AutoCloner

Multiple sequence alignment - TraesCS3A01G342400

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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	TraesCS3A01G342400	chr3A	100.000	2287	0	0	1	2287	589398365	589396079	0.000000e+00	4224
1	TraesCS3A01G342400	chr3D	92.289	830	59	5	877	1703	55164714	55165541	0.000000e+00	1173
2	TraesCS3A01G342400	chr3D	96.407	668	24	0	215	882	124068585	124067918	0.000000e+00	1101
3	TraesCS3A01G342400	chr3D	87.456	853	79	15	870	1698	45633088	45632240	0.000000e+00	957
4	TraesCS3A01G342400	chr3D	85.160	593	28	19	1709	2287	447993231	447992685	9.230000e-154	553
5	TraesCS3A01G342400	chr3D	99.074	216	2	0	1	216	543909792	543910007	2.760000e-104	388
6	TraesCS3A01G342400	chr3D	97.778	225	4	1	1	224	539887000	539886776	9.910000e-104	387
7	TraesCS3A01G342400	chr3D	98.624	218	2	1	1	218	583076390	583076606	3.560000e-103	385
8	TraesCS3A01G342400	chr5D	95.373	670	30	1	215	883	39089942	39090611	0.000000e+00	1064
9	TraesCS3A01G342400	chr5D	94.469	669	33	2	215	882	353957429	353958094	0.000000e+00	1027
10	TraesCS3A01G342400	chr5D	94.320	669	36	2	215	882	201829085	201829752	0.000000e+00	1024
11	TraesCS3A01G342400	chr5D	88.848	825	70	15	877	1685	369344432	369345250	0.000000e+00	994
12	TraesCS3A01G342400	chr5D	87.380	832	84	16	877	1698	416790816	416791636	0.000000e+00	935
13	TraesCS3A01G342400	chr4D	94.619	669	34	2	215	882	345354947	345355614	0.000000e+00	1035
14	TraesCS3A01G342400	chr6B	94.603	667	35	1	217	882	149421505	149420839	0.000000e+00	1031
15	TraesCS3A01G342400	chr7D	94.461	668	37	0	215	882	116614254	116613587	0.000000e+00	1029
16	TraesCS3A01G342400	chr7D	94.337	671	35	2	215	882	561525100	561524430	0.000000e+00	1026
17	TraesCS3A01G342400	chr7D	88.249	834	76	13	870	1685	571475901	571476730	0.000000e+00	977
18	TraesCS3A01G342400	chr7D	99.070	215	2	0	1	215	247736308	247736522	9.910000e-104	387
19	TraesCS3A01G342400	chr2D	87.599	887	96	7	1	882	469180607	469181484	0.000000e+00	1016
20	TraesCS3A01G342400	chr2D	99.070	215	2	0	1	215	576892585	576892371	9.910000e-104	387
21	TraesCS3A01G342400	chr2D	97.758	223	3	2	1	222	148362340	148362119	1.280000e-102	383
22	TraesCS3A01G342400	chr3B	88.494	817	76	15	880	1685	782819771	782820580	0.000000e+00	972
23	TraesCS3A01G342400	chr3B	86.719	512	28	20	1778	2276	587569371	587568887	1.200000e-147	532
24	TraesCS3A01G342400	chr5B	88.171	820	76	14	882	1685	34491267	34492081	0.000000e+00	957
25	TraesCS3A01G342400	chr5A	87.500	824	84	14	877	1686	78333619	78334437	0.000000e+00	933
26	TraesCS3A01G342400	chr4B	88.000	800	82	9	910	1699	656166295	656165500	0.000000e+00	933
27	TraesCS3A01G342400	chr1D	97.345	226	4	2	1	225	210215607	210215383	1.280000e-102	383
28	TraesCS3A01G342400	chr1D	94.937	237	9	3	1	237	22878312	22878545	3.590000e-98	368

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	TraesCS3A01G342400	chr3A	589396079	589398365	2286	True	4224	4224	100.000	1	2287	1	chr3A.!!$R1	2286
1	TraesCS3A01G342400	chr3D	55164714	55165541	827	False	1173	1173	92.289	877	1703	1	chr3D.!!$F1	826
2	TraesCS3A01G342400	chr3D	124067918	124068585	667	True	1101	1101	96.407	215	882	1	chr3D.!!$R2	667
3	TraesCS3A01G342400	chr3D	45632240	45633088	848	True	957	957	87.456	870	1698	1	chr3D.!!$R1	828
4	TraesCS3A01G342400	chr3D	447992685	447993231	546	True	553	553	85.160	1709	2287	1	chr3D.!!$R3	578
5	TraesCS3A01G342400	chr5D	39089942	39090611	669	False	1064	1064	95.373	215	883	1	chr5D.!!$F1	668
6	TraesCS3A01G342400	chr5D	353957429	353958094	665	False	1027	1027	94.469	215	882	1	chr5D.!!$F3	667
7	TraesCS3A01G342400	chr5D	201829085	201829752	667	False	1024	1024	94.320	215	882	1	chr5D.!!$F2	667
8	TraesCS3A01G342400	chr5D	369344432	369345250	818	False	994	994	88.848	877	1685	1	chr5D.!!$F4	808
9	TraesCS3A01G342400	chr5D	416790816	416791636	820	False	935	935	87.380	877	1698	1	chr5D.!!$F5	821
10	TraesCS3A01G342400	chr4D	345354947	345355614	667	False	1035	1035	94.619	215	882	1	chr4D.!!$F1	667
11	TraesCS3A01G342400	chr6B	149420839	149421505	666	True	1031	1031	94.603	217	882	1	chr6B.!!$R1	665
12	TraesCS3A01G342400	chr7D	116613587	116614254	667	True	1029	1029	94.461	215	882	1	chr7D.!!$R1	667
13	TraesCS3A01G342400	chr7D	561524430	561525100	670	True	1026	1026	94.337	215	882	1	chr7D.!!$R2	667
14	TraesCS3A01G342400	chr7D	571475901	571476730	829	False	977	977	88.249	870	1685	1	chr7D.!!$F2	815
15	TraesCS3A01G342400	chr2D	469180607	469181484	877	False	1016	1016	87.599	1	882	1	chr2D.!!$F1	881
16	TraesCS3A01G342400	chr3B	782819771	782820580	809	False	972	972	88.494	880	1685	1	chr3B.!!$F1	805
17	TraesCS3A01G342400	chr5B	34491267	34492081	814	False	957	957	88.171	882	1685	1	chr5B.!!$F1	803
18	TraesCS3A01G342400	chr5A	78333619	78334437	818	False	933	933	87.500	877	1686	1	chr5A.!!$F1	809
19	TraesCS3A01G342400	chr4B	656165500	656166295	795	True	933	933	88.000	910	1699	1	chr4B.!!$R1	789

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
86	87	0.034896	ACTCCATCAACCGCGTTCTT	59.965	50.0	4.92	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1963	2016	0.106619	AGAGTACGGGACCAGCTAGG	60.107	60.0	0.0	0.0	45.67	3.02	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
31	32	4.170062	CGTCCGTTCGGCGCTAGA	62.170	66.667	7.64	4.43	39.71	2.43
32	33	2.412112	GTCCGTTCGGCGCTAGAT	59.588	61.111	7.64	0.00	39.71	1.98
33	34	1.657794	GTCCGTTCGGCGCTAGATC	60.658	63.158	7.64	5.92	39.71	2.75
34	35	2.726180	CCGTTCGGCGCTAGATCG	60.726	66.667	21.14	21.14	39.71	3.69
35	36	2.726180	CGTTCGGCGCTAGATCGG	60.726	66.667	20.67	9.02	0.00	4.18
36	37	2.719979	GTTCGGCGCTAGATCGGA	59.280	61.111	7.64	0.00	0.00	4.55
37	38	1.286260	GTTCGGCGCTAGATCGGAT	59.714	57.895	7.64	0.00	0.00	4.18
38	39	0.729816	GTTCGGCGCTAGATCGGATC	60.730	60.000	7.64	10.02	0.00	3.36
39	40	0.889638	TTCGGCGCTAGATCGGATCT	60.890	55.000	22.96	22.96	43.33	2.75
41	42	0.455295	CGGCGCTAGATCGGATCTTC	60.455	60.000	24.36	15.48	40.76	2.87
42	43	0.109039	GGCGCTAGATCGGATCTTCC	60.109	60.000	24.36	16.11	40.76	3.46
79	80	1.531264	CGAGTACGACTCCATCAACCG	60.531	57.143	8.73	0.00	42.12	4.44
86	87	0.034896	ACTCCATCAACCGCGTTCTT	59.965	50.000	4.92	0.00	0.00	2.52
87	88	0.443869	CTCCATCAACCGCGTTCTTG	59.556	55.000	4.92	3.62	0.00	3.02
101	103	1.529865	GTTCTTGTAACGCTTCCGCTT	59.470	47.619	0.00	0.00	38.22	4.68
102	104	2.728690	TCTTGTAACGCTTCCGCTTA	57.271	45.000	0.00	0.00	38.22	3.09
121	123	5.050490	GCTTAGCGATCTTCAAGGTTATGA	58.950	41.667	0.00	0.00	0.00	2.15
133	135	3.567478	AGGTTATGAAGATGCACTCCC	57.433	47.619	0.00	0.00	0.00	4.30
134	136	3.118531	AGGTTATGAAGATGCACTCCCT	58.881	45.455	0.00	0.00	0.00	4.20
136	138	3.135530	GGTTATGAAGATGCACTCCCTCT	59.864	47.826	0.00	0.00	0.00	3.69
153	155	2.287547	CCTCTCTCTCGTTGCTAGCATC	60.288	54.545	20.13	17.01	0.00	3.91
184	186	3.513912	TGATCTTGGTGACACGTAGGAAT	59.486	43.478	0.00	0.00	42.67	3.01
185	187	4.020573	TGATCTTGGTGACACGTAGGAATT	60.021	41.667	0.00	0.00	42.67	2.17
186	188	4.345859	TCTTGGTGACACGTAGGAATTT	57.654	40.909	0.00	0.00	42.67	1.82
414	419	4.844420	GGAGACGGCCTGATTCAG	57.156	61.111	6.70	6.70	0.00	3.02
441	446	1.466360	GCGAATGATGTCAACTGCCAC	60.466	52.381	0.00	0.00	0.00	5.01
477	482	2.612972	GGTCAGGAATCAGCGTCTTCAA	60.613	50.000	0.00	0.00	0.00	2.69
492	497	5.290386	CGTCTTCAACTCTTCTTTAGTGGT	58.710	41.667	0.00	0.00	0.00	4.16
512	517	3.691118	GGTCTTCATGAGCACTGCATTAA	59.309	43.478	3.30	0.00	42.34	1.40
550	555	0.811616	GCATGGAGCCGAAGTTCGAT	60.812	55.000	26.37	14.25	43.74	3.59
610	615	1.614241	CCGACCACCCGAGGAAGAAT	61.614	60.000	0.00	0.00	0.00	2.40
620	625	1.207791	GAGGAAGAATGCCCTCCAGA	58.792	55.000	0.00	0.00	42.35	3.86
724	730	1.726352	AGAGAGGGGGTGGGTAAGTAA	59.274	52.381	0.00	0.00	0.00	2.24
731	737	1.917568	GGGTGGGTAAGTAATGGTGGA	59.082	52.381	0.00	0.00	0.00	4.02
858	868	3.688235	TCCATGAATTGTGTGCAGATCA	58.312	40.909	0.00	0.00	0.00	2.92
934	950	4.827481	CGCAACTACGGCCACTAT	57.173	55.556	2.24	0.00	0.00	2.12
1031	1052	0.179094	TTCACCAAGCACTTCGTCGT	60.179	50.000	0.00	0.00	0.00	4.34
1035	1056	0.319211	CCAAGCACTTCGTCGTGGTA	60.319	55.000	10.81	0.00	44.08	3.25
1038	1059	1.007038	GCACTTCGTCGTGGTACCA	60.007	57.895	11.60	11.60	35.47	3.25
1161	1190	3.875727	CAGCCGTTCATCAGATCAAGATT	59.124	43.478	0.00	0.00	0.00	2.40
1185	1214	1.967319	ACATGGTGACGTTCAAGCTT	58.033	45.000	0.00	0.00	0.00	3.74
1221	1257	5.984695	CCCTCAAGGTCATATCTTCGATA	57.015	43.478	0.00	0.00	0.00	2.92
1280	1316	3.134127	GAAGCCTTCGCCGCCAAT	61.134	61.111	0.00	0.00	34.57	3.16
1289	1325	2.590092	GCCGCCAATGAGTAGGGT	59.410	61.111	0.00	0.00	0.00	4.34
1290	1326	1.077716	GCCGCCAATGAGTAGGGTT	60.078	57.895	0.00	0.00	0.00	4.11
1298	1334	0.844661	ATGAGTAGGGTTGGGCCACA	60.845	55.000	5.23	0.00	39.65	4.17
1307	1343	0.890683	GTTGGGCCACATCTTTCCAG	59.109	55.000	5.23	0.00	0.00	3.86
1320	1356	3.538591	TCTTTCCAGCGTACTATCGAGA	58.461	45.455	0.00	0.00	0.00	4.04
1329	1365	3.487042	GCGTACTATCGAGACTGCTTTGA	60.487	47.826	0.00	0.00	0.00	2.69
1370	1412	4.025229	GCGTTGAACTGTTATGAAGTGTGA	60.025	41.667	0.00	0.00	0.00	3.58
1440	1488	4.943093	TGTTGTGCTTATGATGTGTGCTAT	59.057	37.500	0.00	0.00	0.00	2.97
1460	1508	0.465460	ATGGTTGTGCCGAAGTGTGT	60.465	50.000	0.00	0.00	41.21	3.72
1570	1622	1.067916	CAGGCAACCAAACACCAGC	59.932	57.895	0.00	0.00	37.17	4.85
1578	1630	1.423541	ACCAAACACCAGCCAGTATGA	59.576	47.619	0.00	0.00	39.69	2.15
1666	1718	2.363038	GCATTTGCATAGCCAGATTGGA	59.637	45.455	0.00	0.00	39.60	3.53
1705	1757	2.877582	GGTACGGTAGCGCACACG	60.878	66.667	18.54	13.35	44.07	4.49
1758	1810	2.830827	CCACACCCAACCGCAACA	60.831	61.111	0.00	0.00	0.00	3.33
1789	1841	0.521735	GTGAAATCGCCAACAGGACC	59.478	55.000	0.00	0.00	0.00	4.46
1818	1870	2.108976	GGCGAATGAGGGCGATCA	59.891	61.111	0.00	0.00	0.00	2.92
1819	1871	1.302033	GGCGAATGAGGGCGATCAT	60.302	57.895	0.00	0.00	41.72	2.45
1820	1872	1.294659	GGCGAATGAGGGCGATCATC	61.295	60.000	4.54	0.00	39.00	2.92
1836	1888	4.462133	GATCATCCATCCATCATCATCCC	58.538	47.826	0.00	0.00	0.00	3.85
1845	1897	3.074390	TCCATCATCATCCCCCATGTTAC	59.926	47.826	0.00	0.00	33.66	2.50
1846	1898	3.074985	CCATCATCATCCCCCATGTTACT	59.925	47.826	0.00	0.00	33.66	2.24
1847	1899	3.862877	TCATCATCCCCCATGTTACTG	57.137	47.619	0.00	0.00	33.66	2.74
1848	1900	3.122480	TCATCATCCCCCATGTTACTGT	58.878	45.455	0.00	0.00	33.66	3.55
1849	1901	4.302930	TCATCATCCCCCATGTTACTGTA	58.697	43.478	0.00	0.00	33.66	2.74
1853	1905	6.182507	TCATCCCCCATGTTACTGTATTAC	57.817	41.667	0.00	0.00	33.66	1.89
1932	1984	3.283684	CCCCGTCGCACTTGCAAA	61.284	61.111	0.00	0.00	42.21	3.68
1939	1991	2.829206	CGCACTTGCAAACCGTGGA	61.829	57.895	16.37	0.00	42.21	4.02
1980	2033	1.757340	GCCTAGCTGGTCCCGTACT	60.757	63.158	0.00	0.00	38.35	2.73
1981	2034	1.736365	GCCTAGCTGGTCCCGTACTC	61.736	65.000	0.00	0.00	38.35	2.59
1982	2035	0.106619	CCTAGCTGGTCCCGTACTCT	60.107	60.000	0.00	0.00	0.00	3.24
2001	2056	2.187100	CTGGGGAAGAAGAGAAGAGCT	58.813	52.381	0.00	0.00	0.00	4.09
2074	2142	2.507102	ATTCGCCAGCTCGACGTG	60.507	61.111	0.00	0.00	38.30	4.49
2146	2214	3.745803	GACGGAGGAACGCGGACT	61.746	66.667	12.47	4.89	37.37	3.85
2152	2220	0.038526	GAGGAACGCGGACTGAAGAA	60.039	55.000	12.47	0.00	0.00	2.52
2204	2272	3.595108	GACTGGAAAAGGCGCGTGC	62.595	63.158	13.78	13.78	41.71	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	3.528009	GATTCAAATCGCGGAAGATCC	57.472	47.619	6.13	0.00	0.00	3.36
51	52	2.277756	GTCGTACTCGCGGCGATT	60.278	61.111	26.60	22.48	37.00	3.34
55	56	2.985486	GATGGAGTCGTACTCGCGGC	62.985	65.000	6.13	0.00	45.96	6.53
57	58	0.098200	TTGATGGAGTCGTACTCGCG	59.902	55.000	0.00	0.00	45.96	5.87
58	59	1.546834	GTTGATGGAGTCGTACTCGC	58.453	55.000	8.33	3.96	45.96	5.03
110	112	4.517285	GGAGTGCATCTTCATAACCTTGA	58.483	43.478	0.00	0.00	0.00	3.02
116	118	4.293494	AGAGAGGGAGTGCATCTTCATAA	58.707	43.478	0.00	0.00	0.00	1.90
121	123	2.387757	GAGAGAGAGGGAGTGCATCTT	58.612	52.381	0.00	0.00	0.00	2.40
133	135	2.618241	AGATGCTAGCAACGAGAGAGAG	59.382	50.000	23.54	0.00	0.00	3.20
134	136	2.616376	GAGATGCTAGCAACGAGAGAGA	59.384	50.000	23.54	0.00	0.00	3.10
136	138	1.678627	GGAGATGCTAGCAACGAGAGA	59.321	52.381	23.54	0.00	0.00	3.10
153	155	5.355596	GTGTCACCAAGATCAATCTAGGAG	58.644	45.833	0.00	0.00	35.76	3.69
186	188	6.015350	TGGGGAACGTAGCAATAATTCAAAAA	60.015	34.615	0.00	0.00	0.00	1.94
196	198	1.530323	GTGTTGGGGAACGTAGCAAT	58.470	50.000	0.00	0.00	0.00	3.56
197	199	0.881159	CGTGTTGGGGAACGTAGCAA	60.881	55.000	0.00	0.00	35.13	3.91
414	419	4.875713	ACATCATTCGCCGGGCCC	62.876	66.667	13.57	13.57	0.00	5.80
420	425	0.099436	GGCAGTTGACATCATTCGCC	59.901	55.000	0.00	0.00	0.00	5.54
477	482	6.672266	TCATGAAGACCACTAAAGAAGAGT	57.328	37.500	0.00	0.00	0.00	3.24
492	497	6.519679	AATTTAATGCAGTGCTCATGAAGA	57.480	33.333	17.60	0.00	0.00	2.87
512	517	1.086696	CCGGACATGCAGAACGAATT	58.913	50.000	0.00	0.00	0.00	2.17
610	615	1.279025	GGGGTATTGTCTGGAGGGCA	61.279	60.000	0.00	0.00	0.00	5.36
620	625	1.007607	CCCTTCCCTTGGGGTATTGT	58.992	55.000	5.78	0.00	44.74	2.71
724	730	2.038863	TTACTCACCCTGTCCACCAT	57.961	50.000	0.00	0.00	0.00	3.55
731	737	4.077626	TCCCCCTATATTTACTCACCCTGT	60.078	45.833	0.00	0.00	0.00	4.00
858	868	3.135530	GTGCCCATCTCATTACTCTCCTT	59.864	47.826	0.00	0.00	0.00	3.36
1031	1052	1.541670	GCTTGAACTCCGTTGGTACCA	60.542	52.381	11.60	11.60	0.00	3.25
1035	1056	0.468226	TGAGCTTGAACTCCGTTGGT	59.532	50.000	0.00	0.00	35.72	3.67
1038	1059	1.048601	TCCTGAGCTTGAACTCCGTT	58.951	50.000	0.00	0.00	35.72	4.44
1135	1164	1.086067	ATCTGATGAACGGCTGCGTG	61.086	55.000	0.00	0.00	0.00	5.34
1161	1190	0.682292	TGAACGTCACCATGTAGCCA	59.318	50.000	0.00	0.00	0.00	4.75
1185	1214	1.304217	GAGGGTGTCGGGAGTGAGA	60.304	63.158	0.00	0.00	0.00	3.27
1221	1257	2.494471	TGACGACCTCAATACCATCGTT	59.506	45.455	0.00	0.00	45.39	3.85
1280	1316	0.844661	ATGTGGCCCAACCCTACTCA	60.845	55.000	0.00	0.00	37.83	3.41
1289	1325	0.899717	GCTGGAAAGATGTGGCCCAA	60.900	55.000	0.00	0.00	0.00	4.12
1290	1326	1.304381	GCTGGAAAGATGTGGCCCA	60.304	57.895	0.00	0.00	0.00	5.36
1298	1334	4.023878	GTCTCGATAGTACGCTGGAAAGAT	60.024	45.833	0.00	0.00	37.40	2.40
1307	1343	2.759538	AAGCAGTCTCGATAGTACGC	57.240	50.000	0.00	0.00	37.40	4.42
1320	1356	5.789643	ACCATAAACATGTTCAAAGCAGT	57.210	34.783	12.39	0.98	0.00	4.40
1329	1365	6.682746	TCAACGCATAAACCATAAACATGTT	58.317	32.000	4.92	4.92	0.00	2.71
1390	1433	7.841956	AGTACAAACAGAGCATCAACTAGTAT	58.158	34.615	0.00	0.00	37.82	2.12
1392	1435	6.015010	AGAGTACAAACAGAGCATCAACTAGT	60.015	38.462	0.00	0.00	37.82	2.57
1411	1459	5.639506	ACACATCATAAGCACAACAGAGTAC	59.360	40.000	0.00	0.00	0.00	2.73
1440	1488	1.202710	ACACACTTCGGCACAACCATA	60.203	47.619	0.00	0.00	39.03	2.74
1521	1573	1.956477	GACAAACTCAAGGCATGGTGT	59.044	47.619	0.00	0.00	0.00	4.16
1570	1622	1.586422	CACGGGCAGAATCATACTGG	58.414	55.000	0.00	0.00	36.09	4.00
1643	1695	5.656436	TCCAATCTGGCTATGCAAATGCAA	61.656	41.667	12.67	1.58	45.84	4.08
1666	1718	4.816385	CCGGTATTGCATACACTTCTTCAT	59.184	41.667	0.00	0.00	37.48	2.57
1728	1780	3.569210	TGTGGTGGACAGCCTGGG	61.569	66.667	0.00	0.00	34.31	4.45
1743	1795	1.822186	GTCTGTTGCGGTTGGGTGT	60.822	57.895	0.00	0.00	0.00	4.16
1758	1810	0.949105	GATTTCACGTGGCGGTGTCT	60.949	55.000	17.00	0.00	39.00	3.41
1810	1862	0.325933	TGATGGATGGATGATCGCCC	59.674	55.000	2.33	0.00	30.87	6.13
1817	1869	2.357881	GGGGGATGATGATGGATGGATG	60.358	54.545	0.00	0.00	0.00	3.51
1818	1870	1.928077	GGGGGATGATGATGGATGGAT	59.072	52.381	0.00	0.00	0.00	3.41
1819	1871	1.375610	GGGGGATGATGATGGATGGA	58.624	55.000	0.00	0.00	0.00	3.41
1820	1872	1.078115	TGGGGGATGATGATGGATGG	58.922	55.000	0.00	0.00	0.00	3.51
1836	1888	4.134563	GCCAGGTAATACAGTAACATGGG	58.865	47.826	14.96	2.03	43.49	4.00
1845	1897	1.269102	CGTCTCGGCCAGGTAATACAG	60.269	57.143	2.24	0.00	0.00	2.74
1846	1898	0.742505	CGTCTCGGCCAGGTAATACA	59.257	55.000	2.24	0.00	0.00	2.29
1847	1899	0.596859	GCGTCTCGGCCAGGTAATAC	60.597	60.000	2.24	0.00	0.00	1.89
1848	1900	1.737816	GCGTCTCGGCCAGGTAATA	59.262	57.895	2.24	0.00	0.00	0.98
1849	1901	2.499685	GCGTCTCGGCCAGGTAAT	59.500	61.111	2.24	0.00	0.00	1.89
1892	1944	4.803426	CTCCGCTCCGCTGTCCAC	62.803	72.222	0.00	0.00	0.00	4.02
1910	1962	4.096003	AAGTGCGACGGGGATGGG	62.096	66.667	0.00	0.00	0.00	4.00
1925	1977	2.903547	CGGGTCCACGGTTTGCAAG	61.904	63.158	0.00	0.00	0.00	4.01
1963	2016	0.106619	AGAGTACGGGACCAGCTAGG	60.107	60.000	0.00	0.00	45.67	3.02
1964	2017	1.025812	CAGAGTACGGGACCAGCTAG	58.974	60.000	0.00	0.00	0.00	3.42
1965	2018	0.395311	CCAGAGTACGGGACCAGCTA	60.395	60.000	0.00	0.00	33.26	3.32
1966	2019	1.682684	CCAGAGTACGGGACCAGCT	60.683	63.158	0.00	0.00	33.26	4.24
1967	2020	2.893398	CCAGAGTACGGGACCAGC	59.107	66.667	0.00	0.00	33.26	4.85
1980	2033	2.183679	GCTCTTCTCTTCTTCCCCAGA	58.816	52.381	0.00	0.00	0.00	3.86
1981	2034	2.187100	AGCTCTTCTCTTCTTCCCCAG	58.813	52.381	0.00	0.00	0.00	4.45
1982	2035	2.334006	AGCTCTTCTCTTCTTCCCCA	57.666	50.000	0.00	0.00	0.00	4.96
1987	2042	4.458642	GGCAATCAAAGCTCTTCTCTTCTT	59.541	41.667	0.00	0.00	0.00	2.52
2141	2209	2.049433	ACCGCGTTCTTCAGTCCG	60.049	61.111	4.92	0.00	0.00	4.79
2146	2214	1.006571	GAGGACACCGCGTTCTTCA	60.007	57.895	4.92	0.00	31.49	3.02
2170	2238	4.193334	TCTGGAGCACGCCGATCG	62.193	66.667	8.51	8.51	45.38	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.