AutoCloner

Multiple sequence alignment - TraesCS4A01G156800

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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	TraesCS4A01G156800	chr4A	100.000	2694	0	0	1	2694	313750722	313753415	0.000000e+00	4975.0
1	TraesCS4A01G156800	chr4A	94.583	2695	118	7	1	2694	313762438	313765105	0.000000e+00	4143.0
2	TraesCS4A01G156800	chr4A	83.346	1291	181	31	1422	2694	309531554	309530280	0.000000e+00	1162.0
3	TraesCS4A01G156800	chr4A	95.599	659	25	4	1	656	313758239	313758896	0.000000e+00	1053.0
4	TraesCS4A01G156800	chr4A	89.181	342	32	5	1	339	466898580	466898919	3.210000e-114	422.0
5	TraesCS4A01G156800	chr4A	88.012	342	36	5	1	339	466906374	466906713	1.500000e-107	399.0
6	TraesCS4A01G156800	chr4A	90.508	295	28	0	997	1291	383180866	383181160	9.040000e-105	390.0
7	TraesCS4A01G156800	chr4A	79.757	494	59	19	1348	1806	370133832	370134319	1.200000e-83	320.0
8	TraesCS4A01G156800	chr4A	78.032	437	82	14	1	433	69284485	69284911	2.060000e-66	263.0
9	TraesCS4A01G156800	chr4A	88.806	134	11	4	474	606	243223265	243223135	7.720000e-36	161.0
10	TraesCS4A01G156800	chr4A	91.453	117	9	1	613	728	575183268	575183384	2.780000e-35	159.0
11	TraesCS4A01G156800	chr4A	85.556	90	8	5	436	524	297573345	297573260	3.690000e-14	89.8
12	TraesCS4A01G156800	chr4A	92.500	40	2	1	547	585	427076118	427076079	3.750000e-04	56.5
13	TraesCS4A01G156800	chr1A	88.116	1279	140	10	1422	2694	201871654	201870382	0.000000e+00	1509.0
14	TraesCS4A01G156800	chr1A	87.647	1279	145	11	1422	2694	201896153	201894882	0.000000e+00	1474.0
15	TraesCS4A01G156800	chr1A	83.423	1297	171	36	1422	2694	329767531	329766255	0.000000e+00	1164.0
16	TraesCS4A01G156800	chr1A	91.463	164	14	0	1333	1496	233464444	233464281	2.700000e-55	226.0
17	TraesCS4A01G156800	chr1A	83.696	92	15	0	724	815	424631462	424631371	1.330000e-13	87.9
18	TraesCS4A01G156800	chr7A	85.352	1379	159	37	1332	2688	112636286	112637643	0.000000e+00	1387.0
19	TraesCS4A01G156800	chr7A	89.527	296	26	5	997	1290	382179355	382179647	1.180000e-98	370.0
20	TraesCS4A01G156800	chr7A	89.153	295	31	1	997	1291	671011277	671011570	1.520000e-97	366.0
21	TraesCS4A01G156800	chr7A	87.500	88	8	1	452	536	198244352	198244439	6.140000e-17	99.0
22	TraesCS4A01G156800	chr7A	85.227	88	10	2	452	536	198236488	198236575	1.330000e-13	87.9
23	TraesCS4A01G156800	chr4D	84.578	1232	160	22	1484	2694	104798073	104799295	0.000000e+00	1195.0
24	TraesCS4A01G156800	chr5D	84.398	1237	155	25	1484	2694	335209631	335210855	0.000000e+00	1181.0
25	TraesCS4A01G156800	chr3A	82.426	1360	191	35	1332	2667	297357211	297358546	0.000000e+00	1144.0
26	TraesCS4A01G156800	chr3A	84.726	347	38	12	2	338	487162795	487163136	1.550000e-87	333.0
27	TraesCS4A01G156800	chr3A	83.069	378	49	13	2	373	151252999	151252631	2.000000e-86	329.0
28	TraesCS4A01G156800	chr3A	87.013	154	17	3	604	756	237410970	237410819	1.280000e-38	171.0
29	TraesCS4A01G156800	chr3A	93.043	115	8	0	834	948	401042917	401043031	4.610000e-38	169.0
30	TraesCS4A01G156800	chr3A	90.323	124	12	0	612	735	237433029	237432906	2.150000e-36	163.0
31	TraesCS4A01G156800	chr3A	86.986	146	17	2	805	948	316592787	316592932	2.150000e-36	163.0
32	TraesCS4A01G156800	chr3A	86.000	150	19	2	805	952	264177574	264177723	2.780000e-35	159.0
33	TraesCS4A01G156800	chr3A	75.168	298	56	15	1	286	699351453	699351162	1.010000e-24	124.0
34	TraesCS4A01G156800	chr3A	92.500	40	2	1	547	585	260324716	260324677	3.750000e-04	56.5
35	TraesCS4A01G156800	chr2A	87.838	370	41	3	1332	1699	315745476	315745843	5.330000e-117	431.0
36	TraesCS4A01G156800	chr2A	83.704	405	53	12	2	396	250681856	250682257	1.180000e-98	370.0
37	TraesCS4A01G156800	chr2A	93.333	165	11	0	1332	1496	361431155	361431319	7.450000e-61	244.0
38	TraesCS4A01G156800	chr2A	91.018	167	15	0	1332	1498	268640810	268640644	2.700000e-55	226.0
39	TraesCS4A01G156800	chr2A	85.650	223	21	3	806	1017	305271666	305271444	9.710000e-55	224.0
40	TraesCS4A01G156800	chr2A	86.207	87	7	5	436	521	204722225	204722307	3.690000e-14	89.8
41	TraesCS4A01G156800	chr2A	86.207	87	7	5	436	521	204756964	204757046	3.690000e-14	89.8
42	TraesCS4A01G156800	chr3D	92.542	295	22	0	997	1291	49329832	49329538	8.920000e-115	424.0
43	TraesCS4A01G156800	chr1D	90.508	295	28	0	997	1291	186717078	186717372	9.040000e-105	390.0
44	TraesCS4A01G156800	chr6A	89.655	290	30	0	997	1286	121360667	121360956	1.180000e-98	370.0
45	TraesCS4A01G156800	chr6A	89.456	294	30	1	997	1290	319327536	319327828	1.180000e-98	370.0
46	TraesCS4A01G156800	chr6A	83.796	216	20	8	821	1024	244167153	244167365	9.840000e-45	191.0
47	TraesCS4A01G156800	chr6A	84.456	193	15	6	843	1024	21501063	21500875	2.760000e-40	176.0
48	TraesCS4A01G156800	chr4B	89.153	295	30	2	997	1291	409693855	409693563	1.520000e-97	366.0
49	TraesCS4A01G156800	chr4B	83.333	168	15	12	550	715	602110640	602110484	2.800000e-30	143.0
50	TraesCS4A01G156800	chr4B	82.738	168	16	11	550	715	602105328	602105172	1.300000e-28	137.0
51	TraesCS4A01G156800	chr5A	92.241	232	16	2	2	232	63444497	63444727	7.190000e-86	327.0
52	TraesCS4A01G156800	chr5A	89.163	203	22	0	612	814	84653023	84653225	1.240000e-63	254.0
53	TraesCS4A01G156800	chr5A	91.515	165	14	0	1332	1496	168464847	168464683	7.500000e-56	228.0
54	TraesCS4A01G156800	chr5A	92.157	153	12	0	612	764	84618205	84618357	1.620000e-52	217.0
55	TraesCS4A01G156800	chr5A	90.323	124	11	1	805	927	173823694	173823571	7.720000e-36	161.0
56	TraesCS4A01G156800	chr5A	89.516	124	12	1	805	927	181864241	181864118	3.590000e-34	156.0
57	TraesCS4A01G156800	chr5A	90.909	110	9	1	611	719	348234675	348234566	2.160000e-31	147.0
58	TraesCS4A01G156800	chrUn	79.412	408	64	15	1	402	56303012	56303405	1.230000e-68	270.0

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	TraesCS4A01G156800	chr4A	313750722	313753415	2693	False	4975	4975	100.000	1	2694	1	chr4A.!!$F2	2693
1	TraesCS4A01G156800	chr4A	313758239	313765105	6866	False	2598	4143	95.091	1	2694	2	chr4A.!!$F8	2693
2	TraesCS4A01G156800	chr4A	309530280	309531554	1274	True	1162	1162	83.346	1422	2694	1	chr4A.!!$R3	1272
3	TraesCS4A01G156800	chr1A	201870382	201871654	1272	True	1509	1509	88.116	1422	2694	1	chr1A.!!$R1	1272
4	TraesCS4A01G156800	chr1A	201894882	201896153	1271	True	1474	1474	87.647	1422	2694	1	chr1A.!!$R2	1272
5	TraesCS4A01G156800	chr1A	329766255	329767531	1276	True	1164	1164	83.423	1422	2694	1	chr1A.!!$R4	1272
6	TraesCS4A01G156800	chr7A	112636286	112637643	1357	False	1387	1387	85.352	1332	2688	1	chr7A.!!$F1	1356
7	TraesCS4A01G156800	chr4D	104798073	104799295	1222	False	1195	1195	84.578	1484	2694	1	chr4D.!!$F1	1210
8	TraesCS4A01G156800	chr5D	335209631	335210855	1224	False	1181	1181	84.398	1484	2694	1	chr5D.!!$F1	1210
9	TraesCS4A01G156800	chr3A	297357211	297358546	1335	False	1144	1144	82.426	1332	2667	1	chr3A.!!$F2	1335

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
806	5006	0.391597	GGTCGACCAGGTTTCACTCA	59.608	55.0	29.75	0.0	35.64	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1741	5957	0.678395	ACGATGGCATGGCAAACAAA	59.322	45.0	27.04	0.86	0.0	2.83	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	2.621055	TCACCCATAAACACACTTGCAC	59.379	45.455	0.00	0.00	0.00	4.57
170	171	3.467374	TTTTTGGGCGCTTCAAAATCT	57.533	38.095	28.31	0.00	41.72	2.40
329	4529	8.689707	TTTCCCTAACCCTCTCTTTCTATTTA	57.310	34.615	0.00	0.00	0.00	1.40
433	4633	2.284699	AACCTCCTACGCTGGCCT	60.285	61.111	3.32	0.00	0.00	5.19
434	4634	2.660064	AACCTCCTACGCTGGCCTG	61.660	63.158	3.32	4.26	0.00	4.85
509	4709	0.965439	GATCCCATCTCACTCCCTCG	59.035	60.000	0.00	0.00	0.00	4.63
521	4721	4.148825	CCCTCGTCTCCCCTTGCG	62.149	72.222	0.00	0.00	0.00	4.85
552	4752	1.271597	CCCATCCCGATTGATCCCTTC	60.272	57.143	0.00	0.00	0.00	3.46
573	4773	1.305046	TCCCCTTCGTCCTCCTCAC	60.305	63.158	0.00	0.00	0.00	3.51
575	4775	2.182030	CCTTCGTCCTCCTCACGC	59.818	66.667	0.00	0.00	37.18	5.34
597	4797	3.402681	CACCCCGTGCCAGATCCT	61.403	66.667	0.00	0.00	0.00	3.24
610	4810	2.117865	CAGATCCTCTCTGCCTCCTTT	58.882	52.381	0.00	0.00	44.73	3.11
621	4821	2.034048	GCCTCCTTTCCCTCCTAGCG	62.034	65.000	0.00	0.00	0.00	4.26
651	4851	3.834799	CACCTCGCCCGACCCTAC	61.835	72.222	0.00	0.00	0.00	3.18
659	4859	3.387947	CCGACCCTACGCCACCTT	61.388	66.667	0.00	0.00	0.00	3.50
697	4897	3.057547	CTCGTCGGAGGAGCACCAG	62.058	68.421	14.05	0.00	38.94	4.00
698	4898	3.062466	CGTCGGAGGAGCACCAGA	61.062	66.667	2.07	0.00	38.94	3.86
703	4903	1.904032	GGAGGAGCACCAGAAGGAG	59.096	63.158	2.07	0.00	38.69	3.69
715	4915	0.401395	AGAAGGAGGGGAACACCACA	60.401	55.000	0.00	0.00	42.91	4.17
758	4958	4.394712	CGCCCCTGAGCTCCGTTT	62.395	66.667	12.15	0.00	0.00	3.60
759	4959	2.747855	GCCCCTGAGCTCCGTTTG	60.748	66.667	12.15	0.00	0.00	2.93
806	5006	0.391597	GGTCGACCAGGTTTCACTCA	59.608	55.000	29.75	0.00	35.64	3.41
819	5019	0.817654	TCACTCATCTTCGCCATCGT	59.182	50.000	0.00	0.00	36.96	3.73
894	5094	4.825679	AGCCCCTGCCTCCCCTAC	62.826	72.222	0.00	0.00	38.69	3.18
953	5153	4.056125	CGCCTCCTCTGCGTCACA	62.056	66.667	0.00	0.00	46.59	3.58
972	5172	4.660938	GGTGGGCCGCCTTGTTCT	62.661	66.667	28.90	0.00	0.00	3.01
982	5182	2.471255	CCTTGTTCTAGGGCTTGCG	58.529	57.895	0.00	0.00	0.00	4.85
1006	5206	1.097547	CCATCCCAAGTCCATGTCGC	61.098	60.000	0.00	0.00	0.00	5.19
1076	5276	1.239347	GTCGCTCAAGCCTTTTTCCT	58.761	50.000	0.00	0.00	37.91	3.36
1082	5282	1.499007	TCAAGCCTTTTTCCTCACCCT	59.501	47.619	0.00	0.00	0.00	4.34
1092	5292	1.073722	CCTCACCCTGCTGCTTTCA	59.926	57.895	0.00	0.00	0.00	2.69
1097	5297	0.106519	ACCCTGCTGCTTTCAGTTGT	60.107	50.000	0.00	0.00	42.29	3.32
1106	5306	3.843999	TGCTTTCAGTTGTTGTTGGTTC	58.156	40.909	0.00	0.00	0.00	3.62
1138	5338	1.672356	GGACATGTTGCTGCGGACT	60.672	57.895	0.00	0.00	0.00	3.85
1142	5342	2.894257	ATGTTGCTGCGGACTCCCA	61.894	57.895	0.00	0.00	0.00	4.37
1185	5385	1.329906	CGTGAACGACTACTCGGCTAT	59.670	52.381	0.00	0.00	44.80	2.97
1228	5428	1.206523	GAATCGCTAAGTACCGCACC	58.793	55.000	0.00	0.00	0.00	5.01
1237	5437	2.048033	TACCGCACCGAAACGCAT	60.048	55.556	0.00	0.00	0.00	4.73
1306	5506	2.262915	CGCGCCAAGTTCCTCTCT	59.737	61.111	0.00	0.00	0.00	3.10
1307	5507	2.097038	CGCGCCAAGTTCCTCTCTG	61.097	63.158	0.00	0.00	0.00	3.35
1308	5508	1.293498	GCGCCAAGTTCCTCTCTGA	59.707	57.895	0.00	0.00	0.00	3.27
1309	5509	1.016653	GCGCCAAGTTCCTCTCTGAC	61.017	60.000	0.00	0.00	0.00	3.51
1310	5510	0.318441	CGCCAAGTTCCTCTCTGACA	59.682	55.000	0.00	0.00	0.00	3.58
1311	5511	1.802069	GCCAAGTTCCTCTCTGACAC	58.198	55.000	0.00	0.00	0.00	3.67
1312	5512	1.937108	GCCAAGTTCCTCTCTGACACG	60.937	57.143	0.00	0.00	0.00	4.49
1313	5513	1.423395	CAAGTTCCTCTCTGACACGC	58.577	55.000	0.00	0.00	0.00	5.34
1314	5514	0.039074	AAGTTCCTCTCTGACACGCG	60.039	55.000	3.53	3.53	0.00	6.01
1315	5515	2.089349	GTTCCTCTCTGACACGCGC	61.089	63.158	5.73	0.00	0.00	6.86
1316	5516	3.282745	TTCCTCTCTGACACGCGCC	62.283	63.158	5.73	0.00	0.00	6.53
1317	5517	4.056125	CCTCTCTGACACGCGCCA	62.056	66.667	5.73	0.30	0.00	5.69
1318	5518	2.049156	CTCTCTGACACGCGCCAA	60.049	61.111	5.73	0.00	0.00	4.52
1319	5519	2.049156	TCTCTGACACGCGCCAAG	60.049	61.111	5.73	0.00	0.00	3.61
1320	5520	2.356313	CTCTGACACGCGCCAAGT	60.356	61.111	5.73	0.00	0.00	3.16
1321	5521	1.956170	CTCTGACACGCGCCAAGTT	60.956	57.895	5.73	0.00	0.00	2.66
1322	5522	1.891060	CTCTGACACGCGCCAAGTTC	61.891	60.000	5.73	0.00	0.00	3.01
1323	5523	2.954753	CTGACACGCGCCAAGTTCC	61.955	63.158	5.73	0.00	0.00	3.62
1324	5524	2.665185	GACACGCGCCAAGTTCCT	60.665	61.111	5.73	0.00	0.00	3.36
1325	5525	2.665185	ACACGCGCCAAGTTCCTC	60.665	61.111	5.73	0.00	0.00	3.71
1326	5526	2.357517	CACGCGCCAAGTTCCTCT	60.358	61.111	5.73	0.00	0.00	3.69
1327	5527	2.048127	ACGCGCCAAGTTCCTCTC	60.048	61.111	5.73	0.00	0.00	3.20
1328	5528	2.262915	CGCGCCAAGTTCCTCTCT	59.737	61.111	0.00	0.00	0.00	3.10
1346	5546	4.383173	TCTCTGACAAGTGTACGACTACA	58.617	43.478	0.00	0.00	33.09	2.74
1393	5593	3.691342	CGACCCTCGAAGGCACCA	61.691	66.667	0.00	0.00	43.74	4.17
1630	5833	2.474410	ACCAGAACCATTCCGAGAAC	57.526	50.000	0.00	0.00	0.00	3.01
1639	5842	0.949105	ATTCCGAGAACGCACGCTTT	60.949	50.000	0.00	0.00	38.29	3.51
1672	5876	3.562779	GAGACGACCGCCCGTGAAA	62.563	63.158	5.09	0.00	43.49	2.69
1706	5920	3.569701	TGATGTATGAGATGCTCGTGCTA	59.430	43.478	11.19	0.00	40.48	3.49
1741	5957	0.808125	TGTTGCTTGCACGTTGTTCT	59.192	45.000	0.00	0.00	0.00	3.01
1831	6058	2.034558	CCGCACACTTGTTCTTTTCCAT	59.965	45.455	0.00	0.00	0.00	3.41
1947	6179	8.294577	TGACAAATGCTTCATAATATGCTCATC	58.705	33.333	0.00	0.00	0.00	2.92
2598	6848	3.298619	CCTCCCATATTGCCATGTCAAA	58.701	45.455	0.00	0.00	0.00	2.69
2641	6897	3.363341	AACCGTTGTTTGGCTATGTTG	57.637	42.857	0.00	0.00	0.00	3.33
2655	6911	0.388659	ATGTTGCCGCTTTTGCTCAA	59.611	45.000	0.00	0.00	44.80	3.02
2657	6913	0.249031	GTTGCCGCTTTTGCTCAACT	60.249	50.000	12.26	0.00	44.85	3.16
2676	6932	5.126545	TCAACTCCTCTTATAGCGTTGCTAA	59.873	40.000	2.23	0.00	44.62	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	5.945784	TGAACTAGAAAAGACATGGGGAATG	59.054	40.000	0.00	0.00	42.48	2.67
159	160	7.907214	TGAACTAGGACTAAGATTTTGAAGC	57.093	36.000	0.00	0.00	0.00	3.86
213	214	9.428097	AGTTGCCTGATTGAAAGATTTAAATTC	57.572	29.630	1.43	0.00	0.00	2.17
377	4577	5.395768	GGCTGGCTTATCTCTTGTCTCTTTA	60.396	44.000	0.00	0.00	0.00	1.85
385	4585	1.673168	GTGGGCTGGCTTATCTCTTG	58.327	55.000	0.00	0.00	0.00	3.02
386	4586	0.548510	GGTGGGCTGGCTTATCTCTT	59.451	55.000	0.00	0.00	0.00	2.85
390	4590	0.398318	CCTAGGTGGGCTGGCTTATC	59.602	60.000	0.00	0.00	0.00	1.75
411	4611	2.687566	AGCGTAGGAGGTTGGGGG	60.688	66.667	0.00	0.00	0.00	5.40
412	4612	2.584608	CAGCGTAGGAGGTTGGGG	59.415	66.667	0.00	0.00	0.00	4.96
433	4633	4.552365	GCGCAGATGGCCTAGGCA	62.552	66.667	34.09	20.63	44.11	4.75
459	4659	1.144716	TTAGATCTGGGCGCTGCTG	59.855	57.895	7.64	0.00	0.00	4.41
521	4721	2.111251	GGATGGGGTTCTAGCGGC	59.889	66.667	0.00	0.00	0.00	6.53
526	4726	2.184088	TCAATCGGGATGGGGTTCTA	57.816	50.000	0.00	0.00	0.00	2.10
552	4752	0.753848	GAGGAGGACGAAGGGGAGAG	60.754	65.000	0.00	0.00	0.00	3.20
597	4797	0.618968	GGAGGGAAAGGAGGCAGAGA	60.619	60.000	0.00	0.00	0.00	3.10
697	4897	0.698818	ATGTGGTGTTCCCCTCCTTC	59.301	55.000	0.00	0.00	0.00	3.46
698	4898	0.698818	GATGTGGTGTTCCCCTCCTT	59.301	55.000	0.00	0.00	0.00	3.36
703	4903	2.750237	GGCGATGTGGTGTTCCCC	60.750	66.667	0.00	0.00	0.00	4.81
953	5153	4.299796	AACAAGGCGGCCCACCAT	62.300	61.111	17.02	0.00	34.57	3.55
967	5167	1.295423	GACCGCAAGCCCTAGAACA	59.705	57.895	0.00	0.00	0.00	3.18
968	5168	1.810030	CGACCGCAAGCCCTAGAAC	60.810	63.158	0.00	0.00	0.00	3.01
981	5181	2.511600	GACTTGGGATGGCGACCG	60.512	66.667	0.00	0.00	0.00	4.79
982	5182	2.124695	GGACTTGGGATGGCGACC	60.125	66.667	0.00	0.00	0.00	4.79
991	5191	2.438434	GGGCGACATGGACTTGGG	60.438	66.667	0.00	0.00	0.00	4.12
1076	5276	0.183492	AACTGAAAGCAGCAGGGTGA	59.817	50.000	2.13	0.00	46.26	4.02
1082	5282	2.417107	CCAACAACAACTGAAAGCAGCA	60.417	45.455	0.00	0.00	46.26	4.41
1092	5292	2.672760	GCCAAACGAACCAACAACAACT	60.673	45.455	0.00	0.00	0.00	3.16
1097	5297	1.067821	GATGGCCAAACGAACCAACAA	59.932	47.619	10.96	0.00	36.94	2.83
1106	5306	1.105457	ATGTCCATGATGGCCAAACG	58.895	50.000	10.96	0.00	37.47	3.60
1138	5338	2.569853	CCATGGTGTAGTTGTACTGGGA	59.430	50.000	2.57	0.00	0.00	4.37
1142	5342	5.393787	CGTATCACCATGGTGTAGTTGTACT	60.394	44.000	37.49	17.42	45.55	2.73
1185	5385	4.462834	CAGGATGTAGAGGTACACTTGTCA	59.537	45.833	0.00	0.00	42.06	3.58
1228	5428	2.222213	TCCTTGTTGTACATGCGTTTCG	59.778	45.455	0.00	0.00	0.00	3.46
1237	5437	1.129917	TCGGGGTTCCTTGTTGTACA	58.870	50.000	0.00	0.00	0.00	2.90
1270	5470	0.966920	GTGTCGGAGAGGAACTTGGA	59.033	55.000	0.00	0.00	41.55	3.53
1306	5506	2.970324	GGAACTTGGCGCGTGTCA	60.970	61.111	8.43	0.00	0.00	3.58
1307	5507	2.665185	AGGAACTTGGCGCGTGTC	60.665	61.111	8.43	0.00	27.25	3.67
1308	5508	2.665185	GAGGAACTTGGCGCGTGT	60.665	61.111	8.43	0.00	41.55	4.49
1309	5509	2.357517	AGAGGAACTTGGCGCGTG	60.358	61.111	8.43	0.00	41.55	5.34
1310	5510	2.048127	GAGAGGAACTTGGCGCGT	60.048	61.111	8.43	0.00	41.55	6.01
1311	5511	2.097038	CAGAGAGGAACTTGGCGCG	61.097	63.158	0.00	0.00	41.55	6.86
1312	5512	1.016653	GTCAGAGAGGAACTTGGCGC	61.017	60.000	0.00	0.00	41.55	6.53
1313	5513	0.318441	TGTCAGAGAGGAACTTGGCG	59.682	55.000	0.00	0.00	41.55	5.69
1314	5514	2.224402	ACTTGTCAGAGAGGAACTTGGC	60.224	50.000	0.00	0.00	41.55	4.52
1315	5515	3.181461	ACACTTGTCAGAGAGGAACTTGG	60.181	47.826	0.00	0.00	41.55	3.61
1316	5516	4.065321	ACACTTGTCAGAGAGGAACTTG	57.935	45.455	0.00	0.00	41.55	3.16
1317	5517	4.261656	CGTACACTTGTCAGAGAGGAACTT	60.262	45.833	0.00	0.00	41.55	2.66
1318	5518	9.787232	TAGTCGTACACTTGTCAGAGAGGAACT	62.787	44.444	3.77	0.00	37.88	3.01
1319	5519	3.252701	TCGTACACTTGTCAGAGAGGAAC	59.747	47.826	0.00	0.00	0.00	3.62
1320	5520	3.252701	GTCGTACACTTGTCAGAGAGGAA	59.747	47.826	0.00	0.00	0.00	3.36
1321	5521	2.812591	GTCGTACACTTGTCAGAGAGGA	59.187	50.000	0.00	0.00	0.00	3.71
1322	5522	2.814919	AGTCGTACACTTGTCAGAGAGG	59.185	50.000	0.00	0.00	26.56	3.69
1323	5523	4.451435	TGTAGTCGTACACTTGTCAGAGAG	59.549	45.833	3.77	0.00	36.43	3.20
1324	5524	4.383173	TGTAGTCGTACACTTGTCAGAGA	58.617	43.478	3.77	0.00	36.43	3.10
1325	5525	4.744136	TGTAGTCGTACACTTGTCAGAG	57.256	45.455	3.77	0.00	36.43	3.35
1346	5546	0.319083	TAGTTGTCGCATCGTTGGGT	59.681	50.000	9.98	0.00	37.12	4.51
1350	5550	1.544691	AGAGGTAGTTGTCGCATCGTT	59.455	47.619	0.00	0.00	0.00	3.85
1393	5593	0.389948	GCGAGGAACTTGACGTCCAT	60.390	55.000	14.12	0.00	44.22	3.41
1592	5795	2.083002	GTTCGACGAGGGAAGTAGAGT	58.917	52.381	0.00	0.00	0.00	3.24
1630	5833	2.222953	GGTTATACCTTCAAAGCGTGCG	60.223	50.000	0.00	0.00	34.73	5.34
1639	5842	2.026641	CGTCTCGGGGTTATACCTTCA	58.973	52.381	0.00	0.00	38.64	3.02
1672	5876	4.162888	TCTCATACATCACACATGCCTTCT	59.837	41.667	0.00	0.00	0.00	2.85
1741	5957	0.678395	ACGATGGCATGGCAAACAAA	59.322	45.000	27.04	0.86	0.00	2.83
1831	6058	3.489229	CGGTAACTCGATTGAGATGCTGA	60.489	47.826	17.27	0.00	45.57	4.26
2164	6406	3.431766	GCACTCCCGTTTATGTACTGGAT	60.432	47.826	0.00	0.00	32.05	3.41
2166	6408	2.277084	GCACTCCCGTTTATGTACTGG	58.723	52.381	0.00	0.00	0.00	4.00
2167	6409	2.671396	GTGCACTCCCGTTTATGTACTG	59.329	50.000	10.32	0.00	0.00	2.74
2598	6848	2.359037	GCTAGGTAGGTGGGTTAGAGGT	60.359	54.545	0.00	0.00	0.00	3.85
2641	6897	1.081175	GGAGTTGAGCAAAAGCGGC	60.081	57.895	0.00	0.00	0.00	6.53
2655	6911	5.793030	ATTAGCAACGCTATAAGAGGAGT	57.207	39.130	0.00	0.00	41.01	3.85
2657	6913	4.750098	GCAATTAGCAACGCTATAAGAGGA	59.250	41.667	0.00	0.00	41.01	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.