AutoCloner

Multiple sequence alignment - TraesCS3D01G013300

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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	TraesCS3D01G013300	chr3D	100.000	3341	0	0	1	3341	4820489	4817149	0.000000e+00	6170.0
1	TraesCS3D01G013300	chr3D	98.891	451	5	0	2825	3275	4674525	4674075	0.000000e+00	806.0
2	TraesCS3D01G013300	chr3D	91.124	507	35	4	392	897	4677281	4676784	0.000000e+00	678.0
3	TraesCS3D01G013300	chr3D	92.401	329	24	1	1013	1340	4819307	4818979	5.050000e-128	468.0
4	TraesCS3D01G013300	chr3D	92.401	329	24	1	1183	1511	4819477	4819150	5.050000e-128	468.0
5	TraesCS3D01G013300	chr3D	73.818	592	135	19	1632	2219	1873064	1872489	2.020000e-52	217.0
6	TraesCS3D01G013300	chr3D	95.902	122	4	1	872	992	4674644	4674523	2.630000e-46	196.0
7	TraesCS3D01G013300	chr3D	92.222	90	6	1	2955	3043	9761604	9761693	3.500000e-25	126.0
8	TraesCS3D01G013300	chr3A	93.324	2202	87	21	1094	3249	10441555	10439368	0.000000e+00	3197.0
9	TraesCS3D01G013300	chr3A	93.823	2137	73	20	1183	3275	10474668	10472547	0.000000e+00	3160.0
10	TraesCS3D01G013300	chr3A	86.294	715	56	23	165	853	10442373	10441675	0.000000e+00	739.0
11	TraesCS3D01G013300	chr3A	84.615	481	49	9	870	1340	10474812	10474347	3.930000e-124	455.0
12	TraesCS3D01G013300	chr3A	89.458	332	22	6	1013	1340	10441466	10441144	1.120000e-109	407.0
13	TraesCS3D01G013300	chr3A	89.200	250	24	1	1265	1511	10441555	10441306	3.240000e-80	309.0
14	TraesCS3D01G013300	chr3A	73.684	589	129	20	1629	2210	7158416	7158985	4.370000e-49	206.0
15	TraesCS3D01G013300	chr3A	86.335	161	18	2	1354	1511	10474668	10474509	4.430000e-39	172.0
16	TraesCS3D01G013300	chrUn	85.466	2133	211	49	392	2481	236969569	236971645	0.000000e+00	2130.0
17	TraesCS3D01G013300	chrUn	86.853	928	76	30	2385	3275	35391339	35390421	0.000000e+00	996.0
18	TraesCS3D01G013300	chrUn	85.468	929	71	30	2385	3275	35985889	35984987	0.000000e+00	909.0
19	TraesCS3D01G013300	chrUn	91.707	627	42	7	2595	3218	35389033	35388414	0.000000e+00	861.0
20	TraesCS3D01G013300	chrUn	93.258	534	16	8	1966	2481	35392178	35391647	0.000000e+00	769.0
21	TraesCS3D01G013300	chrUn	92.705	329	23	1	1183	1511	236970151	236970478	1.080000e-129	473.0
22	TraesCS3D01G013300	chrUn	89.666	329	33	1	1013	1340	236970321	236970649	5.160000e-113	418.0
23	TraesCS3D01G013300	chrUn	87.912	364	31	7	568	919	36023024	36023386	1.850000e-112	416.0
24	TraesCS3D01G013300	chrUn	95.477	199	8	1	2483	2680	35391608	35391410	1.930000e-82	316.0
25	TraesCS3D01G013300	chrUn	79.202	351	66	5	1	345	35408370	35408021	1.550000e-58	237.0
26	TraesCS3D01G013300	chrUn	78.342	374	74	4	1	368	236969083	236969455	5.570000e-58	235.0
27	TraesCS3D01G013300	chrUn	95.270	148	7	0	2484	2631	236971993	236972140	5.570000e-58	235.0
28	TraesCS3D01G013300	chrUn	96.124	129	5	0	3213	3341	35588702	35588830	9.390000e-51	211.0
29	TraesCS3D01G013300	chrUn	87.898	157	10	2	915	1062	302609580	302609424	3.430000e-40	176.0
30	TraesCS3D01G013300	chrUn	88.312	154	9	2	915	1059	340428023	340428176	3.430000e-40	176.0
31	TraesCS3D01G013300	chrUn	91.139	79	7	0	3097	3175	35389032	35388954	1.270000e-19	108.0
32	TraesCS3D01G013300	chrUn	93.443	61	4	0	2483	2543	236971685	236971745	1.280000e-14	91.6
33	TraesCS3D01G013300	chrUn	97.872	47	1	0	3276	3322	35390206	35390160	7.680000e-12	82.4
34	TraesCS3D01G013300	chrUn	97.500	40	0	1	2642	2680	35985999	35985960	2.150000e-07	67.6
35	TraesCS3D01G013300	chr7D	77.124	459	82	18	1772	2223	552955947	552955505	9.260000e-61	244.0
36	TraesCS3D01G013300	chr7D	75.000	264	45	11	414	675	239515417	239515173	5.900000e-18	102.0
37	TraesCS3D01G013300	chr7B	75.045	561	114	21	1686	2237	598469156	598468613	1.550000e-58	237.0
38	TraesCS3D01G013300	chr7B	75.506	494	92	20	1740	2223	644530431	644529957	7.260000e-52	215.0
39	TraesCS3D01G013300	chr7B	74.126	286	64	7	11	288	705129584	705129301	3.520000e-20	110.0
40	TraesCS3D01G013300	chr7A	76.471	459	85	18	1772	2223	638702476	638702034	9.330000e-56	228.0
41	TraesCS3D01G013300	chr4B	76.899	316	56	11	417	726	587467938	587467634	2.670000e-36	163.0
42	TraesCS3D01G013300	chr3B	91.765	85	4	3	3194	3276	154605133	154605050	7.570000e-22	115.0
43	TraesCS3D01G013300	chr4A	92.405	79	4	2	3195	3272	737235902	737235979	9.800000e-21	111.0
44	TraesCS3D01G013300	chr2A	91.139	79	5	2	3195	3272	402688279	402688356	4.560000e-19	106.0
45	TraesCS3D01G013300	chr5B	77.876	113	24	1	410	521	572941430	572941318	5.980000e-08	69.4

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	TraesCS3D01G013300	chr3D	4817149	4820489	3340	True	2368.666667	6170	94.934000	1	3341	3	chr3D.!!$R3	3340
1	TraesCS3D01G013300	chr3D	4674075	4677281	3206	True	560.000000	806	95.305667	392	3275	3	chr3D.!!$R2	2883
2	TraesCS3D01G013300	chr3D	1872489	1873064	575	True	217.000000	217	73.818000	1632	2219	1	chr3D.!!$R1	587
3	TraesCS3D01G013300	chr3A	10472547	10474812	2265	True	1262.333333	3160	88.257667	870	3275	3	chr3A.!!$R2	2405
4	TraesCS3D01G013300	chr3A	10439368	10442373	3005	True	1163.000000	3197	89.569000	165	3249	4	chr3A.!!$R1	3084
5	TraesCS3D01G013300	chr3A	7158416	7158985	569	False	206.000000	206	73.684000	1629	2210	1	chr3A.!!$F1	581
6	TraesCS3D01G013300	chrUn	236969083	236972140	3057	False	597.100000	2130	89.148667	1	2631	6	chrUn.!!$F4	2630
7	TraesCS3D01G013300	chrUn	35388414	35392178	3764	True	522.066667	996	92.717667	1966	3322	6	chrUn.!!$R3	1356
8	TraesCS3D01G013300	chrUn	35984987	35985999	1012	True	488.300000	909	91.484000	2385	3275	2	chrUn.!!$R4	890
9	TraesCS3D01G013300	chr7B	598468613	598469156	543	True	237.000000	237	75.045000	1686	2237	1	chr7B.!!$R1	551

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	End Stability	Orientation
310	316	0.108520	GAACCAACGACGAGGCCATA	60.109	55.000	5.01	2.74	F
581	693	0.895100	GAGCAACATGTCAAGGGGCA	60.895	55.000	0.00	5.36	F
995	3362	1.003580	TCGAAATCTGAAGCTTGCCCT	59.996	47.619	2.10	5.19	F
1939	4527	1.038681	TATGAAGGCCTACGACCGCA	61.039	55.000	5.16	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1559	4132	1.137086	CCCTGGACGACGATCTTGATT	59.863	52.381	0.00	0.00	0.00	2.57	R
1939	4527	1.183676	AGGTCGTAGGAGTTGCCGTT	61.184	55.000	0.00	0.00	43.43	4.44	R
2128	4716	1.885850	GGTTGTCCGCGTTGTCAGT	60.886	57.895	4.92	0.00	0.00	3.41	R
3320	8137	1.878088	GAGTCACATATGGCCATGCTG	59.122	52.381	29.04	24.91	0.00	4.41	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
25	26	3.376935	CTTCTCGAGCATGGCGGGT	62.377	63.158	7.81	0.00	0.00	5.28
43	44	1.228184	TAGCGGATCCGAGTCCTCC	60.228	63.158	37.64	17.49	42.83	4.30
44	45	1.991339	TAGCGGATCCGAGTCCTCCA	61.991	60.000	37.64	8.05	42.83	3.86
47	48	1.857318	CGGATCCGAGTCCTCCATCG	61.857	65.000	30.62	0.00	42.83	3.84
71	72	2.158986	CGATATGCCCCAGGATCTCATC	60.159	54.545	0.00	0.00	0.00	2.92
85	87	4.820744	CATCCCACCGGGCCCAAG	62.821	72.222	24.92	15.59	43.94	3.61
94	96	2.922234	GGGCCCAAGGAGGAGATG	59.078	66.667	19.95	0.00	41.22	2.90
99	101	1.144936	CCAAGGAGGAGATGGTCGC	59.855	63.158	0.00	0.00	41.22	5.19
101	103	2.066999	AAGGAGGAGATGGTCGCCC	61.067	63.158	0.00	0.00	37.00	6.13
109	111	2.045438	ATGGTCGCCCGCATTTCA	60.045	55.556	0.00	0.00	0.00	2.69
110	112	2.051804	GATGGTCGCCCGCATTTCAG	62.052	60.000	0.00	0.00	0.00	3.02
117	119	2.331893	CCCGCATTTCAGTTCGCCA	61.332	57.895	0.00	0.00	0.00	5.69
120	122	1.866237	GCATTTCAGTTCGCCACGA	59.134	52.632	0.00	0.00	0.00	4.35
122	124	1.148310	CATTTCAGTTCGCCACGACT	58.852	50.000	0.00	0.00	34.89	4.18
124	126	1.495584	TTTCAGTTCGCCACGACTGC	61.496	55.000	11.90	0.00	36.12	4.40
137	139	1.519719	GACTGCGAGGAGAATGCCT	59.480	57.895	0.00	0.00	42.17	4.75
142	144	0.809241	GCGAGGAGAATGCCTGACAG	60.809	60.000	0.00	0.00	38.73	3.51
143	145	0.534412	CGAGGAGAATGCCTGACAGT	59.466	55.000	0.93	0.00	38.73	3.55
145	147	1.552337	GAGGAGAATGCCTGACAGTGA	59.448	52.381	0.00	0.00	38.73	3.41
146	148	2.170187	GAGGAGAATGCCTGACAGTGAT	59.830	50.000	0.00	0.00	38.73	3.06
148	150	2.200067	GAGAATGCCTGACAGTGATCG	58.800	52.381	0.00	0.00	0.00	3.69
151	153	0.176680	ATGCCTGACAGTGATCGGAC	59.823	55.000	0.00	0.00	0.00	4.79
153	155	0.179124	GCCTGACAGTGATCGGACTC	60.179	60.000	0.00	0.00	0.00	3.36
155	157	0.805614	CTGACAGTGATCGGACTCGT	59.194	55.000	0.00	0.00	37.69	4.18
267	269	4.456806	GTGTCTGAACGCCTTGGT	57.543	55.556	0.00	0.00	0.00	3.67
288	294	2.574929	CGTGCAGCCCCTACGTTA	59.425	61.111	0.00	0.00	33.48	3.18
310	316	0.108520	GAACCAACGACGAGGCCATA	60.109	55.000	5.01	0.00	0.00	2.74
466	575	1.070786	GTGAAGGCTTCGGACACCA	59.929	57.895	21.42	0.51	0.00	4.17
501	610	2.048222	ATGTGAGACGGTGGCACG	60.048	61.111	12.17	9.61	35.37	5.34
516	625	2.641559	ACGTCGAGTCCCGTGAAC	59.358	61.111	0.00	0.00	39.75	3.18
517	626	2.501222	CGTCGAGTCCCGTGAACG	60.501	66.667	0.00	0.00	39.75	3.95
581	693	0.895100	GAGCAACATGTCAAGGGGCA	60.895	55.000	0.00	0.00	0.00	5.36
646	765	5.741011	TCCGCTTAGATTAGGTTTGACATT	58.259	37.500	0.00	0.00	0.00	2.71
651	770	7.260603	GCTTAGATTAGGTTTGACATTGCATT	58.739	34.615	0.00	0.00	0.00	3.56
659	785	7.424227	AGGTTTGACATTGCATTTAATTGTG	57.576	32.000	0.00	0.00	0.00	3.33
685	811	7.122650	GTGGATTTGAGGTTTCATAATTGAGGA	59.877	37.037	0.00	0.00	32.27	3.71
694	820	6.183360	GGTTTCATAATTGAGGAATGCGGTTA	60.183	38.462	0.00	0.00	32.27	2.85
761	905	1.532316	TCGGAGTTTGAGGGGTCGT	60.532	57.895	0.00	0.00	0.00	4.34
762	906	1.080025	CGGAGTTTGAGGGGTCGTC	60.080	63.158	0.00	0.00	0.00	4.20
784	928	2.953466	TGGTGTACCGAGAATGTAGC	57.047	50.000	0.00	0.00	39.43	3.58
799	943	5.595133	AGAATGTAGCTGGTCTTAGAGTACC	59.405	44.000	0.00	0.00	36.24	3.34
850	1042	4.201685	CCAACGCCTAGTATCAAAGTTTCG	60.202	45.833	0.00	0.00	0.00	3.46
983	3350	1.468520	CCACAACCGCATTCGAAATCT	59.531	47.619	0.00	0.00	38.10	2.40
984	3351	2.508867	CACAACCGCATTCGAAATCTG	58.491	47.619	0.00	0.00	38.10	2.90
985	3352	2.159430	CACAACCGCATTCGAAATCTGA	59.841	45.455	0.00	0.00	38.10	3.27
989	3356	1.667724	CCGCATTCGAAATCTGAAGCT	59.332	47.619	0.00	0.00	38.10	3.74
990	3357	2.096496	CCGCATTCGAAATCTGAAGCTT	59.904	45.455	0.00	0.00	38.10	3.74
991	3358	3.096461	CGCATTCGAAATCTGAAGCTTG	58.904	45.455	2.10	0.00	38.10	4.01
992	3359	2.850647	GCATTCGAAATCTGAAGCTTGC	59.149	45.455	2.10	0.00	0.00	4.01
993	3360	3.432782	CATTCGAAATCTGAAGCTTGCC	58.567	45.455	2.10	0.00	0.00	4.52
994	3361	1.453155	TCGAAATCTGAAGCTTGCCC	58.547	50.000	2.10	0.00	0.00	5.36
995	3362	1.003580	TCGAAATCTGAAGCTTGCCCT	59.996	47.619	2.10	0.00	0.00	5.19
1018	3414	4.169271	TGGACGACCAAGACTCGT	57.831	55.556	3.49	0.00	46.86	4.18
1022	3418	4.436653	CGACCAAGACTCGTCGTC	57.563	61.111	14.01	0.38	45.20	4.20
1034	3430	4.867599	GTCGTCGGCCGGTGGATC	62.868	72.222	27.83	7.73	37.11	3.36
1036	3432	4.143333	CGTCGGCCGGTGGATCTT	62.143	66.667	27.83	0.00	0.00	2.40
1037	3433	2.202892	GTCGGCCGGTGGATCTTC	60.203	66.667	27.83	1.14	0.00	2.87
1038	3434	3.467226	TCGGCCGGTGGATCTTCC	61.467	66.667	27.83	0.00	36.96	3.46
1039	3435	4.891727	CGGCCGGTGGATCTTCCG	62.892	72.222	20.10	17.55	40.17	4.30
1043	3439	2.107141	CGGTGGATCTTCCGGCTC	59.893	66.667	16.99	0.00	40.17	4.70
1044	3440	2.506472	GGTGGATCTTCCGGCTCC	59.494	66.667	0.00	0.44	40.17	4.70
1045	3441	2.066999	GGTGGATCTTCCGGCTCCT	61.067	63.158	0.00	0.00	40.17	3.69
1046	3442	1.443828	GTGGATCTTCCGGCTCCTC	59.556	63.158	0.00	0.00	40.17	3.71
1047	3443	2.127869	TGGATCTTCCGGCTCCTCG	61.128	63.158	0.00	0.00	40.17	4.63
1059	3455	3.071206	TCCTCGGCAGGAGAGCAC	61.071	66.667	5.65	0.00	44.75	4.40
1060	3456	4.504916	CCTCGGCAGGAGAGCACG	62.505	72.222	5.65	0.00	46.23	5.34
1061	3457	3.443925	CTCGGCAGGAGAGCACGA	61.444	66.667	0.00	0.00	46.23	4.35
1062	3458	3.408501	CTCGGCAGGAGAGCACGAG	62.409	68.421	10.63	10.63	46.23	4.18
1063	3459	4.504916	CGGCAGGAGAGCACGAGG	62.505	72.222	0.00	0.00	35.83	4.63
1064	3460	4.828925	GGCAGGAGAGCACGAGGC	62.829	72.222	0.00	0.00	45.30	4.70
1065	3461	4.828925	GCAGGAGAGCACGAGGCC	62.829	72.222	0.00	0.00	46.50	5.19
1066	3462	4.504916	CAGGAGAGCACGAGGCCG	62.505	72.222	0.00	0.00	46.50	6.13
1067	3463	4.742649	AGGAGAGCACGAGGCCGA	62.743	66.667	0.00	0.00	46.50	5.54
1068	3464	4.200283	GGAGAGCACGAGGCCGAG	62.200	72.222	0.00	0.00	46.50	4.63
1069	3465	4.200283	GAGAGCACGAGGCCGAGG	62.200	72.222	0.00	0.00	46.50	4.63
1146	3542	1.238439	CCGGCAAGAAGAGCAAGAAA	58.762	50.000	0.00	0.00	0.00	2.52
1151	3547	2.287915	GCAAGAAGAGCAAGAAACGTCA	59.712	45.455	0.00	0.00	0.00	4.35
1702	4281	3.125573	CGGACGACCTCTCGCTGA	61.126	66.667	1.72	0.00	44.33	4.26
1897	4485	1.294659	CGTGGAGGAGAAGCAGTTGC	61.295	60.000	0.00	0.00	42.49	4.17
1920	4508	2.842496	TCAGAAGCAGATCAAGGTGGAT	59.158	45.455	0.00	0.00	0.00	3.41
1939	4527	1.038681	TATGAAGGCCTACGACCGCA	61.039	55.000	5.16	0.00	0.00	5.69
2137	4728	1.846648	GTGAGCGTCACTGACAACG	59.153	57.895	9.84	0.00	43.73	4.10
2143	4734	1.590525	GTCACTGACAACGCGGACA	60.591	57.895	12.47	3.78	32.09	4.02
2144	4735	1.142097	TCACTGACAACGCGGACAA	59.858	52.632	12.47	0.00	0.00	3.18
2237	4831	4.778143	GGCGTCATTGCCGGGAGT	62.778	66.667	2.18	0.00	46.75	3.85
2383	4997	2.893637	CCAGTTCACGATCGATTTCCT	58.106	47.619	24.34	7.63	0.00	3.36
2481	5102	5.795972	ACATTGATTGGCATGTTGATTTGA	58.204	33.333	0.00	0.00	0.00	2.69
2571	5241	5.973565	GGTCTTGTGAGTTTGAATTTGTGAG	59.026	40.000	0.00	0.00	0.00	3.51
2574	5244	6.826231	TCTTGTGAGTTTGAATTTGTGAGGTA	59.174	34.615	0.00	0.00	0.00	3.08
2615	5285	1.597663	GTTTCCATGCCCGTCGATTAG	59.402	52.381	0.00	0.00	0.00	1.73
3287	6591	7.559897	TGACCAACTTTATAAAGATGATTCCCC	59.440	37.037	27.81	14.48	40.11	4.81
3320	8137	5.401550	TGCGAGAATTTGTCATGGATTTTC	58.598	37.500	0.00	0.00	0.00	2.29
3321	8138	5.048154	TGCGAGAATTTGTCATGGATTTTCA	60.048	36.000	0.00	0.00	0.00	2.69
3335	8152	3.322828	GGATTTTCAGCATGGCCATATGT	59.677	43.478	20.30	2.44	36.16	2.29
3339	8156	1.491754	TCAGCATGGCCATATGTGACT	59.508	47.619	20.30	6.55	36.16	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	1.228184	GGAGGACTCGGATCCGCTA	60.228	63.158	29.62	12.52	44.22	4.26
48	49	1.078143	GATCCTGGGGCATATCGGC	60.078	63.158	0.00	0.00	40.20	5.54
49	50	0.539051	GAGATCCTGGGGCATATCGG	59.461	60.000	0.00	0.00	0.00	4.18
50	51	1.269958	TGAGATCCTGGGGCATATCG	58.730	55.000	0.00	0.00	0.00	2.92
76	77	2.770048	ATCTCCTCCTTGGGCCCG	60.770	66.667	19.37	2.86	36.20	6.13
99	101	2.331893	TGGCGAACTGAAATGCGGG	61.332	57.895	0.00	0.00	0.00	6.13
101	103	1.509787	CGTGGCGAACTGAAATGCG	60.510	57.895	0.00	0.00	0.00	4.73
117	119	1.153745	GCATTCTCCTCGCAGTCGT	60.154	57.895	0.00	0.00	36.96	4.34
120	122	1.220206	CAGGCATTCTCCTCGCAGT	59.780	57.895	0.00	0.00	33.25	4.40
122	124	1.219124	GTCAGGCATTCTCCTCGCA	59.781	57.895	0.00	0.00	33.25	5.10
124	126	0.534412	ACTGTCAGGCATTCTCCTCG	59.466	55.000	4.53	0.00	33.25	4.63
137	139	1.199327	GAACGAGTCCGATCACTGTCA	59.801	52.381	0.00	0.00	37.50	3.58
142	144	0.802607	GGCAGAACGAGTCCGATCAC	60.803	60.000	0.00	0.00	39.62	3.06
143	145	1.511305	GGCAGAACGAGTCCGATCA	59.489	57.895	0.00	0.00	39.62	2.92
145	147	2.044555	TCGGCAGAACGAGTCCGAT	61.045	57.895	0.00	0.00	44.99	4.18
153	155	1.328680	CAATGGATTCTCGGCAGAACG	59.671	52.381	2.25	0.00	41.64	3.95
155	157	1.382522	GCAATGGATTCTCGGCAGAA	58.617	50.000	2.63	2.63	43.06	3.02
267	269	3.702048	GTAGGGGCTGCACGTCCA	61.702	66.667	0.00	0.00	39.98	4.02
288	294	1.445582	GCCTCGTCGTTGGTTCGAT	60.446	57.895	8.35	0.00	41.78	3.59
349	359	1.967535	CTCCCTCTGCTTGACACGA	59.032	57.895	0.00	0.00	0.00	4.35
466	575	3.118112	CACATGCCCTACTCTTCCTCATT	60.118	47.826	0.00	0.00	0.00	2.57
517	626	3.343421	GTCACGCACCGGTTCACC	61.343	66.667	2.97	0.00	0.00	4.02
533	642	1.139058	GGGATTGAGTAGGACATGCGT	59.861	52.381	0.00	0.00	0.00	5.24
626	738	6.194796	TGCAATGTCAAACCTAATCTAAGC	57.805	37.500	0.00	0.00	0.00	3.09
646	765	6.164876	CCTCAAATCCACACAATTAAATGCA	58.835	36.000	0.00	0.00	0.00	3.96
651	770	7.353414	TGAAACCTCAAATCCACACAATTAA	57.647	32.000	0.00	0.00	0.00	1.40
659	785	7.122650	TCCTCAATTATGAAACCTCAAATCCAC	59.877	37.037	0.00	0.00	34.49	4.02
744	888	1.080025	GACGACCCCTCAAACTCCG	60.080	63.158	0.00	0.00	0.00	4.63
761	905	4.619863	GCTACATTCTCGGTACACCAAAGA	60.620	45.833	0.00	0.00	35.14	2.52
762	906	3.617263	GCTACATTCTCGGTACACCAAAG	59.383	47.826	0.00	0.00	35.14	2.77
784	928	7.042335	CCAAAACATAGGTACTCTAAGACCAG	58.958	42.308	0.00	0.00	41.75	4.00
799	943	6.537453	TCTCTCCTCTCTTCCAAAACATAG	57.463	41.667	0.00	0.00	0.00	2.23
850	1042	2.280186	CGGCGGCAGGAGATAACC	60.280	66.667	10.53	0.00	0.00	2.85
983	3350	1.228956	ATGGCAAGGGCAAGCTTCA	60.229	52.632	0.00	0.00	42.43	3.02
984	3351	1.217244	CATGGCAAGGGCAAGCTTC	59.783	57.895	0.00	0.00	42.43	3.86
985	3352	2.288025	CCATGGCAAGGGCAAGCTT	61.288	57.895	0.00	0.00	42.43	3.74
989	3356	2.676121	CGTCCATGGCAAGGGCAA	60.676	61.111	14.36	0.00	42.43	4.52
990	3357	3.645660	TCGTCCATGGCAAGGGCA	61.646	61.111	14.36	0.00	43.71	5.36
991	3358	3.134127	GTCGTCCATGGCAAGGGC	61.134	66.667	6.96	6.03	40.13	5.19
992	3359	2.438434	GGTCGTCCATGGCAAGGG	60.438	66.667	6.96	5.53	0.00	3.95
993	3360	1.303236	TTGGTCGTCCATGGCAAGG	60.303	57.895	6.96	1.41	43.91	3.61
994	3361	0.321564	TCTTGGTCGTCCATGGCAAG	60.322	55.000	18.09	18.09	43.91	4.01
995	3362	0.605319	GTCTTGGTCGTCCATGGCAA	60.605	55.000	6.96	4.13	43.91	4.52
1019	3415	4.143333	AAGATCCACCGGCCGACG	62.143	66.667	30.73	17.26	43.80	5.12
1020	3416	2.202892	GAAGATCCACCGGCCGAC	60.203	66.667	30.73	10.34	0.00	4.79
1021	3417	3.467226	GGAAGATCCACCGGCCGA	61.467	66.667	30.73	6.75	36.28	5.54
1022	3418	4.891727	CGGAAGATCCACCGGCCG	62.892	72.222	21.04	21.04	44.59	6.13
1027	3423	2.034048	GAGGAGCCGGAAGATCCACC	62.034	65.000	5.05	0.00	38.70	4.61
1028	3424	1.443828	GAGGAGCCGGAAGATCCAC	59.556	63.158	5.05	1.00	38.70	4.02
1029	3425	2.127869	CGAGGAGCCGGAAGATCCA	61.128	63.158	5.05	0.00	38.70	3.41
1030	3426	2.731374	CGAGGAGCCGGAAGATCC	59.269	66.667	5.05	6.47	37.13	3.36
1043	3439	4.504916	CGTGCTCTCCTGCCGAGG	62.505	72.222	0.00	0.00	39.30	4.63
1044	3440	3.408501	CTCGTGCTCTCCTGCCGAG	62.409	68.421	10.85	10.85	42.39	4.63
1045	3441	3.443925	CTCGTGCTCTCCTGCCGA	61.444	66.667	0.00	0.00	35.55	5.54
1046	3442	4.504916	CCTCGTGCTCTCCTGCCG	62.505	72.222	0.00	0.00	0.00	5.69
1047	3443	4.828925	GCCTCGTGCTCTCCTGCC	62.829	72.222	0.00	0.00	36.87	4.85
1048	3444	4.828925	GGCCTCGTGCTCTCCTGC	62.829	72.222	0.00	0.00	40.92	4.85
1049	3445	4.504916	CGGCCTCGTGCTCTCCTG	62.505	72.222	0.00	0.00	40.92	3.86
1050	3446	4.742649	TCGGCCTCGTGCTCTCCT	62.743	66.667	0.00	0.00	40.92	3.69
1051	3447	4.200283	CTCGGCCTCGTGCTCTCC	62.200	72.222	0.00	0.00	40.92	3.71
1052	3448	4.200283	CCTCGGCCTCGTGCTCTC	62.200	72.222	0.00	0.00	40.92	3.20
1129	3525	1.604278	ACGTTTCTTGCTCTTCTTGCC	59.396	47.619	0.00	0.00	0.00	4.52
1559	4132	1.137086	CCCTGGACGACGATCTTGATT	59.863	52.381	0.00	0.00	0.00	2.57
1702	4281	2.099831	GACGACGCCGATCGACTT	59.900	61.111	18.66	0.00	45.13	3.01
1724	4303	2.723273	TCAGGATCTCGTGCAGACTTA	58.277	47.619	0.00	0.00	32.26	2.24
1897	4485	3.008330	CCACCTTGATCTGCTTCTGAAG	58.992	50.000	13.02	13.02	0.00	3.02
1900	4488	2.775911	TCCACCTTGATCTGCTTCTG	57.224	50.000	0.00	0.00	0.00	3.02
1939	4527	1.183676	AGGTCGTAGGAGTTGCCGTT	61.184	55.000	0.00	0.00	43.43	4.44
2128	4716	1.885850	GGTTGTCCGCGTTGTCAGT	60.886	57.895	4.92	0.00	0.00	3.41
2383	4997	4.986659	GCCTACTAGTGAAAACAGAACGAA	59.013	41.667	5.39	0.00	0.00	3.85
2571	5241	6.525280	ACGTTTGCAAATTCGATAAACATACC	59.475	34.615	23.86	2.87	32.36	2.73
2574	5244	7.358848	GGAAACGTTTGCAAATTCGATAAACAT	60.359	33.333	25.29	2.23	32.36	2.71
2615	5285	6.595772	ACTCATCTTTGCGACTCAAATATC	57.404	37.500	0.00	0.00	43.14	1.63
3320	8137	1.878088	GAGTCACATATGGCCATGCTG	59.122	52.381	29.04	24.91	0.00	4.41
3321	8138	2.267174	GAGTCACATATGGCCATGCT	57.733	50.000	29.04	12.67	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.