Locus 3623

Sequence ID 3R_DroMel_CAF1
Location 9,776,683 – 9,776,793
Length 110
Max. P 0.787413
window5832 window5833

overview

Window 2

Location 9,776,683 – 9,776,793
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -44.20
Consensus MFE -27.76
Energy contribution -29.47
Covariance contribution 1.70
Combinations/Pair 1.29
Mean z-score -1.69
Structure conservation index 0.63
SVM decision value 0.37
SVM RNA-class probability 0.708882
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9776683 110 + 27905053
UGCCGUGGCACCGAUGCGGUUGAGGAUGCGGCCUGGCCAGGGGCGAUAGCGGCGCAACUUGGCGAACACAAAGUCGCCAAUGGUGAAAUUAGGCAUCUUGGCUCGGCGAC
.((((.(((...((((((((((......)))))(.((((..((((((...(.(((......)))....)...))))))..)))).)......)))))...)))))))... ( -44.10)
>DroGri_CAF1 86103 97 + 1
CAUUUUGCCC---UCGUCUUGCAGAAUACGCGCCGGCCACGCACAAAAGCCGGGCACCUUGGCGAACACAAAGUCUCCCACUUUGAUU----------UGGUACGGUGAC
.(((((((..---.......)))))))...(((((((((.........((((((...)))))).....((((((.....))))))...----------)))).))))).. ( -27.60)
>DroSec_CAF1 99875 110 + 1
UGCCGUGGCACCGAUGCGUUUCAGGAUGCGGCCUGGCCAGGGGCGAUAGCCGCGCACCUUGGCAAACACAAAGUCGCCAAUGGUGAAAUUAGGCAUCUUGGCACGGCGAC
.((((((.((..(((((((((((((......))))((((((((((.......))).)))))))))))......(((((...)))))......))))).)).))))))... ( -50.10)
>DroSim_CAF1 100471 110 + 1
UGCCGUGGCACCGAUGCGUUUCAGGAUGCGGCCUGGCCAGGGGCGAUAGCCGCGCACCUUGGCGAACACAAAGUCGCCAAUGGUGAAAUUAAGCAUCUUGGCACGGCGAC
.(((((((((....)))...((((((((((((...))).(.(((....))).).(((((((((((........))))))).)))).......)))))))))))))))... ( -52.40)
>DroEre_CAF1 104164 110 + 1
UGCCGUAGCACCGACGCGGUUCAGGAUGCGGGCUGGCCAGGCGCGAUACCCGCGCACCUUAGCGAACACAAAGUCGCCGAUCGUGAAAAUAGGCAUCCUGGCACGUCGGC
(((....)))((((((.(..(((((((((..(((((....(((((.....)))))...)))))..........((((.....))))......)))))))))).)))))). ( -42.70)
>DroYak_CAF1 103581 110 + 1
GGCCGUGGCACCGACGCGGUUUAGGAUGCGGGCUGGCCAGGCGCGAUACCCGCGCACCUUGGCGAACACAAAGUCGCCAAUCGUGAAAAUAGGCAUCCUGGCACGGCGAC
.((((((.(((((...))))..(((((((.((....))..(((((.....)))))...(((((((........)))))))............)))))))).))))))... ( -48.30)
>consensus
UGCCGUGGCACCGACGCGGUUCAGGAUGCGGCCUGGCCAGGCGCGAUAGCCGCGCACCUUGGCGAACACAAAGUCGCCAAUGGUGAAAUUAGGCAUCUUGGCACGGCGAC
(((((((((......))....(((((((((.(((.....))).)........(((...(((((((........)))))))..))).......)))))))).))))))).. (-27.76 = -29.47 +   1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,776,683 – 9,776,793
Length 110
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -43.82
Consensus MFE -29.17
Energy contribution -30.63
Covariance contribution 1.46
Combinations/Pair 1.27
Mean z-score -1.70
Structure conservation index 0.67
SVM decision value 0.58
SVM RNA-class probability 0.787413
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9776683 110 - 27905053
GUCGCCGAGCCAAGAUGCCUAAUUUCACCAUUGGCGACUUUGUGUUCGCCAAGUUGCGCCGCUAUCGCCCCUGGCCAGGCCGCAUCCUCAACCGCAUCGGUGCCACGGCA
...((((.((...(((((............((((((((.....).)))))))..((((((((((.......))))..)).)))).........)))))...))..)))). ( -36.10)
>DroGri_CAF1 86103 97 - 1
GUCACCGUACCA----------AAUCAAAGUGGGAGACUUUGUGUUCGCCAAGGUGCCCGGCUUUUGUGCGUGGCCGGCGCGUAUUCUGCAAGACGA---GGGCAAAAUG
(((..(((....----------........((((..((((((.(....))))))).))))((....(((((((.....)))))))...))...))).---.)))...... ( -28.30)
>DroSec_CAF1 99875 110 - 1
GUCGCCGUGCCAAGAUGCCUAAUUUCACCAUUGGCGACUUUGUGUUUGCCAAGGUGCGCGGCUAUCGCCCCUGGCCAGGCCGCAUCCUGAAACGCAUCGGUGCCACGGCA
...((((((.((.(((((.......((((.((((((((.....).))))))))))).((((((...(((...)))..))))))..........)))))..)).)))))). ( -49.60)
>DroSim_CAF1 100471 110 - 1
GUCGCCGUGCCAAGAUGCUUAAUUUCACCAUUGGCGACUUUGUGUUCGCCAAGGUGCGCGGCUAUCGCCCCUGGCCAGGCCGCAUCCUGAAACGCAUCGGUGCCACGGCA
...((((((.((.(((((.......((((.((((((((.....).))))))))))).((((((...(((...)))..))))))..........)))))..)).)))))). ( -52.10)
>DroEre_CAF1 104164 110 - 1
GCCGACGUGCCAGGAUGCCUAUUUUCACGAUCGGCGACUUUGUGUUCGCUAAGGUGCGCGGGUAUCGCGCCUGGCCAGCCCGCAUCCUGAACCGCGUCGGUGCUACGGCA
(((((((((.((((((((.......(((((..(....).)))))...((((.((((((.......))))))))))......))))))))...)))))))))((....)). ( -50.40)
>DroYak_CAF1 103581 110 - 1
GUCGCCGUGCCAGGAUGCCUAUUUUCACGAUUGGCGACUUUGUGUUCGCCAAGGUGCGCGGGUAUCGCGCCUGGCCAGCCCGCAUCCUAAACCGCGUCGGUGCCACGGCC
...((((((.((((((((............((((((((.....).)))))))((((((((.....)))))...))).....)))))))..((((...))))).)))))). ( -46.40)
>consensus
GUCGCCGUGCCAAGAUGCCUAAUUUCACCAUUGGCGACUUUGUGUUCGCCAAGGUGCGCGGCUAUCGCCCCUGGCCAGCCCGCAUCCUGAAACGCAUCGGUGCCACGGCA
...((((((.((.(((((..............((((((.....).))))).(((...((((((...((.....))..))))))..))).....)))))..)).)))))). (-29.17 = -30.63 +   1.46)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:00 2006