AutoCloner

Multiple sequence alignment - TraesCS3D01G070500

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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	TraesCS3D01G070500	chr3D	100.000	3245	0	0	1	3245	31651609	31654853	0.000000e+00	5993.0
1	TraesCS3D01G070500	chr3D	90.840	131	11	1	26	155	141357712	141357582	1.200000e-39	174.0
2	TraesCS3D01G070500	chr3D	97.297	37	0	1	874	910	31652451	31652486	9.720000e-06	62.1
3	TraesCS3D01G070500	chr3D	97.297	37	0	1	843	878	31652482	31652518	9.720000e-06	62.1
4	TraesCS3D01G070500	chr3A	91.501	2412	189	10	843	3245	266559537	266557133	0.000000e+00	3304.0
5	TraesCS3D01G070500	chr3A	97.350	717	16	2	1	717	51698246	51697533	0.000000e+00	1216.0
6	TraesCS3D01G070500	chr3A	98.551	69	1	0	716	784	51697429	51697361	4.400000e-24	122.0
7	TraesCS3D01G070500	chr7A	89.870	2389	226	10	871	3245	401613302	401615688	0.000000e+00	3057.0
8	TraesCS3D01G070500	chr7A	91.227	1915	157	8	864	2769	26975519	26973607	0.000000e+00	2595.0
9	TraesCS3D01G070500	chr7A	91.771	1203	85	10	1931	3125	9092520	9091324	0.000000e+00	1661.0
10	TraesCS3D01G070500	chr7A	89.600	125	13	0	3121	3245	9069479	9069355	3.350000e-35	159.0
11	TraesCS3D01G070500	chr7A	71.765	595	149	16	1209	1794	449992182	449991598	2.020000e-32	150.0
12	TraesCS3D01G070500	chr7A	97.297	37	0	1	843	878	26975509	26975473	9.720000e-06	62.1
13	TraesCS3D01G070500	chr7B	88.903	2415	250	13	845	3245	405675625	405673215	0.000000e+00	2959.0
14	TraesCS3D01G070500	chr7B	100.000	36	0	0	843	878	405675596	405675561	2.090000e-07	67.6
15	TraesCS3D01G070500	chr6B	92.853	1861	126	4	844	2701	87634122	87635978	0.000000e+00	2693.0
16	TraesCS3D01G070500	chr6B	93.078	549	38	0	2697	3245	87644285	87644833	0.000000e+00	804.0
17	TraesCS3D01G070500	chr6B	81.618	136	13	5	21	155	335091173	335091049	5.730000e-18	102.0
18	TraesCS3D01G070500	chr5B	81.398	1989	343	15	1259	3245	243770509	243772472	0.000000e+00	1598.0
19	TraesCS3D01G070500	chr5B	79.576	377	71	5	873	1245	243768787	243769161	6.900000e-67	265.0
20	TraesCS3D01G070500	chr5B	96.610	59	2	0	843	901	566087719	566087777	7.410000e-17	99.0
21	TraesCS3D01G070500	chr5B	100.000	40	0	0	848	887	689661335	689661296	1.250000e-09	75.0
22	TraesCS3D01G070500	chr2A	90.083	1200	109	7	843	2033	3364438	3365636	0.000000e+00	1548.0
23	TraesCS3D01G070500	chr2A	90.789	1140	104	1	2106	3245	3365878	3367016	0.000000e+00	1522.0
24	TraesCS3D01G070500	chr2B	90.625	928	87	0	2318	3245	104786234	104787161	0.000000e+00	1232.0
25	TraesCS3D01G070500	chr2B	76.084	853	172	23	2201	3040	646410322	646409489	1.800000e-112	416.0
26	TraesCS3D01G070500	chr2B	80.882	136	14	5	21	155	155942117	155941993	2.660000e-16	97.1
27	TraesCS3D01G070500	chr2B	100.000	34	0	0	787	820	492953931	492953898	2.700000e-06	63.9
28	TraesCS3D01G070500	chr6A	95.082	61	3	0	843	903	17593557	17593617	2.660000e-16	97.1
29	TraesCS3D01G070500	chr2D	81.203	133	13	5	21	152	105620956	105621077	2.660000e-16	97.1
30	TraesCS3D01G070500	chr2D	100.000	35	0	0	787	821	420521605	420521571	7.510000e-07	65.8

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	TraesCS3D01G070500	chr3D	31651609	31654853	3244	False	2039.066667	5993	98.1980	1	3245	3	chr3D.!!$F1	3244
1	TraesCS3D01G070500	chr3A	266557133	266559537	2404	True	3304.000000	3304	91.5010	843	3245	1	chr3A.!!$R1	2402
2	TraesCS3D01G070500	chr3A	51697361	51698246	885	True	669.000000	1216	97.9505	1	784	2	chr3A.!!$R2	783
3	TraesCS3D01G070500	chr7A	401613302	401615688	2386	False	3057.000000	3057	89.8700	871	3245	1	chr7A.!!$F1	2374
4	TraesCS3D01G070500	chr7A	9091324	9092520	1196	True	1661.000000	1661	91.7710	1931	3125	1	chr7A.!!$R2	1194
5	TraesCS3D01G070500	chr7A	26973607	26975519	1912	True	1328.550000	2595	94.2620	843	2769	2	chr7A.!!$R4	1926
6	TraesCS3D01G070500	chr7B	405673215	405675625	2410	True	1513.300000	2959	94.4515	843	3245	2	chr7B.!!$R1	2402
7	TraesCS3D01G070500	chr6B	87634122	87635978	1856	False	2693.000000	2693	92.8530	844	2701	1	chr6B.!!$F1	1857
8	TraesCS3D01G070500	chr6B	87644285	87644833	548	False	804.000000	804	93.0780	2697	3245	1	chr6B.!!$F2	548
9	TraesCS3D01G070500	chr5B	243768787	243772472	3685	False	931.500000	1598	80.4870	873	3245	2	chr5B.!!$F2	2372
10	TraesCS3D01G070500	chr2A	3364438	3367016	2578	False	1535.000000	1548	90.4360	843	3245	2	chr2A.!!$F1	2402
11	TraesCS3D01G070500	chr2B	104786234	104787161	927	False	1232.000000	1232	90.6250	2318	3245	1	chr2B.!!$F1	927
12	TraesCS3D01G070500	chr2B	646409489	646410322	833	True	416.000000	416	76.0840	2201	3040	1	chr2B.!!$R3	839

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
633	634	0.099968	CGATTGGAAGCCATGCACAG	59.900	55.0	0.0	0.0	31.53	3.66	F
2178	3799	0.246086	AGCGAAGGAGAGCAGAACAG	59.754	55.0	0.0	0.0	35.48	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2180	3801	0.108567	GGTCGAAGCTGTCTCTTCCC	60.109	60.0	0.0	0.0	39.33	3.97	R
2988	4615	0.322008	CCTCCACAGTTTCCTCAGCC	60.322	60.0	0.0	0.0	0.00	4.85	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
24	25	4.568956	TGTCGCATATACGGTAGCTACTA	58.431	43.478	22.74	9.39	0.00	1.82
69	70	2.490903	GTTGCCTGCTCTGTGATTTCAT	59.509	45.455	0.00	0.00	0.00	2.57
102	103	6.938030	TGGTTTAATTCGTTTATGACCTCTGT	59.062	34.615	0.00	0.00	32.00	3.41
145	146	3.771479	TGCACCAAGATACTCACTCAGAT	59.229	43.478	0.00	0.00	0.00	2.90
149	150	4.141981	ACCAAGATACTCACTCAGATGCAG	60.142	45.833	0.00	0.00	0.00	4.41
392	393	7.330262	AGAAACTGGAACACATTTTTGAATGT	58.670	30.769	0.00	0.00	43.64	2.71
412	413	9.936759	TGAATGTTATGACTAACTGATGTACAA	57.063	29.630	0.00	0.00	38.44	2.41
605	606	3.660177	AGCTAGACCTCTAGATGGGATCA	59.340	47.826	12.72	0.00	46.80	2.92
606	607	4.107149	AGCTAGACCTCTAGATGGGATCAA	59.893	45.833	12.72	0.00	46.80	2.57
629	630	1.226773	GTGCGATTGGAAGCCATGC	60.227	57.895	0.00	0.00	31.53	4.06
633	634	0.099968	CGATTGGAAGCCATGCACAG	59.900	55.000	0.00	0.00	31.53	3.66
651	652	1.952296	CAGTTGCTTGAGTTGCTTCCT	59.048	47.619	0.00	0.00	0.00	3.36
784	890	3.868835	AGTTAACGCTTGCGTTAAACAG	58.131	40.909	37.40	6.62	43.16	3.16
785	891	3.556775	AGTTAACGCTTGCGTTAAACAGA	59.443	39.130	37.40	22.84	43.16	3.41
786	892	2.663279	AACGCTTGCGTTAAACAGAG	57.337	45.000	28.18	0.00	0.00	3.35
787	893	1.860676	ACGCTTGCGTTAAACAGAGA	58.139	45.000	15.19	0.00	0.00	3.10
788	894	2.413837	ACGCTTGCGTTAAACAGAGAT	58.586	42.857	15.19	0.00	0.00	2.75
789	895	2.157668	ACGCTTGCGTTAAACAGAGATG	59.842	45.455	15.19	0.00	0.00	2.90
790	896	2.474526	CGCTTGCGTTAAACAGAGATGG	60.475	50.000	6.86	0.00	0.00	3.51
791	897	2.742053	GCTTGCGTTAAACAGAGATGGA	59.258	45.455	0.00	0.00	0.00	3.41
792	898	3.424962	GCTTGCGTTAAACAGAGATGGAC	60.425	47.826	0.00	0.00	0.00	4.02
793	899	2.333926	TGCGTTAAACAGAGATGGACG	58.666	47.619	0.00	0.00	0.00	4.79
794	900	2.288579	TGCGTTAAACAGAGATGGACGT	60.289	45.455	0.00	0.00	0.00	4.34
795	901	2.735134	GCGTTAAACAGAGATGGACGTT	59.265	45.455	0.00	0.00	0.00	3.99
796	902	3.423123	GCGTTAAACAGAGATGGACGTTG	60.423	47.826	0.00	0.00	0.00	4.10
797	903	3.985279	CGTTAAACAGAGATGGACGTTGA	59.015	43.478	0.00	0.00	0.00	3.18
798	904	4.090066	CGTTAAACAGAGATGGACGTTGAG	59.910	45.833	0.00	0.00	0.00	3.02
799	905	5.227908	GTTAAACAGAGATGGACGTTGAGA	58.772	41.667	0.00	0.00	0.00	3.27
800	906	4.336889	AAACAGAGATGGACGTTGAGAA	57.663	40.909	0.00	0.00	0.00	2.87
801	907	3.305398	ACAGAGATGGACGTTGAGAAC	57.695	47.619	0.00	0.00	0.00	3.01
802	908	2.628178	ACAGAGATGGACGTTGAGAACA	59.372	45.455	0.00	0.00	0.00	3.18
803	909	3.069586	ACAGAGATGGACGTTGAGAACAA	59.930	43.478	0.00	0.00	0.00	2.83
814	920	3.685139	TTGAGAACAACTAGCTGGAGG	57.315	47.619	3.17	0.00	0.00	4.30
815	921	1.276421	TGAGAACAACTAGCTGGAGGC	59.724	52.381	3.17	0.00	42.19	4.70
825	931	2.596776	GCTGGAGGCTACAGGAAGA	58.403	57.895	27.50	0.00	36.48	2.87
826	932	0.905357	GCTGGAGGCTACAGGAAGAA	59.095	55.000	27.50	0.00	36.48	2.52
827	933	1.134551	GCTGGAGGCTACAGGAAGAAG	60.135	57.143	27.50	1.96	36.48	2.85
828	934	2.461695	CTGGAGGCTACAGGAAGAAGA	58.538	52.381	19.53	0.00	32.38	2.87
829	935	2.834549	CTGGAGGCTACAGGAAGAAGAA	59.165	50.000	19.53	0.00	32.38	2.52
830	936	2.834549	TGGAGGCTACAGGAAGAAGAAG	59.165	50.000	0.00	0.00	0.00	2.85
831	937	3.100671	GGAGGCTACAGGAAGAAGAAGA	58.899	50.000	0.00	0.00	0.00	2.87
832	938	3.515901	GGAGGCTACAGGAAGAAGAAGAA	59.484	47.826	0.00	0.00	0.00	2.52
833	939	4.382577	GGAGGCTACAGGAAGAAGAAGAAG	60.383	50.000	0.00	0.00	0.00	2.85
834	940	4.421131	AGGCTACAGGAAGAAGAAGAAGA	58.579	43.478	0.00	0.00	0.00	2.87
835	941	5.029474	AGGCTACAGGAAGAAGAAGAAGAT	58.971	41.667	0.00	0.00	0.00	2.40
836	942	5.128663	AGGCTACAGGAAGAAGAAGAAGATC	59.871	44.000	0.00	0.00	0.00	2.75
837	943	5.105146	GGCTACAGGAAGAAGAAGAAGATCA	60.105	44.000	0.00	0.00	0.00	2.92
838	944	5.810074	GCTACAGGAAGAAGAAGAAGATCAC	59.190	44.000	0.00	0.00	0.00	3.06
839	945	5.159273	ACAGGAAGAAGAAGAAGATCACC	57.841	43.478	0.00	0.00	0.00	4.02
840	946	4.594920	ACAGGAAGAAGAAGAAGATCACCA	59.405	41.667	0.00	0.00	0.00	4.17
841	947	5.177326	CAGGAAGAAGAAGAAGATCACCAG	58.823	45.833	0.00	0.00	0.00	4.00
912	1019	2.083715	GGGTTCCCCTTGATCCACA	58.916	57.895	0.00	0.00	41.34	4.17
947	1054	1.338105	CCTCACGCCAGATCTTTGTGA	60.338	52.381	16.43	16.43	37.89	3.58
974	1081	2.033448	TGGTGTGATTCCCCGTGC	59.967	61.111	0.00	0.00	0.00	5.34
990	1097	4.767255	GCCTGCACTCACCGAGGG	62.767	72.222	0.00	0.00	35.94	4.30
1041	1148	3.371097	GATGTCCTCGAAGGCCGCA	62.371	63.158	0.00	0.00	34.61	5.69
1043	1150	3.760035	GTCCTCGAAGGCCGCAGA	61.760	66.667	0.00	0.00	34.61	4.26
1068	1184	2.484062	GGCGGAACATGCATCTGGG	61.484	63.158	0.00	0.00	0.00	4.45
1076	1192	3.377253	ACATGCATCTGGGAGTTTCAT	57.623	42.857	0.00	0.00	0.00	2.57
1117	1233	2.720605	GCGCGGTACTAGAGGACC	59.279	66.667	8.83	0.20	0.00	4.46
1125	1241	2.223994	GGTACTAGAGGACCGATTTGCC	60.224	54.545	0.00	0.00	0.00	4.52
1275	2725	5.221621	GGCTCTCTACAAGGCTATGAGAAAT	60.222	44.000	9.01	0.00	36.45	2.17
1341	2791	3.625649	AATCTCTTCCTGGCTCAGTTC	57.374	47.619	0.00	0.00	0.00	3.01
1401	2851	3.668447	CCCATGGATATTCAGGAACTCG	58.332	50.000	15.22	0.00	34.60	4.18
1431	2881	6.143206	TGTTCTGGAGGAGTATGATGGATTA	58.857	40.000	0.00	0.00	0.00	1.75
1437	2887	6.270000	TGGAGGAGTATGATGGATTAACGAAT	59.730	38.462	0.00	0.00	0.00	3.34
1440	2890	7.509546	AGGAGTATGATGGATTAACGAATGTT	58.490	34.615	0.00	0.00	42.19	2.71
1546	2996	4.261572	CGGAGAAAATTGCAAAGAAGGTGA	60.262	41.667	1.71	0.00	0.00	4.02
1613	3063	2.860136	CAACGAAATATCTGCGAGCTCA	59.140	45.455	15.40	0.00	0.00	4.26
1715	3166	6.954232	AGTATGAAAAACTCCCCGATTTCTA	58.046	36.000	0.00	0.00	33.90	2.10
1740	3191	2.307496	TTTGTGGGCTGATTGGACAT	57.693	45.000	0.00	0.00	0.00	3.06
1803	3254	2.806434	TGTGAATGGGGAGAATGGTTG	58.194	47.619	0.00	0.00	0.00	3.77
1869	3320	2.038295	CAGAGAAGAAAGGACTGCAGGT	59.962	50.000	19.93	3.31	0.00	4.00
1875	3326	1.003580	GAAAGGACTGCAGGTGATGGA	59.996	52.381	19.93	0.00	0.00	3.41
1881	3332	1.541118	TGCAGGTGATGGAAGGGGA	60.541	57.895	0.00	0.00	0.00	4.81
1918	3370	2.569404	AGAAACCCTCGAGAGCAGAATT	59.431	45.455	15.71	0.00	0.00	2.17
1940	3392	3.176411	TGAATGAGGACAGAGATGTGGT	58.824	45.455	0.00	0.00	0.00	4.16
2021	3473	4.962362	GGATGGAAAGGTTAATGGTCCAAT	59.038	41.667	0.00	0.00	41.54	3.16
2091	3549	5.242615	TGTTAATGACAAGGTGCAAATGCTA	59.757	36.000	6.97	0.00	37.34	3.49
2145	3766	1.344438	ACGATGAGCACTCCACAGAAA	59.656	47.619	0.00	0.00	0.00	2.52
2178	3799	0.246086	AGCGAAGGAGAGCAGAACAG	59.754	55.000	0.00	0.00	35.48	3.16
2180	3801	0.108424	CGAAGGAGAGCAGAACAGGG	60.108	60.000	0.00	0.00	0.00	4.45
2196	3817	1.219393	GGGGGAAGAGACAGCTTCG	59.781	63.158	0.00	0.00	44.04	3.79
2276	3899	1.450312	GAACTGTCGGGGCATCCTG	60.450	63.158	0.00	0.00	40.84	3.86
2324	3947	4.339530	TCTGGATATATAGAGGCGACATGC	59.660	45.833	0.00	0.00	45.38	4.06
2397	4020	3.573967	AGGTTTTGATGAAAAGGATGCGT	59.426	39.130	0.00	0.00	31.57	5.24
2550	4175	0.921896	ATGGGGATGAGTGGAGGTTG	59.078	55.000	0.00	0.00	0.00	3.77
2556	4181	0.326264	ATGAGTGGAGGTTGACTGGC	59.674	55.000	0.00	0.00	0.00	4.85
2769	4395	2.758979	CTCGCTAGAAGACTTGGGGTAA	59.241	50.000	0.00	0.00	34.09	2.85
2884	4511	1.152881	GGCCTATGCAACCTGGAGG	60.153	63.158	0.00	0.00	40.13	4.30
3134	4761	1.134371	GGTATTGAAGGAGCCTCGCTT	60.134	52.381	0.00	0.00	39.88	4.68
3202	4830	1.007271	CTGACTCCTGACGTGCGTT	60.007	57.895	0.00	0.00	0.00	4.84
3223	4851	3.281727	TGCAACAGAAGGAGTTGTCTT	57.718	42.857	7.74	0.00	46.09	3.01
3228	4856	6.017109	TGCAACAGAAGGAGTTGTCTTTATTC	60.017	38.462	7.74	0.00	46.09	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	8.681486	ACGGTAGGTTTATTTTCAGTTAAAGT	57.319	30.769	0.00	0.00	0.00	2.66
69	70	9.602568	TCATAAACGAATTAAACCATGCTACTA	57.397	29.630	0.00	0.00	0.00	1.82
102	103	5.241285	TGCATGCTTGTCTCTGAATAAAACA	59.759	36.000	20.33	0.00	0.00	2.83
115	116	3.012518	AGTATCTTGGTGCATGCTTGTC	58.987	45.455	20.33	6.72	0.00	3.18
145	146	6.499106	TTACAAGATATCCTGGATTCTGCA	57.501	37.500	15.55	0.00	0.00	4.41
149	150	9.678260	ATGCTAATTACAAGATATCCTGGATTC	57.322	33.333	15.55	11.79	0.00	2.52
466	467	3.769536	TCACATCGCATACAGTACAGTG	58.230	45.455	0.42	0.00	0.00	3.66
538	539	6.782000	CCCATTCCTGGATGAAAATGGTAATA	59.218	38.462	18.50	0.00	46.37	0.98
539	540	5.603813	CCCATTCCTGGATGAAAATGGTAAT	59.396	40.000	18.50	0.00	46.37	1.89
540	541	4.961730	CCCATTCCTGGATGAAAATGGTAA	59.038	41.667	18.50	0.00	46.37	2.85
541	542	4.545678	CCCATTCCTGGATGAAAATGGTA	58.454	43.478	18.50	0.00	46.37	3.25
605	606	1.589716	GCTTCCAATCGCACCTGCTT	61.590	55.000	0.00	0.00	39.32	3.91
606	607	2.042831	GCTTCCAATCGCACCTGCT	61.043	57.895	0.00	0.00	39.32	4.24
629	630	2.542411	GGAAGCAACTCAAGCAACTGTG	60.542	50.000	0.00	0.00	0.00	3.66
633	634	1.949525	TGAGGAAGCAACTCAAGCAAC	59.050	47.619	2.98	0.00	41.66	4.17
651	652	4.204799	CAAATGATCATTCTGGCTCCTGA	58.795	43.478	20.95	0.00	0.00	3.86
721	827	6.653020	TCAGTACATGGGATCCATATTATGC	58.347	40.000	15.23	2.31	43.15	3.14
793	899	4.416513	GCCTCCAGCTAGTTGTTCTCAAC	61.417	52.174	5.81	3.31	44.98	3.18
794	900	2.289694	GCCTCCAGCTAGTTGTTCTCAA	60.290	50.000	5.81	0.00	38.99	3.02
795	901	1.276421	GCCTCCAGCTAGTTGTTCTCA	59.724	52.381	5.81	0.00	38.99	3.27
796	902	2.017138	GCCTCCAGCTAGTTGTTCTC	57.983	55.000	5.81	0.00	38.99	2.87
807	913	0.905357	TTCTTCCTGTAGCCTCCAGC	59.095	55.000	0.00	0.00	44.25	4.85
808	914	2.461695	TCTTCTTCCTGTAGCCTCCAG	58.538	52.381	0.00	0.00	0.00	3.86
809	915	2.623418	TCTTCTTCCTGTAGCCTCCA	57.377	50.000	0.00	0.00	0.00	3.86
810	916	3.100671	TCTTCTTCTTCCTGTAGCCTCC	58.899	50.000	0.00	0.00	0.00	4.30
811	917	4.464597	TCTTCTTCTTCTTCCTGTAGCCTC	59.535	45.833	0.00	0.00	0.00	4.70
812	918	4.421131	TCTTCTTCTTCTTCCTGTAGCCT	58.579	43.478	0.00	0.00	0.00	4.58
813	919	4.810191	TCTTCTTCTTCTTCCTGTAGCC	57.190	45.455	0.00	0.00	0.00	3.93
814	920	5.810074	GTGATCTTCTTCTTCTTCCTGTAGC	59.190	44.000	0.00	0.00	0.00	3.58
815	921	6.071108	TGGTGATCTTCTTCTTCTTCCTGTAG	60.071	42.308	0.00	0.00	0.00	2.74
816	922	5.780282	TGGTGATCTTCTTCTTCTTCCTGTA	59.220	40.000	0.00	0.00	0.00	2.74
817	923	4.594920	TGGTGATCTTCTTCTTCTTCCTGT	59.405	41.667	0.00	0.00	0.00	4.00
818	924	5.157940	TGGTGATCTTCTTCTTCTTCCTG	57.842	43.478	0.00	0.00	0.00	3.86
819	925	4.843516	ACTGGTGATCTTCTTCTTCTTCCT	59.156	41.667	0.00	0.00	0.00	3.36
820	926	5.159273	ACTGGTGATCTTCTTCTTCTTCC	57.841	43.478	0.00	0.00	0.00	3.46
821	927	6.983890	GGATACTGGTGATCTTCTTCTTCTTC	59.016	42.308	0.00	0.00	0.00	2.87
822	928	6.126911	GGGATACTGGTGATCTTCTTCTTCTT	60.127	42.308	0.00	0.00	0.00	2.52
823	929	5.365314	GGGATACTGGTGATCTTCTTCTTCT	59.635	44.000	0.00	0.00	0.00	2.85
824	930	5.454045	GGGGATACTGGTGATCTTCTTCTTC	60.454	48.000	0.00	0.00	0.00	2.87
825	931	4.410555	GGGGATACTGGTGATCTTCTTCTT	59.589	45.833	0.00	0.00	0.00	2.52
826	932	3.970640	GGGGATACTGGTGATCTTCTTCT	59.029	47.826	0.00	0.00	0.00	2.85
827	933	3.970640	AGGGGATACTGGTGATCTTCTTC	59.029	47.826	0.00	0.00	0.00	2.87
828	934	3.713764	CAGGGGATACTGGTGATCTTCTT	59.286	47.826	0.00	0.00	34.84	2.52
829	935	3.312890	CAGGGGATACTGGTGATCTTCT	58.687	50.000	0.00	0.00	34.84	2.85
830	936	3.760580	CAGGGGATACTGGTGATCTTC	57.239	52.381	0.00	0.00	34.84	2.87
839	945	1.837051	TAGCCGCCAGGGGATACTG	60.837	63.158	4.70	0.00	38.20	2.74
840	946	1.837499	GTAGCCGCCAGGGGATACT	60.837	63.158	18.70	9.67	43.81	2.12
841	947	2.741747	GTAGCCGCCAGGGGATAC	59.258	66.667	12.58	12.58	41.24	2.24
912	1019	0.923358	TGAGGTTTGGGTGGAGTTGT	59.077	50.000	0.00	0.00	0.00	3.32
947	1054	4.145052	GGGAATCACACCAGAGTTCTTTT	58.855	43.478	0.00	0.00	0.00	2.27
974	1081	4.087892	CCCCTCGGTGAGTGCAGG	62.088	72.222	0.00	0.00	0.00	4.85
984	1091	1.825191	CATGCAATCACCCCCTCGG	60.825	63.158	0.00	0.00	37.81	4.63
990	1097	0.729116	CAGTCGACATGCAATCACCC	59.271	55.000	19.50	0.00	0.00	4.61
1068	1184	1.103398	CCCCATCGCCCATGAAACTC	61.103	60.000	0.00	0.00	33.80	3.01
1117	1233	1.664151	GAGGTTAAGTCCGGCAAATCG	59.336	52.381	0.00	0.00	0.00	3.34
1257	2707	5.048921	CCATGCATTTCTCATAGCCTTGTAG	60.049	44.000	0.00	0.00	0.00	2.74
1275	2725	0.256752	CCTGTTCAGGGATCCATGCA	59.743	55.000	21.65	13.35	0.00	3.96
1341	2791	0.251742	TCCAATCCCCCAAGCACAAG	60.252	55.000	0.00	0.00	0.00	3.16
1401	2851	0.398318	ACTCCTCCAGAACAACAGCC	59.602	55.000	0.00	0.00	0.00	4.85
1431	2881	5.050091	CAGCTTGTACTCTTCAACATTCGTT	60.050	40.000	0.00	0.00	35.01	3.85
1437	2887	4.569943	GATCCAGCTTGTACTCTTCAACA	58.430	43.478	0.00	0.00	0.00	3.33
1440	2890	2.826128	ACGATCCAGCTTGTACTCTTCA	59.174	45.455	0.00	0.00	0.00	3.02
1613	3063	6.239204	GGGTGTTTCCAGCTTAACAAATACTT	60.239	38.462	7.24	0.00	39.09	2.24
1715	3166	3.839490	TCCAATCAGCCCACAAAAATCAT	59.161	39.130	0.00	0.00	0.00	2.45
1740	3191	3.483808	TCACCACATTCAGTTACTGCA	57.516	42.857	7.61	0.00	0.00	4.41
1803	3254	1.337167	GGGGCATCAAAGTTCACAAGC	60.337	52.381	0.00	0.00	0.00	4.01
1869	3320	2.918934	TCTGTCAAATCCCCTTCCATCA	59.081	45.455	0.00	0.00	0.00	3.07
1875	3326	2.041755	GTCCCTTCTGTCAAATCCCCTT	59.958	50.000	0.00	0.00	0.00	3.95
1881	3332	4.145052	GGTTTCTGTCCCTTCTGTCAAAT	58.855	43.478	0.00	0.00	0.00	2.32
1918	3370	3.584406	ACCACATCTCTGTCCTCATTCAA	59.416	43.478	0.00	0.00	31.62	2.69
1940	3392	3.011144	TGCCCCTTGATTTAAGTCCATCA	59.989	43.478	0.00	0.00	34.45	3.07
2021	3473	2.554344	GGAAGCCAAGATGTACCACCAA	60.554	50.000	0.00	0.00	0.00	3.67
2028	3480	1.340017	GCACCAGGAAGCCAAGATGTA	60.340	52.381	0.00	0.00	0.00	2.29
2061	3519	4.404073	TGCACCTTGTCATTAACAAAACCT	59.596	37.500	0.00	0.00	46.95	3.50
2070	3528	5.252547	TCTAGCATTTGCACCTTGTCATTA	58.747	37.500	5.20	0.00	45.16	1.90
2091	3549	0.407528	TCTCACCTCCACTGCTCTCT	59.592	55.000	0.00	0.00	0.00	3.10
2104	3725	4.979197	CGTGCTCTTATCAATAGTCTCACC	59.021	45.833	0.00	0.00	0.00	4.02
2145	3766	4.272489	TCCTTCGCTTTGGATCATGAATT	58.728	39.130	0.00	0.00	0.00	2.17
2178	3799	1.219393	CGAAGCTGTCTCTTCCCCC	59.781	63.158	0.00	0.00	39.33	5.40
2180	3801	0.108567	GGTCGAAGCTGTCTCTTCCC	60.109	60.000	0.00	0.00	39.33	3.97
2196	3817	1.067416	TGTCGCCGATATGCTGGTC	59.933	57.895	0.00	0.00	0.00	4.02
2550	4175	1.065551	GGTTCGCCATAAATGCCAGTC	59.934	52.381	0.00	0.00	37.19	3.51
2884	4511	5.248477	TGGGCCTATGATCTGATTTACCTAC	59.752	44.000	4.53	0.00	0.00	3.18
2988	4615	0.322008	CCTCCACAGTTTCCTCAGCC	60.322	60.000	0.00	0.00	0.00	4.85
3117	4744	0.615331	TCAAGCGAGGCTCCTTCAAT	59.385	50.000	9.32	0.00	38.25	2.57
3134	4761	1.126488	CTATGCCTTCCTGAGCCTCA	58.874	55.000	0.00	0.00	0.00	3.86
3202	4830	3.281727	AGACAACTCCTTCTGTTGCAA	57.718	42.857	0.00	0.00	46.03	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.