Locus 4457

Sequence ID	2L_DroMel_CAF1
Location	12,802,714 – 12,802,817
Length	103
Max. P	0.993189

overview

Window 7

Location	12,802,714 – 12,802,817
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-19.96
Consensus MFE	-13.52
Energy contribution	-14.08
Covariance contribution	0.56
Combinations/Pair	1.25
Mean z-score	-2.63
Structure conservation index	0.68
SVM decision value	2.38
SVM RNA-class probability	0.993189
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12802714 103 + 22407834
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCUGGUAAUGCGCCGCCUCUUCUCGCGGCCAAAAGGAUGCU--UC---------------CCCAUCCCCACAUACACUCCUUUAUUUU
....................(((((((....)))(((...((.(((((........)))))))...(((((..--..---------------..)))))))))))).............. ( -20.20)
>DroPse_CAF1 96182 114 + 1
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCUGGUAAUGUGCCGCCUCUCAUCGCUGCCAAACCCAUUCGCAUUUUAUUCCUGGCUUUGCCCACCGCCCCCCUCGCCCCUC------
.......................(((.....((((((...((.((.((........)).))))...)))...)))..........(((..........)))......)))....------ ( -15.40)
>DroSec_CAF1 68345 103 + 1
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCUGGUAAUGCGCCGCCUCUUCUCGCGGCCAAAAGGAUGCU--AC---------------CCCAUCCUCACAUAUACCCCUUUAUUUU
.......................((((....))))((((.((.(((((........)))))))..((((((..--..---------------..))))))......)))).......... ( -22.40)
>DroSim_CAF1 70522 103 + 1
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCUGGUAAUGCGCCGCCUCUUCUCGCGGCCAAAAGGAUGCU--AC---------------CCCAUCCCCACAUAUACCCCUUUAUUUU
.......................((((....))))((((.((.(((((........)))))))...(((((..--..---------------..))))).......)))).......... ( -21.40)
>DroYak_CAF1 71296 106 + 1
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCCGCUGAUGCGCCGCCUCUUCUCGCGGCCAAAAGGAUGCC--UCUCAU--------AAACCCACCCACCCACACACUCCUUU----U
.......................((((((((((..((....))(((((........)))))))))))..))))--......--------..........................----. ( -20.40)
>consensus
CUCAUUUUAAUACACAUUUUUAUGGCACUUUUGCUGGUAAUGCGCCGCCUCUUCUCGCGGCCAAAAGGAUGCU__UC_______________CCCAUCCCCACAUACACCCCUUUAUUUU
.......................((((....))))((((.((.(((((........)))))))...(((((.......................))))).......)))).......... (-13.52 = -14.08 +   0.56)

alignment

secondary structure

dotplot

Window 8

Location	12,802,714 – 12,802,817
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.83
Mean single sequence MFE	-27.12
Consensus MFE	-16.26
Energy contribution	-17.06
Covariance contribution	0.80
Combinations/Pair	1.19
Mean z-score	-2.08
Structure conservation index	0.60
SVM decision value	0.97
SVM RNA-class probability	0.892063
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12802714 103 - 22407834
AAAAUAAAGGAGUGUAUGUGGGGAUGGG---------------GA--AGCAUCCUUUUGGCCGCGAGAAGAGGCGGCGCAUUACCAGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
........(((((((....(((((((..---------------..--..)))))))...(((((........)))))))))).))......((((((((....))).)))))........ ( -27.40)
>DroPse_CAF1 96182 114 - 1
------GAGGGGCGAGGGGGGCGGUGGGCAAAGCCAGGAAUAAAAUGCGAAUGGGUUUGGCAGCGAUGAGAGGCGGCACAUUACCAGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
------..((.((...(..((..(((.((...(((....((....(((.((.....)).)))...))....))).)).)))..))..)....)).))....................... ( -25.30)
>DroSec_CAF1 68345 103 - 1
AAAAUAAAGGGGUAUAUGUGAGGAUGGG---------------GU--AGCAUCCUUUUGGCCGCGAGAAGAGGCGGCGCAUUACCAGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
..........((((.(((((((((((..---------------..--..)))))))...(((((........)))))))))))))......((((((((....))).)))))........ ( -29.10)
>DroSim_CAF1 70522 103 - 1
AAAAUAAAGGGGUAUAUGUGGGGAUGGG---------------GU--AGCAUCCUUUUGGCCGCGAGAAGAGGCGGCGCAUUACCAGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
..........((((.(((((((((((..---------------..--..)))))))...(((((........)))))))))))))......((((((((....))).)))))........ ( -28.30)
>DroYak_CAF1 71296 106 - 1
A----AAAGGAGUGUGUGGGUGGGUGGGUUU--------AUGAGA--GGCAUCCUUUUGGCCGCGAGAAGAGGCGGCGCAUCAGCGGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
.----.....((((..(..((.((((.....--------..((((--((...)))))).(((((........))))).)))).))((((....))))........)..))))........ ( -25.50)
>consensus
AAAAUAAAGGGGUGUAUGUGGGGAUGGG_______________GA__AGCAUCCUUUUGGCCGCGAGAAGAGGCGGCGCAUUACCAGCAAAAGUGCCAUAAAAAUGUGUAUUAAAAUGAG
..........((((.((((..(((((.......................))))).....(((((........)))))))))))))......((((((((....))).)))))........ (-16.26 = -17.06 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:11 2006