Locus 1707

Sequence ID	2L_DroMel_CAF1
Location	4,683,818 – 4,683,932
Length	114
Max. P	0.796090

overview

Window 8

Location	4,683,818 – 4,683,932
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	71.73
Mean single sequence MFE	-31.98
Consensus MFE	-17.91
Energy contribution	-18.42
Covariance contribution	0.50
Combinations/Pair	1.29
Mean z-score	-1.57
Structure conservation index	0.56
SVM decision value	0.60
SVM RNA-class probability	0.796090
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4683818 114 + 22407834
UCAUGAGACUGUUUGUGCUCUGGCUCCUGAUCCAUUUCCUGGACCUUUUCAAUUUCGAUGGUGAGGAGAUCGAGAGCCUUGCGCUUACUGCGCUCCCAUUGCUGGAGAAGCUUC
....(((...((..((((...(((((.(((((....((((.(.((...((......)).))).))))))))).)))))..))))..))....))).....(((.....)))... ( -35.20)
>DroVir_CAF1 130526 90 + 1
------------------------UCCUGAUCCAUGGUCUGCACCUUCUCGAUCUCGAUGGUGAGCAAAUCCAGGGCCUUGCGUUUGGUGCGCUCCCAACGCUGCAGCAUCUUU
------------------------...........((((((((.(...(((....)))(((.((((....(((((((...)).)))))...)))))))..).))))).)))... ( -23.60)
>DroGri_CAF1 116221 90 + 1
------------------------UCCUGAUCCAUGGCCUGCACCUUCUCGAUCUCAAUGGUAAGCAGAUCGAGAGCCUUCCGCUUGGAGCGUUCCCAACGUUGCAGCAUCUUC
------------------------...........(((........((((((((((........).))))))))))))....(((.(.(((((.....))))).))))...... ( -23.70)
>DroEre_CAF1 117177 108 + 1
UCAUGAG------CCUGCUCUUGCUCCUGAUCCAUUUCCUGCACCUUCUCGAUCUCAGUUGUUAGGAGAUCGAGAGCCUUGCGCUUACUGCGCUCCCAUCGCUGUAGAAGCCUC
(((.(((------(........)))).)))..........(((..(((((((((((.........)))))))))))...)))((((.((((((.......)).))))))))... ( -34.60)
>DroYak_CAF1 117825 114 + 1
UCAUGAGUCGGCUCCUGCUCUUGCUCCUGAUCCAUUUCCUGCACCUUCUCAAUCUCGAUGGUCAGGAGGUCGAGAGCCUUGCGCUUACUGCGCUCCCAUUGCUGCAGAAGCUUC
.........((((.((((....((((.(((((....(((((.(((.((........)).))))))))))))).))))...((((.....))))..........)))).)))).. ( -38.70)
>DroMoj_CAF1 138238 90 + 1
------------------------UCCUGGUCCAUGGUCUGCAGCUUCUCGAUCUCGAGCAUGAGCAGGUCGAGCGCCUUGCGCUUGCUGCGCUCCCAACGCUGCAGCAUCUUG
------------------------........((.((((((((((..((((....))))...((((.((.(((((((...)))))))))..)))).....))))))).))).)) ( -36.10)
>consensus
________________________UCCUGAUCCAUGGCCUGCACCUUCUCGAUCUCGAUGGUGAGCAGAUCGAGAGCCUUGCGCUUACUGCGCUCCCAACGCUGCAGAAGCUUC
......................................(((((.((((((((((((........).))))))))))....((((.....)))).......).)))))....... (-17.91 = -18.42 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	4,683,818 – 4,683,932
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	71.73
Mean single sequence MFE	-34.10
Consensus MFE	-16.68
Energy contribution	-18.02
Covariance contribution	1.33
Combinations/Pair	1.11
Mean z-score	-1.69
Structure conservation index	0.49
SVM decision value	0.37
SVM RNA-class probability	0.707596
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4683818 114 - 22407834
GAAGCUUCUCCAGCAAUGGGAGCGCAGUAAGCGCAAGGCUCUCGAUCUCCUCACCAUCGAAAUUGAAAAGGUCCAGGAAAUGGAUCAGGAGCCAGAGCACAAACAGUCUCAUGA
...((((.((((....)))).((((.....))))..(((((..((((((((.(((.(((....)))...)))..))))....))))..))))).))))................ ( -35.30)
>DroVir_CAF1 130526 90 - 1
AAAGAUGCUGCAGCGUUGGGAGCGCACCAAACGCAAGGCCCUGGAUUUGCUCACCAUCGAGAUCGAGAAGGUGCAGACCAUGGAUCAGGA------------------------
...((((((...(((((((.......)).)))))..)))(((((.(((((..(((.(((....)))...))))))))))).)))))....------------------------ ( -28.20)
>DroGri_CAF1 116221 90 - 1
GAAGAUGCUGCAACGUUGGGAACGCUCCAAGCGGAAGGCUCUCGAUCUGCUUACCAUUGAGAUCGAGAAGGUGCAGGCCAUGGAUCAGGA------------------------
.......(((((.((((.(((....))).))))......(((((((((.(........))))))))))...))))).((........)).------------------------ ( -27.10)
>DroEre_CAF1 117177 108 - 1
GAGGCUUCUACAGCGAUGGGAGCGCAGUAAGCGCAAGGCUCUCGAUCUCCUAACAACUGAGAUCGAGAAGGUGCAGGAAAUGGAUCAGGAGCAAGAGCAGG------CUCAUGA
...((((((............((((.....)))).....((((((((((.........)))))))))).(((.((.....)).)))))))))..(((....------))).... ( -35.70)
>DroYak_CAF1 117825 114 - 1
GAAGCUUCUGCAGCAAUGGGAGCGCAGUAAGCGCAAGGCUCUCGACCUCCUGACCAUCGAGAUUGAGAAGGUGCAGGAAAUGGAUCAGGAGCAAGAGCAGGAGCCGACUCAUGA
...((((((((..........((((.....))))...((((..((((((((((((.((........)).))).)))))...)).))..))))....)))))))).......... ( -44.20)
>DroMoj_CAF1 138238 90 - 1
CAAGAUGCUGCAGCGUUGGGAGCGCAGCAAGCGCAAGGCGCUCGACCUGCUCAUGCUCGAGAUCGAGAAGCUGCAGACCAUGGACCAGGA------------------------
.......(((((((((.((((((((.((....))...))))))..)).)).....((((....))))..))))))).((........)).------------------------ ( -34.10)
>consensus
GAAGAUGCUGCAGCGAUGGGAGCGCAGCAAGCGCAAGGCUCUCGAUCUCCUCACCAUCGAGAUCGAGAAGGUGCAGGAAAUGGAUCAGGA________________________
.......(((((.(.......((((.....))))......((((((((.(........)))))))))..).)))))...................................... (-16.68 = -18.02 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:04 2006