Locus 4391

Sequence ID	2R_DroMel_CAF1
Location	14,443,782 – 14,443,900
Length	118
Max. P	0.883141

overview

Window 2

Location	14,443,782 – 14,443,900
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-34.89
Consensus MFE	-20.32
Energy contribution	-21.32
Covariance contribution	1.00
Combinations/Pair	1.21
Mean z-score	-2.29
Structure conservation index	0.58
SVM decision value	0.93
SVM RNA-class probability	0.883141
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14443782 118 + 20766785
AAAGAUCCGCCGGAGAGGAAAUUGCGGGGGGGGGGGGUCCAAAGUCCAUGGAGAGGAAAAUGGAUUUUCCUGCGAUGGAAGCACCCCAAAGGACUGGCCAAAAAGAGCGGAAUCAAUA
...((((((((.....((..(.(.(.(((((((..((((((...(((.......)))...))))))..)))((.......)).))))...).).)..)).....).)))).))).... ( -40.30)
>DroSec_CAF1 75812 111 + 1
AAAGAUCCGCCGGAGAGGAAAUUGCGGGGG------GCCCUAAGUCCAUGGAGAGGAAAAUGGAUUUUCCUGCGAUGGAAGCAACCCAAAGGACUGGCCAAAAAG-GCGGAAUCAAUA
...((((((((.....((...(((((((..------..)))...(((((.(..(((((((....))))))).).))))).)))).(((......))))).....)-)))).))).... ( -37.40)
>DroSim_CAF1 77098 112 + 1
AAAGAUCCGCCGGAGAGGAAAUUGCAGGGG-----CGCCCUAAGUCCAUGGAGAGGAAAAUGGAUUUUCCUGCGAUGGAAGCAACCCAAAGGACUGGCCAAAAAG-GCGGAAUCAAUA
...((((((((.....((...((((((((.-----..))))...(((((.(..(((((((....))))))).).))))).)))).(((......))))).....)-)))).))).... ( -37.70)
>DroEre_CAF1 77348 92 + 1
AAAGAUCCGCUGGGUAGGAAAACGCG--GG------GCUCUAAGUCCAUGGAGAGGAAAACGGAUUUGCCUGUGAUGGUAGCACCCCAAAGGA------------------AUCGGUG
...(((((..((((........((((--((------....(((((((..............))))))))))))).((....)).))))..)).------------------))).... ( -22.04)
>DroYak_CAF1 78100 110 + 1
AAAGAUCCGCCGGAGAGGAAAUUGCGGGGG------GUUCCAAGUCCAUGGGGUGGAAAAUGGAUUUGCCUGUGAUGGGAGCACGCCAAAGGACUAGCCAAA-GG-GCGGCAUCAAUG
...((((((((((.......((..((((.(------(.((((..(((((...)))))...)))).)).))))..)).........))...((.....))...-.)-)))).))).... ( -36.99)
>consensus
AAAGAUCCGCCGGAGAGGAAAUUGCGGGGG______GCCCUAAGUCCAUGGAGAGGAAAAUGGAUUUUCCUGCGAUGGAAGCACCCCAAAGGACUGGCCAAAAAG_GCGGAAUCAAUA
...(((((((..........((((((((((........))(((((((((..........)))))))))))))))))((.......))...................)))).))).... (-20.32 = -21.32 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	14,443,782 – 14,443,900
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	81.05
Mean single sequence MFE	-29.34
Consensus MFE	-15.22
Energy contribution	-17.06
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-2.34
Structure conservation index	0.52
SVM decision value	0.73
SVM RNA-class probability	0.835202
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14443782 118 - 20766785
UAUUGAUUCCGCUCUUUUUGGCCAGUCCUUUGGGGUGCUUCCAUCGCAGGAAAAUCCAUUUUCCUCUCCAUGGACUUUGGACCCCCCCCCCCCGCAAUUUCCUCUCCGGCGGAUCUUU
....(((.(((((......((..(((((..((((((((.......)))((((((....)))))).))))).)))))..((......))............)).....))))))))... ( -29.80)
>DroSec_CAF1 75812 111 - 1
UAUUGAUUCCGC-CUUUUUGGCCAGUCCUUUGGGUUGCUUCCAUCGCAGGAAAAUCCAUUUUCCUCUCCAUGGACUUAGGGC------CCCCCGCAAUUUCCUCUCCGGCGGAUCUUU
....(((.((((-(.....((((((....))))(((((.(((((.(.(((((((....)))))))..).)))))....(((.------..))))))))..)).....))))))))... ( -33.80)
>DroSim_CAF1 77098 112 - 1
UAUUGAUUCCGC-CUUUUUGGCCAGUCCUUUGGGUUGCUUCCAUCGCAGGAAAAUCCAUUUUCCUCUCCAUGGACUUAGGGCG-----CCCCUGCAAUUUCCUCUCCGGCGGAUCUUU
....(((.((((-(......((((((((..((((.(((.......)))((((((....))))))..)))).)))))...)))(-----(....))............))))))))... ( -34.40)
>DroEre_CAF1 77348 92 - 1
CACCGAU------------------UCCUUUGGGGUGCUACCAUCACAGGCAAAUCCGUUUUCCUCUCCAUGGACUUAGAGC------CC--CGCGUUUUCCUACCCAGCGGAUCUUU
....(((------------------((....(((((.(((((((...(((.(((.....))))))....))))...))).))------))--)((.............)))))))... ( -21.52)
>DroYak_CAF1 78100 110 - 1
CAUUGAUGCCGC-CC-UUUGGCUAGUCCUUUGGCGUGCUCCCAUCACAGGCAAAUCCAUUUUCCACCCCAUGGACUUGGAAC------CCCCCGCAAUUUCCUCUCCGGCGGAUCUUU
....(((.((((-(.-....(((((....))))).(((..((......))....((((...((((.....))))..))))..------.....)))...........))))))))... ( -27.20)
>consensus
UAUUGAUUCCGC_CUUUUUGGCCAGUCCUUUGGGGUGCUUCCAUCGCAGGAAAAUCCAUUUUCCUCUCCAUGGACUUAGGGC______CCCCCGCAAUUUCCUCUCCGGCGGAUCUUU
....(((................(((((..((((((((.......)))((((((....)))))).))))).)))))...............((((.............)))))))... (-15.22 = -17.06 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:30 2006