AutoCloner

Multiple sequence alignment - TraesCS3D01G028300

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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	TraesCS3D01G028300	chr3D	100.000	3078	0	0	1	3078	9882924	9879847	0.000000e+00	5685
1	TraesCS3D01G028300	chr3D	88.661	1367	114	17	771	2120	9948679	9947337	0.000000e+00	1628
2	TraesCS3D01G028300	chr3D	95.954	964	31	2	2117	3078	9947303	9946346	0.000000e+00	1557
3	TraesCS3D01G028300	chr3D	89.294	439	42	5	1	438	9949436	9949002	2.090000e-151	545
4	TraesCS3D01G028300	chr3D	84.432	546	65	13	2538	3075	5678923	5678390	1.260000e-143	520
5	TraesCS3D01G028300	chr3D	83.879	428	66	3	1	425	5682765	5682338	3.700000e-109	405
6	TraesCS3D01G028300	chr3D	88.686	274	23	4	2164	2434	5680142	5679874	8.230000e-86	327
7	TraesCS3D01G028300	chr3D	98.438	64	1	0	3015	3078	9907864	9907801	2.510000e-21	113
8	TraesCS3D01G028300	chr3D	98.438	64	1	0	3015	3078	9915508	9915445	2.510000e-21	113
9	TraesCS3D01G028300	chr3D	98.438	64	1	0	3015	3078	9938988	9938925	2.510000e-21	113
10	TraesCS3D01G028300	chr3B	88.274	1373	127	20	771	2120	14112768	14111407	0.000000e+00	1613
11	TraesCS3D01G028300	chr3B	88.698	1336	124	13	771	2085	14066093	14064764	0.000000e+00	1605
12	TraesCS3D01G028300	chr3B	87.828	1372	132	23	772	2120	14023825	14022466	0.000000e+00	1576
13	TraesCS3D01G028300	chr3B	87.163	1371	144	21	771	2120	14106085	14104726	0.000000e+00	1528
14	TraesCS3D01G028300	chr3B	87.071	1369	145	21	771	2120	28541825	28540470	0.000000e+00	1519
15	TraesCS3D01G028300	chr3B	86.944	1371	147	16	771	2120	28409823	28408464	0.000000e+00	1511
16	TraesCS3D01G028300	chr3B	86.890	1373	147	18	771	2120	28563774	28562412	0.000000e+00	1507
17	TraesCS3D01G028300	chr3B	86.560	1369	153	16	771	2120	28518996	28517640	0.000000e+00	1480
18	TraesCS3D01G028300	chr3B	90.000	970	80	9	2117	3075	14111377	14110414	0.000000e+00	1238
19	TraesCS3D01G028300	chr3B	89.311	973	84	9	2117	3075	14104696	14103730	0.000000e+00	1203
20	TraesCS3D01G028300	chr3B	89.175	970	86	11	2117	3075	14022436	14021475	0.000000e+00	1192
21	TraesCS3D01G028300	chr3B	88.648	969	87	13	2117	3075	28540440	28539485	0.000000e+00	1158
22	TraesCS3D01G028300	chr3B	89.714	875	70	8	2117	2975	14064710	14063840	0.000000e+00	1099
23	TraesCS3D01G028300	chr3B	87.539	971	94	14	2117	3075	13993080	13992125	0.000000e+00	1098
24	TraesCS3D01G028300	chr3B	88.610	439	48	2	1	438	13995228	13994791	1.620000e-147	532
25	TraesCS3D01G028300	chr3B	88.610	439	47	3	1	438	14066856	14066420	5.840000e-147	531
26	TraesCS3D01G028300	chr3B	88.047	343	30	6	439	777	28542215	28541880	2.220000e-106	396
27	TraesCS3D01G028300	chr3B	87.683	341	29	6	439	777	13994847	13994518	4.810000e-103	385
28	TraesCS3D01G028300	chr3B	87.209	344	32	7	439	777	14106476	14106140	6.230000e-102	381
29	TraesCS3D01G028300	chr3B	88.350	309	34	2	131	438	14134168	14133861	1.350000e-98	370
30	TraesCS3D01G028300	chr3B	86.804	341	31	6	439	777	28423370	28423042	4.850000e-98	368
31	TraesCS3D01G028300	chr3B	86.804	341	31	6	439	777	28530788	28530460	4.850000e-98	368
32	TraesCS3D01G028300	chr3B	86.510	341	33	6	439	777	28478890	28478561	2.260000e-96	363
33	TraesCS3D01G028300	chr3B	86.510	341	32	6	439	777	28519379	28519051	2.260000e-96	363
34	TraesCS3D01G028300	chr3B	87.702	309	36	2	131	438	14113392	14113085	2.920000e-95	359
35	TraesCS3D01G028300	chr3B	86.217	341	33	6	439	777	28456718	28456390	1.050000e-94	357
36	TraesCS3D01G028300	chr3B	91.071	224	16	1	2191	2414	14222302	14222083	1.790000e-77	300
37	TraesCS3D01G028300	chr3B	86.747	249	30	3	192	438	28542405	28542158	1.090000e-69	274
38	TraesCS3D01G028300	chr3B	79.373	383	38	9	2160	2525	12180472	12180114	6.640000e-57	231
39	TraesCS3D01G028300	chr3B	87.640	178	20	2	251	427	28479021	28478845	4.020000e-49	206
40	TraesCS3D01G028300	chrUn	86.890	1373	147	18	771	2120	307487563	307488925	0.000000e+00	1507
41	TraesCS3D01G028300	chrUn	86.890	1373	147	18	771	2120	328827883	328829245	0.000000e+00	1507
42	TraesCS3D01G028300	chrUn	85.360	444	52	6	1	437	35793613	35794050	6.050000e-122	448
43	TraesCS3D01G028300	chr2A	91.396	953	68	6	2117	3066	19662140	19661199	0.000000e+00	1293
44	TraesCS3D01G028300	chr2A	87.992	1016	98	13	1124	2120	19663184	19662174	0.000000e+00	1179
45	TraesCS3D01G028300	chr2A	87.755	343	31	2	439	781	19663851	19663520	1.030000e-104	390
46	TraesCS3D01G028300	chr3A	83.550	231	20	13	2849	3077	15606597	15606811	1.870000e-47	200

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	TraesCS3D01G028300	chr3D	9879847	9882924	3077	True	5685.000000	5685	100.000000	1	3078	1	chr3D.!!$R1	3077
1	TraesCS3D01G028300	chr3D	9946346	9949436	3090	True	1243.333333	1628	91.303000	1	3078	3	chr3D.!!$R6	3077
2	TraesCS3D01G028300	chr3D	5678390	5682765	4375	True	417.333333	520	85.665667	1	3075	3	chr3D.!!$R5	3074
3	TraesCS3D01G028300	chr3B	28408464	28409823	1359	True	1511.000000	1511	86.944000	771	2120	1	chr3B.!!$R4	1349
4	TraesCS3D01G028300	chr3B	28562412	28563774	1362	True	1507.000000	1507	86.890000	771	2120	1	chr3B.!!$R8	1349
5	TraesCS3D01G028300	chr3B	14021475	14023825	2350	True	1384.000000	1576	88.501500	772	3075	2	chr3B.!!$R10	2303
6	TraesCS3D01G028300	chr3B	14063840	14066856	3016	True	1078.333333	1605	89.007333	1	2975	3	chr3B.!!$R11	2974
7	TraesCS3D01G028300	chr3B	14103730	14113392	9662	True	1053.666667	1613	88.276500	131	3075	6	chr3B.!!$R12	2944
8	TraesCS3D01G028300	chr3B	28517640	28519379	1739	True	921.500000	1480	86.535000	439	2120	2	chr3B.!!$R14	1681
9	TraesCS3D01G028300	chr3B	28539485	28542405	2920	True	836.750000	1519	87.628250	192	3075	4	chr3B.!!$R15	2883
10	TraesCS3D01G028300	chr3B	13992125	13995228	3103	True	671.666667	1098	87.944000	1	3075	3	chr3B.!!$R9	3074
11	TraesCS3D01G028300	chrUn	307487563	307488925	1362	False	1507.000000	1507	86.890000	771	2120	1	chrUn.!!$F2	1349
12	TraesCS3D01G028300	chrUn	328827883	328829245	1362	False	1507.000000	1507	86.890000	771	2120	1	chrUn.!!$F3	1349
13	TraesCS3D01G028300	chr2A	19661199	19663851	2652	True	954.000000	1293	89.047667	439	3066	3	chr2A.!!$R1	2627

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
437	443	0.035534	AGCACATCAACCATGGCGTA	60.036	50.0	13.04	0.0	36.72	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2080	9358	0.322636	AACACAACAACGGTGGACCA	60.323	50.0	4.97	0.0	40.54	4.02	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
57	58	3.194005	TGGGAGCCGATACTTGATTTC	57.806	47.619	0.00	0.00	0.00	2.17
68	69	5.759763	CGATACTTGATTTCCCACATCATCA	59.240	40.000	0.00	0.00	30.63	3.07
117	118	1.597663	ACGTTGTTCAAGCCTTTCTCG	59.402	47.619	0.00	0.00	0.00	4.04
149	150	2.019984	GAGGATGATCTTGGTTGGTGC	58.980	52.381	0.00	0.00	0.00	5.01
177	180	3.580458	CTGGTTATCCCCCTATGTCTCTG	59.420	52.174	0.00	0.00	0.00	3.35
198	201	0.978146	AACCTCCAGCTACGGATGCT	60.978	55.000	2.46	0.00	42.06	3.79
208	211	2.936498	GCTACGGATGCTTGCTTAGAAA	59.064	45.455	8.45	0.00	0.00	2.52
212	215	4.265073	ACGGATGCTTGCTTAGAAATCTT	58.735	39.130	0.00	0.00	0.00	2.40
215	218	5.163723	CGGATGCTTGCTTAGAAATCTTTGA	60.164	40.000	0.00	0.00	0.00	2.69
221	224	6.744993	GCTTGCTTAGAAATCTTTGAACTAGC	59.255	38.462	0.00	0.00	0.00	3.42
223	226	7.986085	TGCTTAGAAATCTTTGAACTAGCTT	57.014	32.000	0.00	0.00	0.00	3.74
227	230	9.818796	CTTAGAAATCTTTGAACTAGCTTGTTC	57.181	33.333	27.44	27.44	44.60	3.18
229	232	6.772716	AGAAATCTTTGAACTAGCTTGTTCCA	59.227	34.615	29.75	20.69	43.96	3.53
299	302	4.464597	CCGAATCAAGGGGTTATTTTTCCA	59.535	41.667	0.00	0.00	0.00	3.53
300	303	5.128663	CCGAATCAAGGGGTTATTTTTCCAT	59.871	40.000	0.00	0.00	0.00	3.41
319	324	3.570975	CCATTCCATGCAAGCAGCTAATA	59.429	43.478	0.00	0.00	45.94	0.98
343	348	0.178947	TTTTTGGCATCGGGGGTCTT	60.179	50.000	0.00	0.00	0.00	3.01
379	385	4.464947	CCTATTCCAGGGATCTTTTGGAC	58.535	47.826	11.30	0.00	40.54	4.02
385	391	0.811281	GGGATCTTTTGGACGCTTGG	59.189	55.000	0.00	0.00	0.00	3.61
428	434	3.248043	TGGTAGCCAGCACATCAAC	57.752	52.632	0.00	0.00	0.00	3.18
429	435	0.322456	TGGTAGCCAGCACATCAACC	60.322	55.000	0.00	0.00	0.00	3.77
430	436	0.322456	GGTAGCCAGCACATCAACCA	60.322	55.000	0.00	0.00	0.00	3.67
431	437	1.683011	GGTAGCCAGCACATCAACCAT	60.683	52.381	0.00	0.00	0.00	3.55
432	438	1.402968	GTAGCCAGCACATCAACCATG	59.597	52.381	0.00	0.00	38.64	3.66
433	439	0.968901	AGCCAGCACATCAACCATGG	60.969	55.000	11.19	11.19	36.72	3.66
434	440	1.514087	CCAGCACATCAACCATGGC	59.486	57.895	13.04	0.00	36.72	4.40
435	441	1.138036	CAGCACATCAACCATGGCG	59.862	57.895	13.04	3.06	36.72	5.69
436	442	1.303561	AGCACATCAACCATGGCGT	60.304	52.632	13.04	0.00	36.72	5.68
437	443	0.035534	AGCACATCAACCATGGCGTA	60.036	50.000	13.04	0.00	36.72	4.42
438	444	0.098728	GCACATCAACCATGGCGTAC	59.901	55.000	13.04	0.00	36.72	3.67
439	445	1.737838	CACATCAACCATGGCGTACT	58.262	50.000	13.04	0.00	36.72	2.73
440	446	2.083774	CACATCAACCATGGCGTACTT	58.916	47.619	13.04	0.00	36.72	2.24
441	447	2.083774	ACATCAACCATGGCGTACTTG	58.916	47.619	13.04	8.73	36.72	3.16
442	448	2.083774	CATCAACCATGGCGTACTTGT	58.916	47.619	13.04	0.00	0.00	3.16
443	449	1.518325	TCAACCATGGCGTACTTGTG	58.482	50.000	13.04	0.00	0.00	3.33
444	450	0.521291	CAACCATGGCGTACTTGTGG	59.479	55.000	13.04	0.00	36.06	4.17
445	451	1.241315	AACCATGGCGTACTTGTGGC	61.241	55.000	13.04	0.00	33.24	5.01
486	493	3.823330	GCAGCCAGCACATCAGCC	61.823	66.667	0.00	0.00	44.79	4.85
487	494	2.360726	CAGCCAGCACATCAGCCA	60.361	61.111	0.00	0.00	34.23	4.75
488	495	1.753078	CAGCCAGCACATCAGCCAT	60.753	57.895	0.00	0.00	34.23	4.40
489	496	1.753078	AGCCAGCACATCAGCCATG	60.753	57.895	0.00	0.00	38.64	3.66
490	497	2.782222	GCCAGCACATCAGCCATGG	61.782	63.158	7.63	7.63	36.72	3.66
506	513	3.595758	GGGCCATGGCGTATGTGC	61.596	66.667	29.90	14.18	43.06	4.57
516	523	1.002250	GCGTATGTGCCGGTCGATAG	61.002	60.000	1.90	0.00	0.00	2.08
549	556	1.741770	GGATGTGTCGTGACCTGGC	60.742	63.158	0.00	0.00	0.00	4.85
555	562	0.249868	TGTCGTGACCTGGCTGAAAG	60.250	55.000	0.00	0.00	0.00	2.62
650	660	3.516300	TCTTTTTATAGGCTCCCACGTGA	59.484	43.478	19.30	0.00	0.00	4.35
678	688	3.746492	GGTGTTATAATCTGGCGATGGAC	59.254	47.826	0.00	0.00	0.00	4.02
692	702	3.368531	GCGATGGACTCAAAAGTACTCCT	60.369	47.826	0.00	0.00	37.24	3.69
721	733	8.893727	GTGTATCAATTAAGCAGGAAACTATGT	58.106	33.333	0.00	0.00	40.21	2.29
835	911	9.672086	GATTAAGAGCACGGCTTATATCTATAG	57.328	37.037	0.00	0.00	39.88	1.31
866	1325	2.255406	TGGGAATGGAAACCACAATGG	58.745	47.619	0.00	0.00	45.02	3.16
885	1344	7.231317	CACAATGGGGAAGCATTTATAGTGTAT	59.769	37.037	0.00	0.00	0.00	2.29
924	1393	2.550830	TTTGTTCTCAGACCTCTGCC	57.449	50.000	0.00	0.00	43.46	4.85
964	1442	3.321968	GGAAAAAGTTTGGCCTGAGACAT	59.678	43.478	3.32	0.00	0.00	3.06
1037	1539	1.931007	GATGGGAGGAGCAGGGCTTT	61.931	60.000	0.00	0.00	39.88	3.51
1275	8484	7.521669	TCTTTCTTTCCTTCTTTCTTCCTCAT	58.478	34.615	0.00	0.00	0.00	2.90
1277	8503	6.439636	TCTTTCCTTCTTTCTTCCTCATGA	57.560	37.500	0.00	0.00	0.00	3.07
1280	8506	5.674052	TCCTTCTTTCTTCCTCATGAGAG	57.326	43.478	24.62	14.21	41.72	3.20
1295	8521	6.016024	CCTCATGAGAGAGATCGATTCTTTCT	60.016	42.308	24.62	16.76	45.93	2.52
1296	8522	6.737118	TCATGAGAGAGATCGATTCTTTCTG	58.263	40.000	16.89	14.84	43.93	3.02
1298	8524	5.889219	TGAGAGAGATCGATTCTTTCTGTG	58.111	41.667	16.89	0.00	43.93	3.66
1301	8527	4.431809	AGAGATCGATTCTTTCTGTGCTG	58.568	43.478	0.00	0.00	33.74	4.41
1303	8529	5.021033	AGATCGATTCTTTCTGTGCTGAT	57.979	39.130	0.00	0.00	0.00	2.90
1305	8531	5.879223	AGATCGATTCTTTCTGTGCTGATTT	59.121	36.000	0.00	0.00	0.00	2.17
1307	8533	7.550551	AGATCGATTCTTTCTGTGCTGATTTAA	59.449	33.333	0.00	0.00	0.00	1.52
1320	8564	3.808618	GCTGATTTAAGGCCATCTCCGAT	60.809	47.826	5.01	0.00	0.00	4.18
1417	8662	4.314440	ATGGCGTGCGTGGACAGT	62.314	61.111	0.00	0.00	0.00	3.55
1597	8842	4.830765	GGCTATGTCGGCGCACCA	62.831	66.667	10.83	1.88	34.57	4.17
1845	9093	0.405585	AAGATGTGGGTCAACCTGGG	59.594	55.000	0.00	0.00	41.11	4.45
1846	9094	1.000896	GATGTGGGTCAACCTGGGG	60.001	63.158	0.00	0.00	41.11	4.96
1847	9095	3.224007	ATGTGGGTCAACCTGGGGC	62.224	63.158	0.00	0.00	41.11	5.80
1848	9096	4.678743	GTGGGTCAACCTGGGGCC	62.679	72.222	0.00	0.00	41.11	5.80
2000	9266	1.900016	CTGGTTCCAGCAGCAGCAA	60.900	57.895	3.17	0.00	45.49	3.91
2001	9267	1.863662	CTGGTTCCAGCAGCAGCAAG	61.864	60.000	3.17	0.00	45.49	4.01
2002	9268	2.633509	GGTTCCAGCAGCAGCAAGG	61.634	63.158	3.17	5.00	45.49	3.61
2009	9287	4.020617	CAGCAGCAAGGGACGGGA	62.021	66.667	0.00	0.00	0.00	5.14
2058	9336	1.065854	CATCGACAAGCTCTCCCCTTT	60.066	52.381	0.00	0.00	0.00	3.11
2080	9358	1.883275	TCCGACGCATTGGTTTGATTT	59.117	42.857	0.00	0.00	0.00	2.17
2090	9369	1.324383	GGTTTGATTTGGTCCACCGT	58.676	50.000	0.00	0.00	39.43	4.83
2093	9372	2.060050	TTGATTTGGTCCACCGTTGT	57.940	45.000	0.00	0.00	39.43	3.32
2276	9638	3.248266	GTCATTCCAACTTGCAAGCATC	58.752	45.455	26.27	3.51	0.00	3.91
2397	9762	5.012664	TGCAGGTTTAGTTGAGGATAGTGAA	59.987	40.000	0.00	0.00	0.00	3.18
2416	9781	4.020128	GTGAAGAAGAAAGGAGGCCTTCTA	60.020	45.833	16.04	0.00	43.92	2.10
2472	9880	2.877786	TGTTGATGCAGCATATAACCCG	59.122	45.455	22.78	0.00	0.00	5.28
2560	10794	3.653835	AAGGGGGAAACTTATCTCTGC	57.346	47.619	0.00	0.00	0.00	4.26
2577	10811	1.334556	CTGCACACTGCTTAAACTGCA	59.665	47.619	0.00	0.00	45.31	4.41
2618	10853	0.250640	CTTTGAGGGCTGCAGTCTGT	60.251	55.000	19.48	5.78	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	0.843984	AACCTGTGCTAACCACCAGT	59.156	50.000	0.00	0.00	44.01	4.00
35	36	2.918712	ATCAAGTATCGGCTCCCAAG	57.081	50.000	0.00	0.00	0.00	3.61
57	58	3.067180	GCTAACACCAATGATGATGTGGG	59.933	47.826	0.00	0.00	36.69	4.61
68	69	3.317993	AGCACGAAAAAGCTAACACCAAT	59.682	39.130	0.00	0.00	39.78	3.16
149	150	0.269173	AGGGGGATAACCAGAGAGGG	59.731	60.000	0.00	0.00	43.89	4.30
177	180	1.538419	GCATCCGTAGCTGGAGGTTAC	60.538	57.143	6.61	0.00	41.78	2.50
198	201	7.986085	AGCTAGTTCAAAGATTTCTAAGCAA	57.014	32.000	0.00	0.00	0.00	3.91
229	232	1.361204	TCCATCTGTCACCACACCAT	58.639	50.000	0.00	0.00	0.00	3.55
299	302	5.595542	TCTTTATTAGCTGCTTGCATGGAAT	59.404	36.000	7.79	1.94	45.94	3.01
300	303	4.949238	TCTTTATTAGCTGCTTGCATGGAA	59.051	37.500	7.79	0.00	45.94	3.53
319	324	1.554617	CCCCCGATGCCAAAAATCTTT	59.445	47.619	0.00	0.00	0.00	2.52
343	348	5.104109	CCTGGAATAGGGTACTGGATTTTGA	60.104	44.000	0.00	0.00	43.33	2.69
379	385	0.039256	CAACAACATGACCCCAAGCG	60.039	55.000	0.00	0.00	0.00	4.68
385	391	4.685628	CAGCAAATAACAACAACATGACCC	59.314	41.667	0.00	0.00	0.00	4.46
427	433	1.674322	GCCACAAGTACGCCATGGT	60.674	57.895	14.67	0.00	32.71	3.55
428	434	2.406616	GGCCACAAGTACGCCATGG	61.407	63.158	7.63	7.63	42.52	3.66
429	435	3.187058	GGCCACAAGTACGCCATG	58.813	61.111	0.00	0.00	42.52	3.66
432	438	1.241315	AACATGGCCACAAGTACGCC	61.241	55.000	8.16	2.07	43.32	5.68
433	439	0.109781	CAACATGGCCACAAGTACGC	60.110	55.000	8.16	0.00	0.00	4.42
434	440	1.234821	ACAACATGGCCACAAGTACG	58.765	50.000	8.16	5.15	0.00	3.67
435	441	2.360801	ACAACAACATGGCCACAAGTAC	59.639	45.455	8.16	0.00	0.00	2.73
436	442	2.660572	ACAACAACATGGCCACAAGTA	58.339	42.857	8.16	0.00	0.00	2.24
437	443	1.484038	ACAACAACATGGCCACAAGT	58.516	45.000	8.16	4.12	0.00	3.16
438	444	2.600470	AACAACAACATGGCCACAAG	57.400	45.000	8.16	3.32	0.00	3.16
439	445	4.679373	AATAACAACAACATGGCCACAA	57.321	36.364	8.16	0.00	0.00	3.33
440	446	4.375272	CAAATAACAACAACATGGCCACA	58.625	39.130	8.16	0.00	0.00	4.17
441	447	3.186205	GCAAATAACAACAACATGGCCAC	59.814	43.478	8.16	0.00	0.00	5.01
442	448	3.070734	AGCAAATAACAACAACATGGCCA	59.929	39.130	8.56	8.56	0.00	5.36
443	449	3.432933	CAGCAAATAACAACAACATGGCC	59.567	43.478	0.00	0.00	0.00	5.36
444	450	3.432933	CCAGCAAATAACAACAACATGGC	59.567	43.478	0.00	0.00	0.00	4.40
445	451	4.448395	CACCAGCAAATAACAACAACATGG	59.552	41.667	0.00	0.00	0.00	3.66
486	493	1.529010	ACATACGCCATGGCCCATG	60.529	57.895	30.21	30.21	41.10	3.66
487	494	1.529010	CACATACGCCATGGCCCAT	60.529	57.895	30.79	20.27	39.13	4.00
488	495	2.124362	CACATACGCCATGGCCCA	60.124	61.111	30.79	18.84	39.13	5.36
489	496	3.595758	GCACATACGCCATGGCCC	61.596	66.667	30.79	5.10	39.13	5.80
506	513	0.738975	TTCTCACTGCTATCGACCGG	59.261	55.000	0.00	0.00	0.00	5.28
516	523	1.078143	ATCCCGCCTTTCTCACTGC	60.078	57.895	0.00	0.00	0.00	4.40
549	556	2.033299	ACAACGCATCACAACCTTTCAG	59.967	45.455	0.00	0.00	0.00	3.02
555	562	0.934436	GCACACAACGCATCACAACC	60.934	55.000	0.00	0.00	0.00	3.77
637	647	0.107508	CATCAATCACGTGGGAGCCT	60.108	55.000	17.00	0.00	0.00	4.58
650	660	5.620206	TCGCCAGATTATAACACCATCAAT	58.380	37.500	0.00	0.00	0.00	2.57
678	688	3.662247	ACACGGAGGAGTACTTTTGAG	57.338	47.619	0.00	0.00	0.00	3.02
692	702	4.746535	TCCTGCTTAATTGATACACGGA	57.253	40.909	0.00	0.00	0.00	4.69
835	911	6.127196	TGGTTTCCATTCCCAAACTTATATGC	60.127	38.462	0.00	0.00	33.70	3.14
866	1325	6.515035	GCCACAATACACTATAAATGCTTCCC	60.515	42.308	0.00	0.00	0.00	3.97
924	1393	1.382420	CAGGAGGTGGGAGAGGAGG	60.382	68.421	0.00	0.00	0.00	4.30
964	1442	2.551504	GGGGAAAGAAAACCGCTGTCTA	60.552	50.000	0.00	0.00	36.42	2.59
1020	1522	2.532715	AAAGCCCTGCTCCTCCCA	60.533	61.111	0.00	0.00	38.25	4.37
1054	1565	2.262915	CGCCTTCTTGGAGCTCGT	59.737	61.111	7.83	0.00	38.35	4.18
1275	8484	5.678361	GCACAGAAAGAATCGATCTCTCTCA	60.678	44.000	0.00	0.00	32.99	3.27
1277	8503	4.402155	AGCACAGAAAGAATCGATCTCTCT	59.598	41.667	0.00	0.00	35.80	3.10
1280	8506	4.428209	TCAGCACAGAAAGAATCGATCTC	58.572	43.478	0.00	0.00	37.42	2.75
1295	8521	3.282021	GAGATGGCCTTAAATCAGCACA	58.718	45.455	3.32	0.00	0.00	4.57
1296	8522	2.620585	GGAGATGGCCTTAAATCAGCAC	59.379	50.000	3.32	0.00	0.00	4.40
1298	8524	1.876156	CGGAGATGGCCTTAAATCAGC	59.124	52.381	3.32	0.00	0.00	4.26
1301	8527	5.067805	ACAAAATCGGAGATGGCCTTAAATC	59.932	40.000	3.32	0.00	45.12	2.17
1303	8529	4.157656	CACAAAATCGGAGATGGCCTTAAA	59.842	41.667	3.32	0.00	45.12	1.52
1305	8531	3.278574	CACAAAATCGGAGATGGCCTTA	58.721	45.455	3.32	0.00	45.12	2.69
1307	8533	1.004745	ACACAAAATCGGAGATGGCCT	59.995	47.619	3.32	0.00	45.12	5.19
1320	8564	2.018727	CTGCAGGCAGGCACACAAAA	62.019	55.000	13.39	0.00	39.25	2.44
1415	8660	1.371558	GGTCGAAGAAGCCACCACT	59.628	57.895	0.00	0.00	39.69	4.00
1417	8662	2.747686	GGGTCGAAGAAGCCACCA	59.252	61.111	0.00	0.00	39.69	4.17
1616	8861	1.292223	CCGAGTGGACGGTGTTGAT	59.708	57.895	0.00	0.00	46.70	2.57
1770	9018	4.934942	CGCACACCACGGACACGA	62.935	66.667	0.00	0.00	44.60	4.35
2009	9287	0.840722	AGGGGAACTTCCATGGACGT	60.841	55.000	17.78	17.78	38.64	4.34
2058	9336	0.533085	TCAAACCAATGCGTCGGACA	60.533	50.000	9.10	0.00	0.00	4.02
2080	9358	0.322636	AACACAACAACGGTGGACCA	60.323	50.000	4.97	0.00	40.54	4.02
2090	9369	4.808414	TTGTTTCCCATCAACACAACAA	57.192	36.364	0.00	0.00	33.81	2.83
2093	9372	3.444034	TCGTTTGTTTCCCATCAACACAA	59.556	39.130	0.00	0.00	33.81	3.33
2383	9748	6.702329	TCCTTTCTTCTTCACTATCCTCAAC	58.298	40.000	0.00	0.00	0.00	3.18
2385	9750	5.423610	CCTCCTTTCTTCTTCACTATCCTCA	59.576	44.000	0.00	0.00	0.00	3.86
2397	9762	4.366267	TGATAGAAGGCCTCCTTTCTTCT	58.634	43.478	5.23	5.82	44.82	2.85
2416	9781	5.582953	TCCTGATTGGGAGATTTGTTTGAT	58.417	37.500	0.00	0.00	36.20	2.57
2472	9880	3.549794	AGCTTCATCAGGAATTACTGCC	58.450	45.455	13.28	0.00	38.36	4.85
2560	10794	8.741101	TTATTATTTGCAGTTTAAGCAGTGTG	57.259	30.769	0.00	0.00	43.75	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.