AutoCloner

Multiple sequence alignment - TraesCS6D01G246400

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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	TraesCS6D01G246400	chr6D	100.000	4244	0	0	1	4244	348859735	348863978	0.000000e+00	7838
1	TraesCS6D01G246400	chr6D	92.170	3346	138	26	10	3273	349029767	349033070	0.000000e+00	4614
2	TraesCS6D01G246400	chr6D	94.418	1469	69	6	1936	3403	350204794	350203338	0.000000e+00	2246
3	TraesCS6D01G246400	chr6D	91.141	666	53	6	3355	4017	348995171	348995833	0.000000e+00	898
4	TraesCS6D01G246400	chr6D	91.156	588	43	8	3355	3940	349176230	349176810	0.000000e+00	789
5	TraesCS6D01G246400	chr6D	94.670	469	23	2	3410	3878	349033143	349033609	0.000000e+00	726
6	TraesCS6D01G246400	chr6D	91.228	513	37	7	3355	3862	348839116	348839625	0.000000e+00	691
7	TraesCS6D01G246400	chr6D	88.398	362	30	4	3883	4244	349035813	349036162	3.920000e-115	425
8	TraesCS6D01G246400	chr6D	90.602	266	21	3	3363	3626	349215284	349215547	2.430000e-92	350
9	TraesCS6D01G246400	chr6A	89.001	3664	211	77	10	3575	495155712	495152143	0.000000e+00	4357
10	TraesCS6D01G246400	chr6A	94.093	1930	105	3	1397	3320	493756075	493758001	0.000000e+00	2924
11	TraesCS6D01G246400	chr6A	93.235	1966	101	19	1444	3403	493842322	493844261	0.000000e+00	2865
12	TraesCS6D01G246400	chr6A	93.045	1898	107	17	1405	3290	494046784	494048668	0.000000e+00	2750
13	TraesCS6D01G246400	chr6A	89.104	569	56	6	3678	4242	494870782	494870216	0.000000e+00	702
14	TraesCS6D01G246400	chr6A	88.204	568	62	5	3679	4242	495144913	495144347	0.000000e+00	673
15	TraesCS6D01G246400	chr6A	84.695	673	59	13	935	1596	494881269	494880630	2.150000e-177	632
16	TraesCS6D01G246400	chr6A	83.161	772	41	31	36	754	494882027	494881292	1.300000e-174	623
17	TraesCS6D01G246400	chr6A	85.202	446	40	18	3136	3575	494878443	494878018	6.520000e-118	435
18	TraesCS6D01G246400	chr6A	96.330	109	4	0	3572	3680	494872969	494872861	3.370000e-41	180
19	TraesCS6D01G246400	chr6A	96.330	109	4	0	3572	3680	495147073	495146965	3.370000e-41	180
20	TraesCS6D01G246400	chr6B	92.295	2518	112	22	785	3276	530853004	530850543	0.000000e+00	3500
21	TraesCS6D01G246400	chr6B	93.211	2018	111	10	1397	3403	529773811	529775813	0.000000e+00	2944
22	TraesCS6D01G246400	chr6B	96.611	1682	53	3	1613	3290	529889861	529891542	0.000000e+00	2787
23	TraesCS6D01G246400	chr6B	82.059	1622	233	37	1648	3246	52086465	52088051	0.000000e+00	1330
24	TraesCS6D01G246400	chr6B	88.140	801	45	19	11	774	530853838	530853051	0.000000e+00	907
25	TraesCS6D01G246400	chr6B	88.516	566	56	9	3363	3927	530850493	530849936	0.000000e+00	676
26	TraesCS6D01G246400	chr6B	87.624	202	8	6	3355	3542	564063523	564063325	7.140000e-53	219

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	TraesCS6D01G246400	chr6D	348859735	348863978	4243	False	7838.000000	7838	100.000000	1	4244	1	chr6D.!!$F2	4243
1	TraesCS6D01G246400	chr6D	350203338	350204794	1456	True	2246.000000	2246	94.418000	1936	3403	1	chr6D.!!$R1	1467
2	TraesCS6D01G246400	chr6D	349029767	349036162	6395	False	1921.666667	4614	91.746000	10	4244	3	chr6D.!!$F6	4234
3	TraesCS6D01G246400	chr6D	348995171	348995833	662	False	898.000000	898	91.141000	3355	4017	1	chr6D.!!$F3	662
4	TraesCS6D01G246400	chr6D	349176230	349176810	580	False	789.000000	789	91.156000	3355	3940	1	chr6D.!!$F4	585
5	TraesCS6D01G246400	chr6D	348839116	348839625	509	False	691.000000	691	91.228000	3355	3862	1	chr6D.!!$F1	507
6	TraesCS6D01G246400	chr6A	495152143	495155712	3569	True	4357.000000	4357	89.001000	10	3575	1	chr6A.!!$R1	3565
7	TraesCS6D01G246400	chr6A	493756075	493758001	1926	False	2924.000000	2924	94.093000	1397	3320	1	chr6A.!!$F1	1923
8	TraesCS6D01G246400	chr6A	493842322	493844261	1939	False	2865.000000	2865	93.235000	1444	3403	1	chr6A.!!$F2	1959
9	TraesCS6D01G246400	chr6A	494046784	494048668	1884	False	2750.000000	2750	93.045000	1405	3290	1	chr6A.!!$F3	1885
10	TraesCS6D01G246400	chr6A	494878018	494882027	4009	True	563.333333	632	84.352667	36	3575	3	chr6A.!!$R3	3539
11	TraesCS6D01G246400	chr6A	494870216	494872969	2753	True	441.000000	702	92.717000	3572	4242	2	chr6A.!!$R2	670
12	TraesCS6D01G246400	chr6A	495144347	495147073	2726	True	426.500000	673	92.267000	3572	4242	2	chr6A.!!$R4	670
13	TraesCS6D01G246400	chr6B	529773811	529775813	2002	False	2944.000000	2944	93.211000	1397	3403	1	chr6B.!!$F2	2006
14	TraesCS6D01G246400	chr6B	529889861	529891542	1681	False	2787.000000	2787	96.611000	1613	3290	1	chr6B.!!$F3	1677
15	TraesCS6D01G246400	chr6B	530849936	530853838	3902	True	1694.333333	3500	89.650333	11	3927	3	chr6B.!!$R2	3916
16	TraesCS6D01G246400	chr6B	52086465	52088051	1586	False	1330.000000	1330	82.059000	1648	3246	1	chr6B.!!$F1	1598

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
230	271	0.107654	GTCCTCGAGGGGGTCAAATG	60.108	60.000	30.80	1.44	35.41	2.32	F
545	608	1.002134	CCACGCCCAGTTCAATCCT	60.002	57.895	0.00	0.00	0.00	3.24	F
1343	1586	0.737219	GCATCCACATCACAGCCTTC	59.263	55.000	0.00	0.00	0.00	3.46	F
2343	2602	0.238289	CCGCGTGCAAGAAAATCAGT	59.762	50.000	4.92	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1324	1567	0.737219	GAAGGCTGTGATGTGGATGC	59.263	55.000	0.00	0.00	3.91	R
1869	2127	1.153289	GGTGACGAGCATCATGCCT	60.153	57.895	5.84	46.52	4.75	R
3198	4201	0.530744	AGTTCTTGACGATGCCGCTA	59.469	50.000	0.00	39.95	4.26	R
3247	4250	0.745845	ATCTTGAAGCCTTGCGCGAT	60.746	50.000	12.10	44.76	4.58	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
74	79	4.843516	AGTCTGGATGAAGGAAGAAAGAGT	59.156	41.667	0.00	0.00	0.00	3.24
77	82	6.153680	GTCTGGATGAAGGAAGAAAGAGTAGA	59.846	42.308	0.00	0.00	0.00	2.59
78	83	6.726299	TCTGGATGAAGGAAGAAAGAGTAGAA	59.274	38.462	0.00	0.00	0.00	2.10
81	86	6.765512	GGATGAAGGAAGAAAGAGTAGAATGG	59.234	42.308	0.00	0.00	0.00	3.16
84	89	6.440647	TGAAGGAAGAAAGAGTAGAATGGCTA	59.559	38.462	0.00	0.00	0.00	3.93
106	112	7.201418	GGCTATACTTCGACACTTTTAGTTGAC	60.201	40.741	0.00	0.00	0.00	3.18
113	119	4.557296	CGACACTTTTAGTTGACGGAGGTA	60.557	45.833	0.00	0.00	0.00	3.08
169	192	4.097437	AGTCGAACGCATATGACCTTAGAA	59.903	41.667	6.97	0.00	31.75	2.10
171	194	3.489785	CGAACGCATATGACCTTAGAACC	59.510	47.826	6.97	0.00	0.00	3.62
209	232	1.693083	GGTGCATACTGACCGTTCGC	61.693	60.000	0.00	0.00	0.00	4.70
230	271	0.107654	GTCCTCGAGGGGGTCAAATG	60.108	60.000	30.80	1.44	35.41	2.32
264	305	3.503363	TCTTCAGCACACATTGATTGACC	59.497	43.478	0.00	0.00	0.00	4.02
330	385	4.759782	TCAGAAGCTCACCTATAAACTGC	58.240	43.478	0.00	0.00	0.00	4.40
351	406	6.701841	ACTGCATGGATACGAAAATACTAGTG	59.298	38.462	5.39	0.00	42.51	2.74
355	410	5.353938	TGGATACGAAAATACTAGTGCACC	58.646	41.667	14.63	0.00	42.51	5.01
416	475	4.283722	AGTTTGACCTACCATCGTTCTCTT	59.716	41.667	0.00	0.00	0.00	2.85
454	513	1.487976	TCATCATCCTTCACAGCCTCC	59.512	52.381	0.00	0.00	0.00	4.30
545	608	1.002134	CCACGCCCAGTTCAATCCT	60.002	57.895	0.00	0.00	0.00	3.24
627	720	1.606601	CTGTGGAGACCGGAGACCA	60.607	63.158	9.46	11.46	0.00	4.02
778	942	6.206243	CAGTTGTTGGTGAGAGAGATTTGATT	59.794	38.462	0.00	0.00	0.00	2.57
779	943	7.388776	CAGTTGTTGGTGAGAGAGATTTGATTA	59.611	37.037	0.00	0.00	0.00	1.75
780	944	8.105829	AGTTGTTGGTGAGAGAGATTTGATTAT	58.894	33.333	0.00	0.00	0.00	1.28
863	1027	1.082300	CGCAGCAGAAACACAGCAG	60.082	57.895	0.00	0.00	33.37	4.24
864	1028	1.371389	GCAGCAGAAACACAGCAGC	60.371	57.895	0.00	0.00	36.57	5.25
865	1029	1.082300	CAGCAGAAACACAGCAGCG	60.082	57.895	0.00	0.00	33.37	5.18
977	1179	1.912371	CTCAAACTTCCGCTTCCGCC	61.912	60.000	0.00	0.00	0.00	6.13
1121	1342	2.231716	TCGTTCTGGAAGGAGGATCA	57.768	50.000	0.00	0.00	29.82	2.92
1122	1343	2.103373	TCGTTCTGGAAGGAGGATCAG	58.897	52.381	0.00	0.00	29.82	2.90
1123	1344	1.827969	CGTTCTGGAAGGAGGATCAGT	59.172	52.381	0.00	0.00	36.25	3.41
1124	1345	3.024547	CGTTCTGGAAGGAGGATCAGTA	58.975	50.000	0.00	0.00	36.25	2.74
1125	1346	3.181485	CGTTCTGGAAGGAGGATCAGTAC	60.181	52.174	0.00	0.00	36.25	2.73
1126	1347	3.757947	TCTGGAAGGAGGATCAGTACA	57.242	47.619	0.00	0.00	36.25	2.90
1127	1348	4.061131	TCTGGAAGGAGGATCAGTACAA	57.939	45.455	0.00	0.00	36.25	2.41
1128	1349	4.624913	TCTGGAAGGAGGATCAGTACAAT	58.375	43.478	0.00	0.00	36.25	2.71
1129	1350	4.406972	TCTGGAAGGAGGATCAGTACAATG	59.593	45.833	0.00	0.00	36.25	2.82
1130	1351	4.361783	TGGAAGGAGGATCAGTACAATGA	58.638	43.478	0.00	0.00	36.25	2.57
1131	1352	4.782691	TGGAAGGAGGATCAGTACAATGAA	59.217	41.667	0.00	0.00	36.25	2.57
1132	1353	5.250543	TGGAAGGAGGATCAGTACAATGAAA	59.749	40.000	0.00	0.00	36.25	2.69
1133	1354	6.180472	GGAAGGAGGATCAGTACAATGAAAA	58.820	40.000	0.00	0.00	36.25	2.29
1134	1355	6.094186	GGAAGGAGGATCAGTACAATGAAAAC	59.906	42.308	0.00	0.00	36.25	2.43
1135	1356	6.126863	AGGAGGATCAGTACAATGAAAACA	57.873	37.500	0.00	0.00	36.25	2.83
1136	1357	6.725364	AGGAGGATCAGTACAATGAAAACAT	58.275	36.000	0.00	0.00	36.25	2.71
1137	1358	7.177878	AGGAGGATCAGTACAATGAAAACATT	58.822	34.615	0.00	0.00	36.25	2.71
1138	1359	7.671398	AGGAGGATCAGTACAATGAAAACATTT	59.329	33.333	0.00	0.00	36.25	2.32
1139	1360	8.306761	GGAGGATCAGTACAATGAAAACATTTT	58.693	33.333	0.00	0.00	36.25	1.82
1140	1361	9.346725	GAGGATCAGTACAATGAAAACATTTTC	57.653	33.333	9.68	9.68	40.26	2.29
1141	1362	8.306761	AGGATCAGTACAATGAAAACATTTTCC	58.693	33.333	13.21	0.00	44.48	3.13
1142	1363	7.273381	GGATCAGTACAATGAAAACATTTTCCG	59.727	37.037	13.21	5.90	44.48	4.30
1143	1364	7.265647	TCAGTACAATGAAAACATTTTCCGA	57.734	32.000	13.21	0.00	44.48	4.55
1144	1365	7.359595	TCAGTACAATGAAAACATTTTCCGAG	58.640	34.615	13.21	6.47	44.48	4.63
1266	1488	8.669243	ACTTACAAGAACACAGAGAAGAAAAAG	58.331	33.333	0.00	0.00	0.00	2.27
1324	1567	4.126437	TGCATATCCTAATCACACAACCG	58.874	43.478	0.00	0.00	0.00	4.44
1341	1584	1.450848	CGCATCCACATCACAGCCT	60.451	57.895	0.00	0.00	0.00	4.58
1343	1586	0.737219	GCATCCACATCACAGCCTTC	59.263	55.000	0.00	0.00	0.00	3.46
1430	1674	1.539388	TGGTTGCTAACAATTCCTGCG	59.461	47.619	0.00	0.00	38.27	5.18
1456	1700	3.942351	TCTGTTGCAGAGTCATGGG	57.058	52.632	0.00	0.00	35.39	4.00
1481	1725	4.713792	AAGGTTCAAGAGGATGACAGTT	57.286	40.909	0.00	0.00	0.00	3.16
1578	1828	9.502091	AAGCTACATGTTCATCTAACTGTTTTA	57.498	29.630	2.30	0.00	38.99	1.52
1579	1829	9.502091	AGCTACATGTTCATCTAACTGTTTTAA	57.498	29.630	2.30	0.00	38.99	1.52
1610	1865	8.149631	ACCAAAAATGTGGATTAAATGGAGAT	57.850	30.769	0.00	0.00	41.65	2.75
1628	1883	5.248477	TGGAGATGAGCTAGTGGTTTAACTT	59.752	40.000	0.00	0.00	0.00	2.66
1869	2127	0.467384	CCCTCGTCGTCTACCTCCTA	59.533	60.000	0.00	0.00	0.00	2.94
2317	2576	1.537397	AAGAGCCTCTGCCAGGTCA	60.537	57.895	0.00	0.00	45.61	4.02
2343	2602	0.238289	CCGCGTGCAAGAAAATCAGT	59.762	50.000	4.92	0.00	0.00	3.41
2490	2749	2.066393	CATGGAGGAGAGGCCGGAA	61.066	63.158	5.05	0.00	43.43	4.30
2748	3013	4.015406	AAGGTGATCGTGCCGGCA	62.015	61.111	29.03	29.03	0.00	5.69
3198	4201	1.068748	ACGCTCAACTTCGTCGTGTAT	60.069	47.619	0.00	0.00	33.09	2.29
3323	4349	6.028258	AGTAATTAGGAGTAGCCAGGTACT	57.972	41.667	9.18	9.18	40.02	2.73
3324	4350	6.442091	AGTAATTAGGAGTAGCCAGGTACTT	58.558	40.000	10.62	0.00	40.02	2.24
3325	4351	6.901857	AGTAATTAGGAGTAGCCAGGTACTTT	59.098	38.462	10.62	4.10	40.02	2.66
3353	4379	3.402628	TGAGAAACTTGTAGCCAGGTC	57.597	47.619	0.00	0.00	29.40	3.85
3392	4428	4.573201	CACAAGACACGGTAGGAAGAAAAA	59.427	41.667	0.00	0.00	0.00	1.94
3403	4439	8.491958	ACGGTAGGAAGAAAAATGTAGGATATT	58.508	33.333	0.00	0.00	0.00	1.28
3464	4504	7.504403	TGGCAGGAACATTTCTTTTGAATTTA	58.496	30.769	0.00	0.00	38.37	1.40
3471	4511	9.597999	GAACATTTCTTTTGAATTTATGTTGGC	57.402	29.630	10.23	0.00	42.58	4.52
3494	4534	4.399303	CGCCCTTTCTTGGATTGTAGAAAT	59.601	41.667	0.00	0.00	39.06	2.17
3690	6814	6.726764	GGATAGTCATGGTAAAGGTAGGATCT	59.273	42.308	0.00	0.00	0.00	2.75
3768	6893	9.675464	AAAATTGTGTCCTTTTCTATATCCGTA	57.325	29.630	0.00	0.00	0.00	4.02
3770	6895	7.414222	TTGTGTCCTTTTCTATATCCGTACT	57.586	36.000	0.00	0.00	0.00	2.73
3848	6974	7.014808	TCCCTAAATTTTCATTTGAAGTCGGTT	59.985	33.333	0.00	0.00	34.29	4.44
3917	9242	9.482627	AATTTGTTTAGCGTGGATTGAAAATTA	57.517	25.926	0.00	0.00	0.00	1.40
4008	9333	4.361971	ACAGCAGCAGCCCAGCAT	62.362	61.111	0.00	0.00	43.56	3.79
4029	9354	2.038975	AAGAGCTACAGGGCCCGA	59.961	61.111	18.44	4.83	0.00	5.14
4049	9374	2.847327	AGGCGGTGATCCTATTGATG	57.153	50.000	0.00	0.00	32.41	3.07
4078	9403	1.672356	GGCGACTGTGCACTGGAAT	60.672	57.895	25.15	6.84	36.28	3.01
4095	9420	2.872858	GGAATTGGATGGCGTTAGAGTC	59.127	50.000	0.00	0.00	0.00	3.36
4180	9505	3.384532	GACGGCGGGGGTAGACAA	61.385	66.667	13.24	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.202151	GGTGAGAGGATATTGTTGGGGAA	59.798	47.826	0.00	0.00	0.00	3.97
1	2	2.777692	GGTGAGAGGATATTGTTGGGGA	59.222	50.000	0.00	0.00	0.00	4.81
2	3	2.158608	GGGTGAGAGGATATTGTTGGGG	60.159	54.545	0.00	0.00	0.00	4.96
3	4	2.509548	TGGGTGAGAGGATATTGTTGGG	59.490	50.000	0.00	0.00	0.00	4.12
4	5	3.931907	TGGGTGAGAGGATATTGTTGG	57.068	47.619	0.00	0.00	0.00	3.77
5	6	5.256474	ACTTTGGGTGAGAGGATATTGTTG	58.744	41.667	0.00	0.00	0.00	3.33
6	7	5.520748	ACTTTGGGTGAGAGGATATTGTT	57.479	39.130	0.00	0.00	0.00	2.83
38	39	1.774254	TCCAGACTTTCCTTCTTGCCA	59.226	47.619	0.00	0.00	0.00	4.92
74	79	6.710597	AAGTGTCGAAGTATAGCCATTCTA	57.289	37.500	0.00	0.00	0.00	2.10
77	82	7.328737	ACTAAAAGTGTCGAAGTATAGCCATT	58.671	34.615	0.00	0.00	0.00	3.16
78	83	6.875076	ACTAAAAGTGTCGAAGTATAGCCAT	58.125	36.000	0.00	0.00	0.00	4.40
81	86	7.461156	CGTCAACTAAAAGTGTCGAAGTATAGC	60.461	40.741	0.00	0.00	0.00	2.97
84	89	5.632347	CCGTCAACTAAAAGTGTCGAAGTAT	59.368	40.000	0.00	0.00	0.00	2.12
106	112	1.754803	TGTTGAGCACCTATACCTCCG	59.245	52.381	0.00	0.00	0.00	4.63
113	119	2.867109	AGCACTTGTTGAGCACCTAT	57.133	45.000	0.00	0.00	34.66	2.57
169	192	2.978824	CTGAACGATGACCCCGGT	59.021	61.111	0.00	0.00	0.00	5.28
171	194	1.361668	CTTGCTGAACGATGACCCCG	61.362	60.000	0.00	0.00	0.00	5.73
209	232	4.753662	TGACCCCCTCGAGGACCG	62.754	72.222	33.39	20.17	38.24	4.79
330	385	6.073765	GGTGCACTAGTATTTTCGTATCCATG	60.074	42.308	17.98	0.00	0.00	3.66
362	417	4.170062	CGCCAAGGCTGCGTGATG	62.170	66.667	10.72	0.00	46.59	3.07
416	475	3.385193	TGAGCTGATTCTGTCAAACGA	57.615	42.857	0.00	0.00	36.14	3.85
627	720	1.818363	CATGCAGCCACTCATCGCT	60.818	57.895	0.00	0.00	35.10	4.93
778	942	8.449423	ACAGGATCCAGTGGCTAATAATAATA	57.551	34.615	15.82	0.00	0.00	0.98
779	943	7.335127	ACAGGATCCAGTGGCTAATAATAAT	57.665	36.000	15.82	0.00	0.00	1.28
780	944	6.763715	ACAGGATCCAGTGGCTAATAATAA	57.236	37.500	15.82	0.00	0.00	1.40
863	1027	3.117171	CTGTCTGTCTGCTGCCGC	61.117	66.667	0.00	0.00	0.00	6.53
864	1028	1.445754	CTCTGTCTGTCTGCTGCCG	60.446	63.158	0.00	0.00	0.00	5.69
865	1029	1.741032	GCTCTGTCTGTCTGCTGCC	60.741	63.158	0.00	0.00	0.00	4.85
977	1179	1.154131	CCGACGAGCTCTGTGTCTG	60.154	63.158	12.85	4.82	0.00	3.51
1127	1348	7.504924	TTGTACTCTCGGAAAATGTTTTCAT	57.495	32.000	17.21	0.00	46.34	2.57
1128	1349	6.928979	TTGTACTCTCGGAAAATGTTTTCA	57.071	33.333	17.21	0.73	46.34	2.69
1129	1350	7.581476	TCATTGTACTCTCGGAAAATGTTTTC	58.419	34.615	9.22	9.22	44.38	2.29
1130	1351	7.504924	TCATTGTACTCTCGGAAAATGTTTT	57.495	32.000	0.00	0.00	0.00	2.43
1131	1352	7.504924	TTCATTGTACTCTCGGAAAATGTTT	57.495	32.000	0.00	0.00	0.00	2.83
1132	1353	7.504924	TTTCATTGTACTCTCGGAAAATGTT	57.495	32.000	0.00	0.00	0.00	2.71
1133	1354	7.228706	AGTTTTCATTGTACTCTCGGAAAATGT	59.771	33.333	0.00	0.00	36.84	2.71
1134	1355	7.535258	CAGTTTTCATTGTACTCTCGGAAAATG	59.465	37.037	0.00	4.31	36.84	2.32
1135	1356	7.444183	TCAGTTTTCATTGTACTCTCGGAAAAT	59.556	33.333	0.00	0.00	36.84	1.82
1136	1357	6.764085	TCAGTTTTCATTGTACTCTCGGAAAA	59.236	34.615	0.00	0.00	33.37	2.29
1137	1358	6.285224	TCAGTTTTCATTGTACTCTCGGAAA	58.715	36.000	0.00	0.00	0.00	3.13
1138	1359	5.849510	TCAGTTTTCATTGTACTCTCGGAA	58.150	37.500	0.00	0.00	0.00	4.30
1139	1360	5.462530	TCAGTTTTCATTGTACTCTCGGA	57.537	39.130	0.00	0.00	0.00	4.55
1140	1361	6.539649	TTTCAGTTTTCATTGTACTCTCGG	57.460	37.500	0.00	0.00	0.00	4.63
1141	1362	6.521133	GCATTTCAGTTTTCATTGTACTCTCG	59.479	38.462	0.00	0.00	0.00	4.04
1142	1363	7.362662	TGCATTTCAGTTTTCATTGTACTCTC	58.637	34.615	0.00	0.00	0.00	3.20
1143	1364	7.275888	TGCATTTCAGTTTTCATTGTACTCT	57.724	32.000	0.00	0.00	0.00	3.24
1144	1365	7.928908	TTGCATTTCAGTTTTCATTGTACTC	57.071	32.000	0.00	0.00	0.00	2.59
1324	1567	0.737219	GAAGGCTGTGATGTGGATGC	59.263	55.000	0.00	0.00	0.00	3.91
1341	1584	2.707257	TCTGGATATGATGCTGCAGGAA	59.293	45.455	13.45	0.00	32.31	3.36
1343	1586	2.812591	GTTCTGGATATGATGCTGCAGG	59.187	50.000	17.12	0.00	32.31	4.85
1456	1700	2.489722	GTCATCCTCTTGAACCTTTGGC	59.510	50.000	0.00	0.00	0.00	4.52
1481	1725	1.993701	TTGAGGAGTGGCACCTGCAA	61.994	55.000	15.27	10.97	44.36	4.08
1579	1829	9.487790	CATTTAATCCACATTTTTGGTAACTGT	57.512	29.630	0.00	0.00	37.93	3.55
1610	1865	7.170320	CGAAACTTAAGTTAAACCACTAGCTCA	59.830	37.037	20.83	0.00	37.25	4.26
1869	2127	1.153289	GGTGACGAGCATCATGCCT	60.153	57.895	5.84	0.00	46.52	4.75
2292	2551	2.977178	CAGAGGCTCTTGAGCGGT	59.023	61.111	15.90	6.23	35.24	5.68
2490	2749	2.604686	TTCCAGGAGGTCGCTGCT	60.605	61.111	0.00	0.00	35.89	4.24
2673	2938	2.756283	AAGGAGGCTAGCGACGCT	60.756	61.111	27.45	27.45	43.41	5.07
3141	4144	2.093106	GCCCAGAAGAAGTAGTCGAGA	58.907	52.381	0.00	0.00	0.00	4.04
3198	4201	0.530744	AGTTCTTGACGATGCCGCTA	59.469	50.000	0.00	0.00	39.95	4.26
3247	4250	0.745845	ATCTTGAAGCCTTGCGCGAT	60.746	50.000	12.10	0.00	44.76	4.58
3334	4360	2.615747	GGGACCTGGCTACAAGTTTCTC	60.616	54.545	0.00	0.00	0.00	2.87
3353	4379	7.152645	GTGTCTTGTGTATATATGTACCTGGG	58.847	42.308	7.12	0.00	0.00	4.45
3403	4439	4.825085	ACGGCCATGAAAAGAAAAGAAGTA	59.175	37.500	2.24	0.00	0.00	2.24
3453	4493	3.370672	GGGCGCCAACATAAATTCAAAAG	59.629	43.478	30.85	0.00	0.00	2.27
3464	4504	1.535204	CCAAGAAAGGGCGCCAACAT	61.535	55.000	30.85	11.24	0.00	2.71
3471	4511	2.985896	TCTACAATCCAAGAAAGGGCG	58.014	47.619	0.00	0.00	0.00	6.13
3690	6814	7.073598	TGAATCCAGTCCCATCAAATAGGATAA	59.926	37.037	0.00	0.00	33.75	1.75
3768	6893	9.673454	GATTACGTATTTGAAAACTCCAAAAGT	57.327	29.630	0.00	0.00	41.10	2.66
3848	6974	9.877178	ATAAAAATAAAAACGGCCACATATTCA	57.123	25.926	2.24	0.00	0.00	2.57
3881	9206	9.217278	TCCACGCTAAACAAATTAGTACAAATA	57.783	29.630	0.00	0.00	42.58	1.40
3891	9216	7.961325	ATTTTCAATCCACGCTAAACAAATT	57.039	28.000	0.00	0.00	0.00	1.82
4008	9333	2.058595	GGCCCTGTAGCTCTTCGGA	61.059	63.158	0.00	0.00	0.00	4.55
4029	9354	2.439507	ACATCAATAGGATCACCGCCTT	59.560	45.455	0.00	0.00	41.83	4.35
4039	9364	3.700539	CCATGGTTGCAACATCAATAGGA	59.299	43.478	29.55	3.40	0.00	2.94
4049	9374	1.081242	CAGTCGCCATGGTTGCAAC	60.081	57.895	21.59	21.59	0.00	4.17
4078	9403	3.733236	CGACTCTAACGCCATCCAA	57.267	52.632	0.00	0.00	0.00	3.53
4130	9455	3.372730	GGAATTGCAGCACGGCCA	61.373	61.111	2.24	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.