AutoCloner

Multiple sequence alignment - TraesCS3D01G281700

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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	TraesCS3D01G281700	chr3D	100.000	7437	0	0	1	7437	389904965	389912401	0.000000e+00	13734.0
1	TraesCS3D01G281700	chr3D	92.157	102	8	0	4233	4334	601221851	601221750	2.160000e-30	145.0
2	TraesCS3D01G281700	chr3A	94.013	3023	94	32	1	2985	510589235	510592208	0.000000e+00	4499.0
3	TraesCS3D01G281700	chr3A	95.940	2586	62	7	4134	6695	510594208	510596774	0.000000e+00	4154.0
4	TraesCS3D01G281700	chr3A	95.250	1158	28	3	2961	4116	510592252	510593384	0.000000e+00	1808.0
5	TraesCS3D01G281700	chr3A	94.417	609	20	3	6842	7436	510597079	510597687	0.000000e+00	924.0
6	TraesCS3D01G281700	chr3A	92.053	151	6	2	6692	6836	510596896	510597046	2.720000e-49	207.0
7	TraesCS3D01G281700	chr3A	90.909	44	2	2	5790	5832	329061380	329061422	2.900000e-04	58.4
8	TraesCS3D01G281700	chr3A	97.059	34	1	0	5799	5832	746355802	746355835	2.900000e-04	58.4
9	TraesCS3D01G281700	chr3B	94.856	2877	107	13	2965	5832	507271611	507274455	0.000000e+00	4455.0
10	TraesCS3D01G281700	chr3B	94.316	2674	84	24	329	2982	507268935	507271560	0.000000e+00	4034.0
11	TraesCS3D01G281700	chr3B	89.418	1049	55	18	6415	7414	507275032	507276073	0.000000e+00	1271.0
12	TraesCS3D01G281700	chr3B	96.074	484	17	2	5978	6461	507274553	507275034	0.000000e+00	787.0
13	TraesCS3D01G281700	chr3B	93.909	197	11	1	107	303	507268583	507268778	5.640000e-76	296.0
14	TraesCS3D01G281700	chr3B	89.899	99	10	0	4233	4331	734993622	734993524	2.180000e-25	128.0
15	TraesCS3D01G281700	chr3B	100.000	37	0	0	9	45	507268549	507268585	1.340000e-07	69.4
16	TraesCS3D01G281700	chr6A	93.097	536	24	6	6842	7365	74501477	74502011	0.000000e+00	773.0
17	TraesCS3D01G281700	chr6A	93.514	185	7	2	6658	6838	74501263	74501446	3.420000e-68	270.0
18	TraesCS3D01G281700	chr6A	100.000	32	0	0	5803	5834	552171459	552171490	8.060000e-05	60.2
19	TraesCS3D01G281700	chr1A	76.977	1151	224	27	1578	2715	534245696	534244574	2.950000e-173	619.0
20	TraesCS3D01G281700	chr1A	74.242	660	143	19	4373	5028	534242870	534242234	1.240000e-62	252.0
21	TraesCS3D01G281700	chr1A	80.952	252	44	4	3088	3336	534244181	534243931	5.890000e-46	196.0
22	TraesCS3D01G281700	chr1A	78.855	227	30	15	1344	1566	534245951	534245739	3.620000e-28	137.0
23	TraesCS3D01G281700	chr1A	84.000	125	17	3	5852	5974	537892323	537892446	4.710000e-22	117.0
24	TraesCS3D01G281700	chr1A	100.000	32	0	0	5803	5834	593649265	593649296	8.060000e-05	60.2
25	TraesCS3D01G281700	chr1D	76.644	1156	231	30	1578	2715	437443872	437445006	2.970000e-168	603.0
26	TraesCS3D01G281700	chr1D	74.208	663	139	25	4373	5028	437446736	437447373	1.600000e-61	248.0
27	TraesCS3D01G281700	chr1D	83.333	252	38	4	3088	3336	437445398	437445648	5.800000e-56	230.0
28	TraesCS3D01G281700	chr1D	77.922	231	30	14	1346	1566	437443601	437443820	2.820000e-24	124.0
29	TraesCS3D01G281700	chr1B	76.404	1157	229	29	1578	2715	592847278	592848409	1.080000e-162	584.0
30	TraesCS3D01G281700	chr1B	83.621	232	36	2	3088	3318	592848803	592849033	4.520000e-52	217.0
31	TraesCS3D01G281700	chr1B	75.980	408	84	12	4373	4776	592850145	592850542	1.640000e-46	198.0
32	TraesCS3D01G281700	chr1B	77.682	233	34	13	1344	1566	592847002	592847226	7.830000e-25	126.0
33	TraesCS3D01G281700	chr1B	85.841	113	16	0	5862	5974	525502030	525502142	3.640000e-23	121.0
34	TraesCS3D01G281700	chr5A	93.478	92	6	0	4238	4329	9653285	9653194	3.620000e-28	137.0
35	TraesCS3D01G281700	chr5A	87.850	107	13	0	4230	4336	544514198	544514092	7.830000e-25	126.0
36	TraesCS3D01G281700	chr5A	97.143	35	0	1	5803	5836	598812855	598812889	2.900000e-04	58.4
37	TraesCS3D01G281700	chr7A	86.400	125	14	3	5852	5974	532464056	532464179	4.680000e-27	134.0
38	TraesCS3D01G281700	chr2D	92.553	94	6	1	4233	4325	382456080	382456173	4.680000e-27	134.0
39	TraesCS3D01G281700	chr6B	85.827	127	15	2	5854	5979	8028990	8029114	1.680000e-26	132.0
40	TraesCS3D01G281700	chr5D	88.785	107	12	0	4230	4336	428676979	428676873	1.680000e-26	132.0
41	TraesCS3D01G281700	chr5D	86.667	120	15	1	5855	5974	443649375	443649257	1.680000e-26	132.0
42	TraesCS3D01G281700	chr2A	87.395	119	9	4	5867	5979	657517752	657517870	1.680000e-26	132.0
43	TraesCS3D01G281700	chr7B	90.722	97	9	0	4233	4329	40191640	40191544	6.060000e-26	130.0
44	TraesCS3D01G281700	chr2B	85.039	127	12	4	5855	5974	572791055	572791181	1.010000e-23	122.0
45	TraesCS3D01G281700	chr6D	100.000	32	0	0	5803	5834	13994229	13994260	8.060000e-05	60.2
46	TraesCS3D01G281700	chr4B	92.308	39	2	1	5790	5828	74557042	74557079	4.000000e-03	54.7

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	TraesCS3D01G281700	chr3D	389904965	389912401	7436	False	13734.000000	13734	100.000000	1	7437	1	chr3D.!!$F1	7436
1	TraesCS3D01G281700	chr3A	510589235	510597687	8452	False	2318.400000	4499	94.334600	1	7436	5	chr3A.!!$F3	7435
2	TraesCS3D01G281700	chr3B	507268549	507276073	7524	False	1818.733333	4455	94.762167	9	7414	6	chr3B.!!$F1	7405
3	TraesCS3D01G281700	chr6A	74501263	74502011	748	False	521.500000	773	93.305500	6658	7365	2	chr6A.!!$F2	707
4	TraesCS3D01G281700	chr1A	534242234	534245951	3717	True	301.000000	619	77.756500	1344	5028	4	chr1A.!!$R1	3684
5	TraesCS3D01G281700	chr1D	437443601	437447373	3772	False	301.250000	603	78.026750	1346	5028	4	chr1D.!!$F1	3682
6	TraesCS3D01G281700	chr1B	592847002	592850542	3540	False	281.250000	584	78.421750	1344	4776	4	chr1B.!!$F2	3432

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
814	977	0.036294	CCCTCTCCTTCCCGTGAAAC	60.036	60.000	0.00	0.00	0.00	2.78	F
2115	2388	1.003718	GAGGAAGGTCGGGTTGGTG	60.004	63.158	0.00	0.00	0.00	4.17	F
2133	2406	2.438021	GGTGTATGTCTTCTATGGGCCA	59.562	50.000	9.61	9.61	0.00	5.36	F
3729	4138	0.543749	AGGATGTAGCAAGGCACTCC	59.456	55.000	0.00	0.00	38.49	3.85	F
5676	7316	0.380378	GAGTTGCTTGCGTTTGTGGA	59.620	50.000	0.00	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2379	2652	0.179023	TGTCTGCTGGCAATGTGTCA	60.179	50.000	0.00	0.00	3.58	R
3000	3392	0.250513	CTGACAGGGGCTTAGGTCAC	59.749	60.000	0.00	35.51	3.67	R
4100	4927	0.394565	AGAGGACAACCAGTGACTGC	59.605	55.000	7.16	38.94	4.40	R
5689	7329	2.949644	GGCTTGTTTGTGTAGTTCCACT	59.050	45.455	0.00	36.30	4.00	R
6965	8880	3.109230	GCATGTTGCTCTAGTTTGACG	57.891	47.619	0.00	40.96	4.35	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
78	83	0.608035	TGGTGCTTGTTCCCGATTCC	60.608	55.000	0.00	0.00	0.00	3.01
90	95	2.165301	CGATTCCTGTCGTTCGGGC	61.165	63.158	3.94	0.00	42.13	6.13
123	128	1.651138	CTCGACGTTGTCTGCTGATTC	59.349	52.381	1.96	0.00	0.00	2.52
136	141	2.108976	GATTCCGGCGATCCTGCA	59.891	61.111	9.30	0.00	36.28	4.41
253	258	2.046892	TTCGCAGCTTGAGCCCTC	60.047	61.111	0.00	0.00	43.38	4.30
310	320	9.584839	CAGCACAAGTTTTTGAATTAATAAAGC	57.415	29.630	0.00	0.00	37.73	3.51
323	333	2.620251	ATAAAGCATGCACGGCTCTA	57.380	45.000	21.98	6.45	41.66	2.43
324	334	1.651987	TAAAGCATGCACGGCTCTAC	58.348	50.000	21.98	0.00	41.66	2.59
325	335	1.361668	AAAGCATGCACGGCTCTACG	61.362	55.000	21.98	0.00	41.66	3.51
331	466	0.528924	TGCACGGCTCTACGTACAAT	59.471	50.000	0.00	0.00	46.75	2.71
338	473	3.124636	CGGCTCTACGTACAATTTTGCTT	59.875	43.478	0.00	0.00	0.00	3.91
394	530	4.827481	ACGTCACGTGCTTTCAGT	57.173	50.000	11.67	1.24	39.18	3.41
395	531	3.951115	ACGTCACGTGCTTTCAGTA	57.049	47.368	11.67	0.00	39.18	2.74
396	532	1.484356	ACGTCACGTGCTTTCAGTAC	58.516	50.000	11.67	0.00	39.18	2.73
499	644	1.725641	TCATCAGCCTGTGTTAAGCG	58.274	50.000	0.00	0.00	0.00	4.68
577	727	2.809601	GCGTAGTGCAGTCCCACG	60.810	66.667	10.33	10.33	45.45	4.94
655	815	1.406539	CCGAGAAAGGCCAATCCATTG	59.593	52.381	5.01	0.00	37.29	2.82
659	819	1.273986	AAAGGCCAATCCATTGCCCC	61.274	55.000	5.01	0.00	36.00	5.80
660	820	3.163563	GGCCAATCCATTGCCCCC	61.164	66.667	0.00	0.00	36.48	5.40
661	821	3.539791	GCCAATCCATTGCCCCCG	61.540	66.667	0.00	0.00	36.48	5.73
662	822	2.043046	CCAATCCATTGCCCCCGT	60.043	61.111	0.00	0.00	36.48	5.28
663	823	1.685421	CCAATCCATTGCCCCCGTT	60.685	57.895	0.00	0.00	36.48	4.44
814	977	0.036294	CCCTCTCCTTCCCGTGAAAC	60.036	60.000	0.00	0.00	0.00	2.78
1276	1459	3.910784	GACCCCGACCCCTACACCA	62.911	68.421	0.00	0.00	0.00	4.17
1277	1460	3.396570	CCCCGACCCCTACACCAC	61.397	72.222	0.00	0.00	0.00	4.16
2115	2388	1.003718	GAGGAAGGTCGGGTTGGTG	60.004	63.158	0.00	0.00	0.00	4.17
2133	2406	2.438021	GGTGTATGTCTTCTATGGGCCA	59.562	50.000	9.61	9.61	0.00	5.36
2309	2582	2.620115	ACATCGACATGGATGGAATTGC	59.380	45.455	14.18	0.00	46.38	3.56
2379	2652	5.819991	AGGGTGTTCATATTTGATGACTGT	58.180	37.500	0.00	0.00	0.00	3.55
2478	2751	3.479979	GGTCCCAACCTCGACCTT	58.520	61.111	0.00	0.00	44.40	3.50
2747	3021	6.449698	CAAGCATCATTATTACCATCAACCC	58.550	40.000	0.00	0.00	0.00	4.11
2750	3024	6.491403	AGCATCATTATTACCATCAACCCTTC	59.509	38.462	0.00	0.00	0.00	3.46
2788	3063	2.486918	TCGCAAGCATGATCATACCAG	58.513	47.619	8.15	0.00	37.18	4.00
2925	3249	7.651808	ACCTGTAATTTGTCAAGAAGTGAATG	58.348	34.615	0.00	0.00	38.23	2.67
3000	3392	5.344743	TGGAATACAGCTAAGGAACTCAG	57.655	43.478	0.00	0.00	38.49	3.35
3005	3397	2.300437	ACAGCTAAGGAACTCAGTGACC	59.700	50.000	0.00	0.00	38.49	4.02
3276	3681	6.662755	TGGTTCCTACATATTTGCAAGAGAT	58.337	36.000	0.00	0.00	0.00	2.75
3327	3736	5.362430	TCCAACCTGTAAGCATCAACTTTTT	59.638	36.000	0.00	0.00	0.00	1.94
3681	4090	5.120399	TCAACAAGTACGAGTTTCAACCAT	58.880	37.500	3.64	0.00	0.00	3.55
3729	4138	0.543749	AGGATGTAGCAAGGCACTCC	59.456	55.000	0.00	0.00	38.49	3.85
3739	4148	1.134699	CAAGGCACTCCGCTATTGAGA	60.135	52.381	0.00	0.00	38.49	3.27
3886	4364	1.471119	AATGATCTGGCAAGCAGTGG	58.529	50.000	0.00	0.00	0.00	4.00
3963	4441	1.118838	GATCTGTCAGCCTAGGCACT	58.881	55.000	34.70	13.55	44.88	4.40
4100	4927	8.553459	ACTCCTGTAGTTAATGATTCAGTTTG	57.447	34.615	0.00	0.00	33.35	2.93
4117	4945	0.546122	TTGCAGTCACTGGTTGTCCT	59.454	50.000	7.00	0.00	34.23	3.85
4129	4957	5.639506	CACTGGTTGTCCTCTTTGTATACAG	59.360	44.000	5.56	0.00	34.23	2.74
4130	4958	5.542635	ACTGGTTGTCCTCTTTGTATACAGA	59.457	40.000	5.56	0.30	34.23	3.41
4193	5827	0.811281	GCCATGCCTCCAACTTGTAC	59.189	55.000	0.00	0.00	0.00	2.90
4325	5960	4.232091	ACACTTATTATGGATCGGAGGGT	58.768	43.478	0.00	0.00	0.00	4.34
4379	6014	9.822185	ATTGTTTTCTAACATCAGCTTCTTTTT	57.178	25.926	0.00	0.00	43.43	1.94
4411	6046	2.420022	GCCGACAGTGCAAGTGATATTT	59.580	45.455	4.35	0.00	40.62	1.40
4447	6082	5.767816	ATAAGTCCAACGCTGAAAACTTT	57.232	34.783	6.54	0.00	0.00	2.66
4751	6386	0.764271	TGGACCTTCTCACATGCACA	59.236	50.000	0.00	0.00	0.00	4.57
5568	7208	3.833442	GTGCCACTAAAATAAGTGCCAC	58.167	45.455	2.84	2.84	45.18	5.01
5607	7247	5.104374	CACCACTGAATACAATTGGAATGC	58.896	41.667	10.83	2.35	34.88	3.56
5608	7248	4.142403	ACCACTGAATACAATTGGAATGCG	60.142	41.667	10.83	1.87	34.88	4.73
5672	7312	0.662619	TGAGGAGTTGCTTGCGTTTG	59.337	50.000	0.00	0.00	0.00	2.93
5673	7313	0.663153	GAGGAGTTGCTTGCGTTTGT	59.337	50.000	0.00	0.00	0.00	2.83
5674	7314	0.381801	AGGAGTTGCTTGCGTTTGTG	59.618	50.000	0.00	0.00	0.00	3.33
5675	7315	0.594796	GGAGTTGCTTGCGTTTGTGG	60.595	55.000	0.00	0.00	0.00	4.17
5676	7316	0.380378	GAGTTGCTTGCGTTTGTGGA	59.620	50.000	0.00	0.00	0.00	4.02
5677	7317	0.814457	AGTTGCTTGCGTTTGTGGAA	59.186	45.000	0.00	0.00	0.00	3.53
5678	7318	0.920664	GTTGCTTGCGTTTGTGGAAC	59.079	50.000	0.00	0.00	34.82	3.62
5679	7319	0.814457	TTGCTTGCGTTTGTGGAACT	59.186	45.000	0.00	0.00	38.04	3.01
5680	7320	1.669604	TGCTTGCGTTTGTGGAACTA	58.330	45.000	0.00	0.00	38.04	2.24
5681	7321	1.332375	TGCTTGCGTTTGTGGAACTAC	59.668	47.619	0.00	0.00	38.04	2.73
5682	7322	1.332375	GCTTGCGTTTGTGGAACTACA	59.668	47.619	0.00	0.00	38.04	2.74
5683	7323	2.853281	GCTTGCGTTTGTGGAACTACAC	60.853	50.000	0.00	0.00	41.68	2.90
5865	7542	4.813161	GGGAGTACCTTTTATTACTTCCGC	59.187	45.833	0.00	0.00	34.81	5.54
5963	7663	7.824779	ACAGATCTAAGACAACTAATTTGGGAC	59.175	37.037	0.00	0.00	39.84	4.46
6079	7779	1.408702	GCAGTGCCAAAAAGAGGAACA	59.591	47.619	2.85	0.00	37.13	3.18
6180	7880	8.094548	AGTGAATTAGCAACTGTGTAGTGATAA	58.905	33.333	0.00	0.00	37.19	1.75
6489	8234	9.463443	AAGCGTTTAATTTAGCATCCATAATTC	57.537	29.630	0.00	0.00	0.00	2.17
6757	8631	6.947733	TGATTAGTGAACCATGTCAGGAAAAT	59.052	34.615	0.00	0.00	0.00	1.82
6774	8648	9.489084	TCAGGAAAATATAATATTGACCACGAG	57.511	33.333	0.00	0.00	0.00	4.18
6838	8714	8.926715	TCGATCTTCATTTTATTCTTTCTCGA	57.073	30.769	0.00	0.00	0.00	4.04
6839	8715	9.534565	TCGATCTTCATTTTATTCTTTCTCGAT	57.465	29.630	0.00	0.00	0.00	3.59
6850	8753	9.973246	TTTATTCTTTCTCGATCTTCATTTTCG	57.027	29.630	0.00	0.00	0.00	3.46
6930	8845	5.359576	TGCACTAATGTCTTTGTTCAAGGTT	59.640	36.000	0.00	0.00	32.64	3.50
6965	8880	7.667043	TGATACAGATTACAACACTTTCACC	57.333	36.000	0.00	0.00	0.00	4.02
7056	8971	7.148289	CCACATACTTATGGATCATCTGCAATC	60.148	40.741	0.00	0.00	38.34	2.67
7365	9281	1.167851	CGAGCAGGCAAAGGAATCAA	58.832	50.000	0.00	0.00	0.00	2.57
7380	9296	3.119495	GGAATCAACCTGGTATGCACAAC	60.119	47.826	0.00	0.00	0.00	3.32
7381	9297	2.647683	TCAACCTGGTATGCACAACA	57.352	45.000	0.00	0.00	0.00	3.33
7382	9298	3.153369	TCAACCTGGTATGCACAACAT	57.847	42.857	0.00	0.00	43.18	2.71
7417	9336	4.385825	ACGGCTGTTTAGATGAAGTGAAA	58.614	39.130	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	61	0.889186	ATCGGGAACAAGCACCACAC	60.889	55.000	0.00	0.00	0.00	3.82
63	68	1.087501	GACAGGAATCGGGAACAAGC	58.912	55.000	0.00	0.00	0.00	4.01
66	71	0.682852	AACGACAGGAATCGGGAACA	59.317	50.000	0.00	0.00	46.56	3.18
67	72	1.356938	GAACGACAGGAATCGGGAAC	58.643	55.000	0.00	0.00	46.56	3.62
78	83	4.452733	GAGGGGCCCGAACGACAG	62.453	72.222	18.95	0.00	0.00	3.51
90	95	1.758906	GTCGAGAAGGAGGGAGGGG	60.759	68.421	0.00	0.00	0.00	4.79
96	101	0.882474	AGACAACGTCGAGAAGGAGG	59.118	55.000	0.00	0.00	37.67	4.30
97	102	1.970447	CAGACAACGTCGAGAAGGAG	58.030	55.000	0.00	0.00	37.67	3.69
123	128	4.899239	GGACTGCAGGATCGCCGG	62.899	72.222	19.93	0.00	39.96	6.13
128	133	3.453070	GAGGCCGGACTGCAGGATC	62.453	68.421	19.29	7.26	0.00	3.36
292	297	7.687757	CCGTGCATGCTTTATTAATTCAAAAAC	59.312	33.333	20.33	0.94	0.00	2.43
310	320	0.179148	TGTACGTAGAGCCGTGCATG	60.179	55.000	0.00	0.00	46.06	4.06
323	333	2.032302	TCGCACAAGCAAAATTGTACGT	59.968	40.909	10.84	0.00	45.67	3.57
324	334	2.645163	TCGCACAAGCAAAATTGTACG	58.355	42.857	5.99	5.99	46.45	3.67
325	335	3.364621	CCATCGCACAAGCAAAATTGTAC	59.635	43.478	0.00	0.00	41.41	2.90
326	336	3.573598	CCATCGCACAAGCAAAATTGTA	58.426	40.909	0.00	0.00	41.41	2.41
331	466	0.318869	CAGCCATCGCACAAGCAAAA	60.319	50.000	0.00	0.00	42.27	2.44
338	473	2.435410	CAGAGCAGCCATCGCACA	60.435	61.111	0.00	0.00	37.52	4.57
625	775	4.129737	TTTCTCGGCTCGGCTCGG	62.130	66.667	0.00	0.00	0.00	4.63
626	776	2.580867	CTTTCTCGGCTCGGCTCG	60.581	66.667	0.00	0.00	0.00	5.03
627	777	2.202810	CCTTTCTCGGCTCGGCTC	60.203	66.667	0.00	0.00	0.00	4.70
628	778	4.459089	GCCTTTCTCGGCTCGGCT	62.459	66.667	0.00	0.00	46.63	5.52
793	956	4.148825	CACGGGAAGGAGAGGGCG	62.149	72.222	0.00	0.00	0.00	6.13
1269	1452	2.177531	CGGTCGTCGGTGGTGTAG	59.822	66.667	0.00	0.00	34.75	2.74
1342	1525	2.878429	GAGGAGCGTCTTGAGCGA	59.122	61.111	0.00	0.00	40.04	4.93
1462	1651	4.496336	GCGATCTGGGGCCTTGCT	62.496	66.667	0.84	0.00	0.00	3.91
2010	2283	1.538204	GGTGCGAACTTCTGTGTGAGA	60.538	52.381	0.00	0.00	0.00	3.27
2115	2388	3.467803	GTGTGGCCCATAGAAGACATAC	58.532	50.000	0.00	0.00	0.00	2.39
2133	2406	1.768684	ATGTCTTCCCTGTGCCGTGT	61.769	55.000	0.00	0.00	0.00	4.49
2309	2582	4.655027	CATGACATTGTCAAGAACATCCG	58.345	43.478	22.44	1.11	45.96	4.18
2379	2652	0.179023	TGTCTGCTGGCAATGTGTCA	60.179	50.000	0.00	0.00	0.00	3.58
2478	2751	4.373156	TCTCGACAGGATGATATGAGGA	57.627	45.455	0.00	0.00	39.69	3.71
2586	2859	5.912149	TTAACCTCAATGCATCCCTATCT	57.088	39.130	0.00	0.00	0.00	1.98
2925	3249	8.572185	TCATCTGAAGTTGCTATACTATGTCTC	58.428	37.037	0.00	0.00	0.00	3.36
3000	3392	0.250513	CTGACAGGGGCTTAGGTCAC	59.749	60.000	0.00	0.00	35.51	3.67
3005	3397	6.681368	GCATTAAAATTCTGACAGGGGCTTAG	60.681	42.308	1.81	0.00	0.00	2.18
3681	4090	3.940229	GGAACCGTCCAATACACCA	57.060	52.632	0.00	0.00	44.26	4.17
3729	4138	7.521529	CCATGTTACCATTATTCTCAATAGCG	58.478	38.462	0.00	0.00	0.00	4.26
3739	4148	4.711355	AGTGCTTGCCATGTTACCATTATT	59.289	37.500	0.00	0.00	0.00	1.40
3886	4364	7.767261	AGTGTATCTGACTGAATACTCTCAAC	58.233	38.462	0.00	0.00	0.00	3.18
3963	4441	5.938125	GGATGTTAGACTTTGAAGCTTACCA	59.062	40.000	0.00	0.00	0.00	3.25
4100	4927	0.394565	AGAGGACAACCAGTGACTGC	59.605	55.000	7.16	0.00	38.94	4.40
4193	5827	9.149225	GGAGATAGTAATTCAACATAGCATGAG	57.851	37.037	0.00	0.00	0.00	2.90
4325	5960	7.499563	TGGTAGAACAACAAGCTAACAATTACA	59.500	33.333	0.00	0.00	29.52	2.41
4379	6014	0.834687	ACTGTCGGCCCTGTAGGAAA	60.835	55.000	0.00	0.00	38.24	3.13
4390	6025	1.656652	ATATCACTTGCACTGTCGGC	58.343	50.000	0.00	0.00	0.00	5.54
4411	6046	5.648178	TGGACTTATTTACACGTGAGCTA	57.352	39.130	25.01	0.55	0.00	3.32
4447	6082	2.748132	CGCCTGCATAATTTGTCCCCTA	60.748	50.000	0.00	0.00	0.00	3.53
4751	6386	6.158695	ACACCATTATCTGTTTCAGGATACCT	59.841	38.462	0.00	0.00	31.51	3.08
5061	6696	6.589523	GCAGATGCTGAAGTATTACTCCTATG	59.410	42.308	0.00	0.00	38.21	2.23
5175	6811	4.852134	TGCAAAAGCTTCAAGCATCTTA	57.148	36.364	13.10	0.00	45.56	2.10
5645	7285	3.411446	CAAGCAACTCCTCACCAATACA	58.589	45.455	0.00	0.00	0.00	2.29
5672	7312	3.942748	TCCACTTGTTTGTGTAGTTCCAC	59.057	43.478	0.00	0.00	36.30	4.02
5673	7313	4.223556	TCCACTTGTTTGTGTAGTTCCA	57.776	40.909	0.00	0.00	36.30	3.53
5674	7314	4.638865	AGTTCCACTTGTTTGTGTAGTTCC	59.361	41.667	0.00	0.00	36.30	3.62
5675	7315	5.813080	AGTTCCACTTGTTTGTGTAGTTC	57.187	39.130	0.00	0.00	36.30	3.01
5676	7316	6.093082	GTGTAGTTCCACTTGTTTGTGTAGTT	59.907	38.462	0.00	0.00	36.30	2.24
5677	7317	5.583457	GTGTAGTTCCACTTGTTTGTGTAGT	59.417	40.000	0.00	0.00	36.30	2.73
5678	7318	5.583061	TGTGTAGTTCCACTTGTTTGTGTAG	59.417	40.000	0.00	0.00	36.30	2.74
5679	7319	5.489249	TGTGTAGTTCCACTTGTTTGTGTA	58.511	37.500	0.00	0.00	36.30	2.90
5680	7320	4.328536	TGTGTAGTTCCACTTGTTTGTGT	58.671	39.130	0.00	0.00	36.30	3.72
5681	7321	4.955925	TGTGTAGTTCCACTTGTTTGTG	57.044	40.909	0.00	0.00	36.30	3.33
5682	7322	5.241949	TGTTTGTGTAGTTCCACTTGTTTGT	59.758	36.000	0.00	0.00	36.30	2.83
5683	7323	5.704888	TGTTTGTGTAGTTCCACTTGTTTG	58.295	37.500	0.00	0.00	36.30	2.93
5684	7324	5.968528	TGTTTGTGTAGTTCCACTTGTTT	57.031	34.783	0.00	0.00	36.30	2.83
5685	7325	5.621329	GCTTGTTTGTGTAGTTCCACTTGTT	60.621	40.000	0.00	0.00	36.30	2.83
5686	7326	4.142469	GCTTGTTTGTGTAGTTCCACTTGT	60.142	41.667	0.00	0.00	36.30	3.16
5687	7327	4.351192	GCTTGTTTGTGTAGTTCCACTTG	58.649	43.478	0.00	0.00	36.30	3.16
5688	7328	3.380320	GGCTTGTTTGTGTAGTTCCACTT	59.620	43.478	0.00	0.00	36.30	3.16
5689	7329	2.949644	GGCTTGTTTGTGTAGTTCCACT	59.050	45.455	0.00	0.00	36.30	4.00
5865	7542	6.598064	ACAAATCTAAGACAACTAATTCGGGG	59.402	38.462	0.00	0.00	0.00	5.73
5963	7663	2.164338	GCCTCTATTCTACTCCCTCCG	58.836	57.143	0.00	0.00	0.00	4.63
6117	7817	6.589907	AGCCGTTCCAAACATATTCAAAATTC	59.410	34.615	0.00	0.00	0.00	2.17
6180	7880	2.554032	GCTGTGCTGTGTTCAAATACCT	59.446	45.455	0.00	0.00	0.00	3.08
6489	8234	6.706270	ACAGTCTACAAGGTACAAAGTGAATG	59.294	38.462	0.00	0.00	0.00	2.67
6497	8242	4.831155	ACAGCTACAGTCTACAAGGTACAA	59.169	41.667	0.00	0.00	0.00	2.41
6570	8315	5.554822	TTCGCTACGCCATTTCTATTTTT	57.445	34.783	0.00	0.00	0.00	1.94
6573	8318	5.057149	AGAATTCGCTACGCCATTTCTATT	58.943	37.500	0.00	0.00	0.00	1.73
6708	8578	6.251376	CACAAACTGTTAAGCAAAGACACTTC	59.749	38.462	0.00	0.00	0.00	3.01
6757	8631	7.606135	TTCCCTTCTCGTGGTCAATATTATA	57.394	36.000	0.00	0.00	0.00	0.98
6774	8648	9.305925	CATCTTTAATAGCATTGTTTTCCCTTC	57.694	33.333	0.00	0.00	0.00	3.46
6842	8718	7.537306	GAATCTGAATTCCGTTTTCGAAAATGA	59.463	33.333	33.90	25.24	43.79	2.57
6843	8719	7.657364	GAATCTGAATTCCGTTTTCGAAAATG	58.343	34.615	28.24	28.24	43.79	2.32
6965	8880	3.109230	GCATGTTGCTCTAGTTTGACG	57.891	47.619	0.00	0.00	40.96	4.35
7365	9281	3.443681	GCTTTATGTTGTGCATACCAGGT	59.556	43.478	0.00	0.00	39.57	4.00
7380	9296	7.985634	AAACAGCCGTTTATTATGCTTTATG	57.014	32.000	0.00	0.00	43.59	1.90
7381	9297	9.116067	TCTAAACAGCCGTTTATTATGCTTTAT	57.884	29.630	5.75	0.00	44.52	1.40
7382	9298	8.495361	TCTAAACAGCCGTTTATTATGCTTTA	57.505	30.769	5.75	0.00	44.52	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.