	484	627	518041053	518040910	1.980000e-47	200.0
22	TraesCS3B01G515200	chr6D	90.210	143	14	0	485	627	343314207	343314065	1.540000e-43	187.0
23	TraesCS3B01G515200	chr1B	86.928	153	11	3	484	627	190317873	190317721	2.600000e-36	163.0
24	TraesCS3B01G515200	chr1B	82.955	88	12	2	287	371	111586403	111586490	3.480000e-10	76.8
25	TraesCS3B01G515200	chr7D	85.057	87	10	2	287	370	573922457	573922543	5.790000e-13	86.1
26	TraesCS3B01G515200	chr7D	82.000	100	14	3	275	370	304554331	304554232	7.490000e-12	82.4
27	TraesCS3B01G515200	chr7D	89.062	64	7	0	522	585	175941642	175941579	2.690000e-11	80.5
28	TraesCS3B01G515200	chr7D	86.957	69	7	2	2925	2992	36013483	36013550	3.480000e-10	76.8
29	TraesCS3B01G515200	chrUn	84.270	89	10	3	285	370	99249780	99249867	2.080000e-12	84.2
30	TraesCS3B01G515200	chr2B	83.158	95	13	2	279	370	240839679	240839773	2.080000e-12	84.2
31	TraesCS3B01G515200	chr2B	83.529	85	12	2	287	371	414150774	414150856	9.690000e-11	78.7
32	TraesCS3B01G515200	chr5D	81.132	106	15	3	287	389	529430403	529430300	2.690000e-11	80.5
33	TraesCS3B01G515200	chr2D	82.759	87	12	2	287	370	427126861	427126775	1.250000e-09	75.0

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	TraesCS3B01G515200	chr3B	757733151	757736406	3255	False	6013.000000	6013	100.0000	1	3256	1	chr3B.!!$F2	3255
1	TraesCS3B01G515200	chr3B	757708078	757709361	1283	False	1160.000000	1160	83.1330	992	2308	1	chr3B.!!$F1	1316
2	TraesCS3B01G515200	chr3B	757738570	757739782	1212	True	1107.000000	1107	83.3060	1048	2256	1	chr3B.!!$R2	1208
3	TraesCS3B01G515200	chr3B	757772177	757773386	1209	True	1075.000000	1075	82.8410	1049	2257	1	chr3B.!!$R3	1208
4	TraesCS3B01G515200	chr3B	685038029	685039270	1241	True	1061.000000	1061	82.3200	994	2243	1	chr3B.!!$R1	1249
5	TraesCS3B01G515200	chr3B	757807616	757808928	1312	False	1020.000000	1020	81.0380	989	2292	1	chr3B.!!$F3	1303
6	TraesCS3B01G515200	chr3A	703269325	703271702	2377	False	3467.000000	3467	92.8540	1	2421	1	chr3A.!!$F2	2420
7	TraesCS3B01G515200	chr3A	703203822	703204994	1172	False	1173.000000	1173	84.7810	997	2198	1	chr3A.!!$F1	1201
8	TraesCS3B01G515200	chr3A	703303039	703304315	1276	True	1107.000000	1107	82.4440	980	2262	1	chr3A.!!$R1	1282
9	TraesCS3B01G515200	chr3A	703300172	703300866	694	False	438.550000	804	92.1955	2461	3253	2	chr3A.!!$F3	792
10	TraesCS3B01G515200	chr3D	570392442	570397125	4683	False	1355.666667	3042	89.7320	1	3253	3	chr3D.!!$F5	3252
11	TraesCS3B01G515200	chr3D	570379564	570380853	1289	False	1256.000000	1256	84.3450	978	2302	1	chr3D.!!$F3	1324
12	TraesCS3B01G515200	chr3D	570281032	570282212	1180	False	1153.000000	1153	84.4010	992	2198	1	chr3D.!!$F1	1206
13	TraesCS3B01G515200	chr3D	570311115	570312272	1157	False	1070.000000	1070	83.4880	1094	2270	1	chr3D.!!$F2	1176
14	TraesCS3B01G515200	chr3D	520190686	520191927	1241	True	1038.000000	1038	82.0190	994	2243	1	chr3D.!!$R1	1249
15	TraesCS3B01G515200	chr3D	570559180	570560489	1309	False	1020.000000	1020	81.0420	993	2292	1	chr3D.!!$F4	1299

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
284	307	0.033405	ATTGATGGCTTGAGCTGGCT	60.033	50.0	0.0	0.0	41.70	4.75	F
1671	2204	0.525668	CTACACGCAGTCGATGGACC	60.526	60.0	4.0	0.0	41.61	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1730	2269	1.376683	GCGGGTGTTGTCCATGCTA	60.377	57.895	0.0	0.0	0.00	3.49	R
2670	3232	0.108186	CTGATGACTAGCCCGTGCAA	60.108	55.000	0.0	0.0	41.13	4.08	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
33	34	6.389830	TGCATGCCCTATTAACATACTTTG	57.610	37.500	16.68	0.00	0.00	2.77
102	104	5.221342	TGCTTCCAAACGTAATTTTCATGGT	60.221	36.000	0.00	0.00	0.00	3.55
197	203	0.738389	GGGTAATGTGCAATCACCCG	59.262	55.000	10.36	0.00	42.46	5.28
208	214	3.128415	TGCAATCACCCGTGTAATTGATG	59.872	43.478	0.00	0.00	30.71	3.07
282	305	1.758936	TGATTGATGGCTTGAGCTGG	58.241	50.000	0.00	0.00	41.70	4.85
284	307	0.033405	ATTGATGGCTTGAGCTGGCT	60.033	50.000	0.00	0.00	41.70	4.75
329	352	8.079211	ACTATCATGCATACGATATTAGGGTT	57.921	34.615	0.00	0.00	0.00	4.11
339	362	9.706691	CATACGATATTAGGGTTTGATACTGTT	57.293	33.333	0.00	0.00	0.00	3.16
440	885	6.141211	CGTTTTGGCATCTCATCAAATTATCG	59.859	38.462	0.00	0.00	31.60	2.92
450	895	4.644234	TCATCAAATTATCGGTTGGCATGT	59.356	37.500	0.00	0.00	0.00	3.21
455	900	7.644490	TCAAATTATCGGTTGGCATGTATTAC	58.356	34.615	0.00	0.00	0.00	1.89
456	901	5.856126	ATTATCGGTTGGCATGTATTACG	57.144	39.130	0.00	0.00	0.00	3.18
458	903	2.542597	TCGGTTGGCATGTATTACGTC	58.457	47.619	0.00	0.00	0.00	4.34
459	904	2.166870	TCGGTTGGCATGTATTACGTCT	59.833	45.455	0.00	0.00	0.00	4.18
460	905	2.284150	CGGTTGGCATGTATTACGTCTG	59.716	50.000	0.00	0.00	0.00	3.51
461	906	3.527533	GGTTGGCATGTATTACGTCTGA	58.472	45.455	0.00	0.00	0.00	3.27
462	907	4.127171	GGTTGGCATGTATTACGTCTGAT	58.873	43.478	0.00	0.00	0.00	2.90
463	908	4.024893	GGTTGGCATGTATTACGTCTGATG	60.025	45.833	0.00	0.00	0.00	3.07
464	909	3.130633	TGGCATGTATTACGTCTGATGC	58.869	45.455	0.00	0.00	36.33	3.91
477	922	3.004210	CGTCTGATGCATACTAGCTGTCT	59.996	47.826	0.00	0.00	34.99	3.41
478	923	4.297510	GTCTGATGCATACTAGCTGTCTG	58.702	47.826	0.00	0.00	34.99	3.51
500	945	2.743664	TGATGAGCAATGCTACACACAC	59.256	45.455	8.12	1.54	39.88	3.82
516	961	1.656594	CACACGACACTGTTTGAACGA	59.343	47.619	0.00	0.00	34.51	3.85
577	1022	2.057137	TGCATGGATTAGCACCCTTC	57.943	50.000	0.00	0.00	35.51	3.46
580	1025	2.811873	GCATGGATTAGCACCCTTCGAT	60.812	50.000	0.00	0.00	0.00	3.59
581	1026	2.910688	TGGATTAGCACCCTTCGATC	57.089	50.000	0.00	0.00	0.00	3.69
585	1030	3.432326	GGATTAGCACCCTTCGATCAGTT	60.432	47.826	0.00	0.00	0.00	3.16
593	1038	0.716108	CTTCGATCAGTTGTCGTGCC	59.284	55.000	0.00	0.00	39.91	5.01
622	1067	2.738643	GCTAGCAAGCTGTCGTCCATAA	60.739	50.000	10.63	0.00	45.85	1.90
623	1068	2.472695	AGCAAGCTGTCGTCCATAAA	57.527	45.000	0.00	0.00	0.00	1.40
624	1069	2.350522	AGCAAGCTGTCGTCCATAAAG	58.649	47.619	0.00	0.00	0.00	1.85
625	1070	2.076863	GCAAGCTGTCGTCCATAAAGT	58.923	47.619	0.00	0.00	0.00	2.66
626	1071	3.056107	AGCAAGCTGTCGTCCATAAAGTA	60.056	43.478	0.00	0.00	0.00	2.24
627	1072	3.871594	GCAAGCTGTCGTCCATAAAGTAT	59.128	43.478	0.00	0.00	0.00	2.12
628	1073	4.332819	GCAAGCTGTCGTCCATAAAGTATT	59.667	41.667	0.00	0.00	0.00	1.89
629	1074	5.522460	GCAAGCTGTCGTCCATAAAGTATTA	59.478	40.000	0.00	0.00	0.00	0.98
650	1095	7.596749	ATTAAAGTAGTTTCGAGGTGTGATG	57.403	36.000	0.00	0.00	0.00	3.07
659	1104	1.003355	AGGTGTGATGCTCCCGTTG	60.003	57.895	0.00	0.00	0.00	4.10
807	1270	5.106197	CCAATTTAACTATGAGCAGCACACA	60.106	40.000	0.00	0.00	0.00	3.72
808	1271	5.808042	ATTTAACTATGAGCAGCACACAG	57.192	39.130	0.00	0.00	0.00	3.66
809	1272	1.446907	AACTATGAGCAGCACACAGC	58.553	50.000	0.00	0.00	46.19	4.40
821	1284	2.357517	CACAGCTGGTCACCGTCC	60.358	66.667	19.93	0.00	0.00	4.79
909	1372	4.442706	CACACGGTGCCTATAAAAGAGAT	58.557	43.478	8.30	0.00	0.00	2.75
926	1393	2.153219	GATGCACACACGCGTCGAAA	62.153	55.000	9.86	0.00	38.11	3.46
1018	1495	1.305297	ATGGCACGACTCCTCCTCA	60.305	57.895	0.00	0.00	0.00	3.86
1316	1811	4.640855	CGACAGGACGTGCACGGT	62.641	66.667	39.21	28.06	44.95	4.83
1574	2073	2.422093	CCAATAAGTTCCTCCTCTGCCC	60.422	54.545	0.00	0.00	0.00	5.36
1671	2204	0.525668	CTACACGCAGTCGATGGACC	60.526	60.000	4.00	0.00	41.61	4.46
1730	2269	3.769844	ACTACATCTCGGTCAAGTCCATT	59.230	43.478	0.00	0.00	0.00	3.16
1753	2292	4.309950	GGACAACACCCGCGTCCT	62.310	66.667	4.92	0.00	44.82	3.85
2273	2826	2.106477	AGAGCTTTTACTGCCTCTGC	57.894	50.000	0.00	0.00	38.26	4.26
2275	2828	0.695347	AGCTTTTACTGCCTCTGCCT	59.305	50.000	0.00	0.00	36.33	4.75
2276	2829	0.807496	GCTTTTACTGCCTCTGCCTG	59.193	55.000	0.00	0.00	36.33	4.85
2280	2833	4.265073	CTTTTACTGCCTCTGCCTGTAAT	58.735	43.478	0.00	0.00	36.23	1.89
2281	2834	5.428253	CTTTTACTGCCTCTGCCTGTAATA	58.572	41.667	0.00	0.00	36.23	0.98
2282	2835	5.429681	TTTACTGCCTCTGCCTGTAATAA	57.570	39.130	0.00	0.00	36.23	1.40
2284	2837	6.740944	TTACTGCCTCTGCCTGTAATAATA	57.259	37.500	0.00	0.00	33.49	0.98
2285	2838	5.630415	ACTGCCTCTGCCTGTAATAATAA	57.370	39.130	0.00	0.00	36.33	1.40
2286	2839	6.001449	ACTGCCTCTGCCTGTAATAATAAA	57.999	37.500	0.00	0.00	36.33	1.40
2287	2840	6.605119	ACTGCCTCTGCCTGTAATAATAAAT	58.395	36.000	0.00	0.00	36.33	1.40
2288	2841	6.712547	ACTGCCTCTGCCTGTAATAATAAATC	59.287	38.462	0.00	0.00	36.33	2.17
2289	2842	6.841601	TGCCTCTGCCTGTAATAATAAATCT	58.158	36.000	0.00	0.00	36.33	2.40
2290	2843	6.712095	TGCCTCTGCCTGTAATAATAAATCTG	59.288	38.462	0.00	0.00	36.33	2.90
2291	2844	6.712547	GCCTCTGCCTGTAATAATAAATCTGT	59.287	38.462	0.00	0.00	0.00	3.41
2320	2873	7.636150	TCTACAAGTGTACTATTGGACTACC	57.364	40.000	13.04	0.00	0.00	3.18
2363	2916	7.723324	TGTAGATTATGTAGTAGCCTGAAACC	58.277	38.462	0.00	0.00	0.00	3.27
2369	2928	0.322008	AGTAGCCTGAAACCAGCTGC	60.322	55.000	8.66	0.00	0.00	5.25
2429	2990	5.350365	TGCTATCTGTTACAAACGGTTCATC	59.650	40.000	0.00	0.00	38.89	2.92
2435	2996	7.484975	TCTGTTACAAACGGTTCATCAAAAAT	58.515	30.769	0.00	0.00	38.89	1.82
2441	3002	4.783764	ACGGTTCATCAAAAATTCCCTC	57.216	40.909	0.00	0.00	0.00	4.30
2540	3102	8.675705	TCAAGCAATTGATTATTCTTCGGATA	57.324	30.769	8.90	0.00	0.00	2.59
2565	3127	2.801679	CAATTTCTTGCCAATGCGTTGT	59.198	40.909	17.19	0.00	41.78	3.32
2581	3143	0.250295	TTGTGGAGCTTTGAGACCGG	60.250	55.000	0.00	0.00	0.00	5.28
2602	3164	3.617284	GGACGGGTAATTGTCATTCCTT	58.383	45.455	0.00	0.00	36.83	3.36
2626	3188	9.787532	CTTAAGCAATTGATTTTTCTTCGGATA	57.212	29.630	15.02	0.00	0.00	2.59
2635	3197	9.840427	TTGATTTTTCTTCGGATAAATTGAGTC	57.160	29.630	0.00	0.00	36.33	3.36
2637	3199	7.429636	TTTTTCTTCGGATAAATTGAGTCGT	57.570	32.000	0.00	0.00	0.00	4.34
2670	3232	3.754965	ACTAGTCACCAACATGTGCATT	58.245	40.909	0.00	0.00	36.17	3.56
2684	3246	1.429423	GCATTTGCACGGGCTAGTC	59.571	57.895	12.74	0.00	41.91	2.59
2685	3247	1.305219	GCATTTGCACGGGCTAGTCA	61.305	55.000	12.74	0.00	41.91	3.41
2687	3249	1.331756	CATTTGCACGGGCTAGTCATC	59.668	52.381	12.74	0.00	41.91	2.92
2688	3250	0.323302	TTTGCACGGGCTAGTCATCA	59.677	50.000	12.74	0.00	41.91	3.07
2689	3251	0.108186	TTGCACGGGCTAGTCATCAG	60.108	55.000	12.74	0.00	41.91	2.90
2690	3252	1.884926	GCACGGGCTAGTCATCAGC	60.885	63.158	0.00	0.00	38.35	4.26
2695	3257	4.427394	GCTAGTCATCAGCCCGTG	57.573	61.111	0.00	0.00	32.68	4.94
2886	4645	7.201232	CGTAAAACGCATCGAAAGAATTTGAAT	60.201	33.333	0.00	0.00	38.23	2.57
2964	4723	2.223665	GCATCTGCATGGGCTAGTTTTC	60.224	50.000	0.00	0.00	41.91	2.29
3024	4783	3.392285	TGTTATCTGCAGCCACCAGATAT	59.608	43.478	9.47	0.00	46.15	1.63
3042	4801	6.183360	CCAGATATACTTGTTGTGTGCAGAAG	60.183	42.308	0.00	0.00	0.00	2.85
3126	4885	9.677567	AACACACATTAGCTTGTTTTATAACTG	57.322	29.630	0.00	0.00	35.24	3.16
3130	4889	9.329913	CACATTAGCTTGTTTTATAACTGTCAC	57.670	33.333	0.00	0.00	35.24	3.67
3131	4890	9.062524	ACATTAGCTTGTTTTATAACTGTCACA	57.937	29.630	0.00	0.00	35.24	3.58
3160	4919	8.984891	TGTTTATATTTCCTCTGCAACAAATG	57.015	30.769	0.00	0.00	0.00	2.32
3202	4961	6.491403	GCATTCAAGATATAACCCAATGTCCT	59.509	38.462	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	5.758924	AGTATGTTTCTTTTGCGAGGAAAC	58.241	37.500	19.29	19.29	44.97	2.78
102	104	7.436376	TGTCGAAATCAATGCACAAATAAAACA	59.564	29.630	0.00	0.00	0.00	2.83
224	233	0.036590	TGTTGCTGCATAGTGAGCCA	59.963	50.000	1.84	0.00	34.04	4.75
403	426	2.596338	AAAACGCCCCTCCCGTTG	60.596	61.111	0.00	0.00	46.90	4.10
440	885	3.527533	TCAGACGTAATACATGCCAACC	58.472	45.455	0.00	0.00	0.00	3.77
450	895	6.206829	ACAGCTAGTATGCATCAGACGTAATA	59.793	38.462	0.19	0.00	30.25	0.98
455	900	3.004210	AGACAGCTAGTATGCATCAGACG	59.996	47.826	0.19	0.00	30.25	4.18
456	901	4.202101	ACAGACAGCTAGTATGCATCAGAC	60.202	45.833	0.19	0.00	43.17	3.51
458	903	4.049869	CACAGACAGCTAGTATGCATCAG	58.950	47.826	0.19	0.00	43.17	2.90
459	904	3.701040	TCACAGACAGCTAGTATGCATCA	59.299	43.478	0.19	0.00	43.17	3.07
460	905	4.313277	TCACAGACAGCTAGTATGCATC	57.687	45.455	0.19	0.00	43.17	3.91
461	906	4.343239	TCATCACAGACAGCTAGTATGCAT	59.657	41.667	3.79	3.79	43.17	3.96
462	907	3.701040	TCATCACAGACAGCTAGTATGCA	59.299	43.478	9.78	0.00	43.17	3.96
463	908	4.297510	CTCATCACAGACAGCTAGTATGC	58.702	47.826	9.78	0.00	43.17	3.14
464	909	4.202090	TGCTCATCACAGACAGCTAGTATG	60.202	45.833	8.69	8.69	44.87	2.39
477	922	2.743664	GTGTGTAGCATTGCTCATCACA	59.256	45.455	25.75	25.75	39.92	3.58
478	923	2.743664	TGTGTGTAGCATTGCTCATCAC	59.256	45.455	15.81	20.49	40.44	3.06
500	945	4.203828	CAGAAATCGTTCAAACAGTGTCG	58.796	43.478	0.00	0.00	36.09	4.35
516	961	1.800805	CTCAGTCACCGTGCAGAAAT	58.199	50.000	0.00	0.00	0.00	2.17
577	1022	1.354337	CCTGGCACGACAACTGATCG	61.354	60.000	0.00	0.00	45.17	3.69
580	1025	2.425592	CCCTGGCACGACAACTGA	59.574	61.111	0.00	0.00	0.00	3.41
581	1026	2.111043	ACCCTGGCACGACAACTG	59.889	61.111	0.00	0.00	0.00	3.16
593	1038	2.439156	GCTTGCTAGCCCACCCTG	60.439	66.667	13.29	0.00	41.74	4.45
622	1067	8.362639	TCACACCTCGAAACTACTTTAATACTT	58.637	33.333	0.00	0.00	0.00	2.24
623	1068	7.889469	TCACACCTCGAAACTACTTTAATACT	58.111	34.615	0.00	0.00	0.00	2.12
624	1069	8.592998	CATCACACCTCGAAACTACTTTAATAC	58.407	37.037	0.00	0.00	0.00	1.89
625	1070	7.277098	GCATCACACCTCGAAACTACTTTAATA	59.723	37.037	0.00	0.00	0.00	0.98
626	1071	6.092259	GCATCACACCTCGAAACTACTTTAAT	59.908	38.462	0.00	0.00	0.00	1.40
627	1072	5.407387	GCATCACACCTCGAAACTACTTTAA	59.593	40.000	0.00	0.00	0.00	1.52
628	1073	4.927425	GCATCACACCTCGAAACTACTTTA	59.073	41.667	0.00	0.00	0.00	1.85
629	1074	3.746492	GCATCACACCTCGAAACTACTTT	59.254	43.478	0.00	0.00	0.00	2.66
643	1088	2.870372	GCAACGGGAGCATCACAC	59.130	61.111	0.00	0.00	39.81	3.82
807	1270	3.991051	CGTGGACGGTGACCAGCT	61.991	66.667	1.11	0.00	38.14	4.24
821	1284	1.063469	GATTAATTGGCGACCACCGTG	59.937	52.381	0.00	0.00	41.15	4.94
897	1360	4.548916	CGCGTGTGTGCATCTCTTTTATAG	60.549	45.833	0.00	0.00	34.15	1.31
909	1372	2.886124	TTTCGACGCGTGTGTGCA	60.886	55.556	20.70	0.00	34.15	4.57
1236	1725	4.078516	GGGTAGGCGTTGGCGAGT	62.079	66.667	0.00	0.00	41.24	4.18
1730	2269	1.376683	GCGGGTGTTGTCCATGCTA	60.377	57.895	0.00	0.00	0.00	3.49
1832	2374	3.751246	TCCACGAACGGGCGGTAG	61.751	66.667	0.00	0.00	35.12	3.18
2308	2861	5.104693	TGTTGGGTATGTGGTAGTCCAATAG	60.105	44.000	0.00	0.00	46.15	1.73
2311	2864	2.980379	TGTTGGGTATGTGGTAGTCCAA	59.020	45.455	0.00	0.00	46.15	3.53
2320	2873	5.610398	TCTACAGCATATGTTGGGTATGTG	58.390	41.667	21.69	5.71	39.96	3.21
2363	2916	3.341823	ACTAAACAAGATGGAGCAGCTG	58.658	45.455	10.11	10.11	27.64	4.24
2369	2928	8.752766	TTTTACTCGTACTAAACAAGATGGAG	57.247	34.615	0.00	0.00	0.00	3.86
2408	2969	7.731882	TTTGATGAACCGTTTGTAACAGATA	57.268	32.000	0.00	0.00	0.00	1.98
2447	3008	9.040939	CGTTAGGAAAATTTGATGAACCTTTTT	57.959	29.630	0.00	0.00	0.00	1.94
2448	3009	8.201464	ACGTTAGGAAAATTTGATGAACCTTTT	58.799	29.630	0.00	0.00	0.00	2.27
2449	3010	7.722363	ACGTTAGGAAAATTTGATGAACCTTT	58.278	30.769	0.00	0.00	0.00	3.11
2450	3011	7.284919	ACGTTAGGAAAATTTGATGAACCTT	57.715	32.000	0.00	0.00	0.00	3.50
2451	3012	6.894339	ACGTTAGGAAAATTTGATGAACCT	57.106	33.333	0.00	0.00	0.00	3.50
2496	3057	5.504173	GCTTGAGGAATAGCAAATCCGTTAC	60.504	44.000	0.00	0.00	40.78	2.50
2540	3102	4.317488	ACGCATTGGCAAGAAATTGATTT	58.683	34.783	5.96	0.00	41.24	2.17
2565	3127	1.535444	TCCCGGTCTCAAAGCTCCA	60.535	57.895	0.00	0.00	0.00	3.86
2581	3143	3.277142	AGGAATGACAATTACCCGTCC	57.723	47.619	0.00	0.00	0.00	4.79
2585	3147	6.524101	TTGCTTAAGGAATGACAATTACCC	57.476	37.500	5.16	0.00	0.00	3.69
2590	3152	9.729281	AAAATCAATTGCTTAAGGAATGACAAT	57.271	25.926	21.23	9.84	36.20	2.71
2670	3232	0.108186	CTGATGACTAGCCCGTGCAA	60.108	55.000	0.00	0.00	41.13	4.08
2684	3246	2.238942	TAACTATGCACGGGCTGATG	57.761	50.000	12.74	0.56	41.91	3.07
2685	3247	3.578716	AGTATAACTATGCACGGGCTGAT	59.421	43.478	12.74	0.00	41.91	2.90
2687	3249	3.386768	AGTATAACTATGCACGGGCTG	57.613	47.619	12.74	3.47	41.91	4.85
2688	3250	4.587684	ACTAAGTATAACTATGCACGGGCT	59.412	41.667	12.74	0.00	41.91	5.19
2689	3251	4.879598	ACTAAGTATAACTATGCACGGGC	58.120	43.478	0.34	0.34	41.68	6.13
2690	3252	7.211966	ACTACTAAGTATAACTATGCACGGG	57.788	40.000	0.00	0.00	32.84	5.28
2691	3253	8.347771	TGAACTACTAAGTATAACTATGCACGG	58.652	37.037	0.00	0.00	33.75	4.94
2692	3254	9.894783	ATGAACTACTAAGTATAACTATGCACG	57.105	33.333	0.00	0.00	33.75	5.34
2849	4608	8.289440	TCGATGCGTTTTACGAGATAATTATT	57.711	30.769	3.04	0.00	46.05	1.40
2867	4626	8.107591	ACAATTATTCAAATTCTTTCGATGCG	57.892	30.769	0.00	0.00	0.00	4.73
2886	4645	7.825331	TGACCCTAATTGAACACAACAATTA	57.175	32.000	0.00	0.00	43.25	1.40
2887	4646	6.723298	TGACCCTAATTGAACACAACAATT	57.277	33.333	0.00	0.00	45.67	2.32
2952	4711	3.252554	ACCATTTGGAAAACTAGCCCA	57.747	42.857	3.01	0.00	38.94	5.36
2953	4712	4.083565	TGTACCATTTGGAAAACTAGCCC	58.916	43.478	3.01	0.00	38.94	5.19
2956	4715	9.840427	CAACTAATGTACCATTTGGAAAACTAG	57.160	33.333	3.01	0.00	38.94	2.57
3006	4765	3.246301	AGTATATCTGGTGGCTGCAGAT	58.754	45.455	20.43	2.39	38.91	2.90
3010	4769	3.199880	ACAAGTATATCTGGTGGCTGC	57.800	47.619	0.00	0.00	0.00	5.25
3024	4783	4.261155	GCAATCTTCTGCACACAACAAGTA	60.261	41.667	0.00	0.00	42.17	2.24
3042	4801	8.922676	GTTTTCATATTGATCATCCATGCAATC	58.077	33.333	0.00	0.00	33.45	2.67
3126	4885	9.076596	GCAGAGGAAATATAAACATTTTGTGAC	57.923	33.333	0.00	0.00	0.00	3.67
3130	4889	9.421806	TGTTGCAGAGGAAATATAAACATTTTG	57.578	29.630	0.00	0.00	0.00	2.44
3131	4890	9.995003	TTGTTGCAGAGGAAATATAAACATTTT	57.005	25.926	0.00	0.00	0.00	1.82
3168	4927	7.448469	GGGTTATATCTTGAATGCCTACACAAT	59.552	37.037	0.00	0.00	0.00	2.71
3169	4928	6.770785	GGGTTATATCTTGAATGCCTACACAA	59.229	38.462	0.00	0.00	0.00	3.33
3170	4929	6.126623	TGGGTTATATCTTGAATGCCTACACA	60.127	38.462	0.00	0.00	0.00	3.72
3171	4930	6.296026	TGGGTTATATCTTGAATGCCTACAC	58.704	40.000	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.