Locus 1817

Sequence ID 3L_DroMel_CAF1
Location 5,100,751 – 5,100,900
Length 149
Max. P 0.986303
window2833 window2834 window2835

overview

Window 3

Location 5,100,751 – 5,100,860
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.52
Mean single sequence MFE -25.52
Consensus MFE -17.42
Energy contribution -17.93
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.68
SVM decision value 0.24
SVM RNA-class probability 0.648947
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100751 109 + 23771897
UACACCAUG-CCACUAUAU--AUUUCGUACACUUCUUGAUGUCGCCCAAGUGGGCGUGGCCAGCGCAAAAGCAA------AAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAA
........(-((((.....--.....(.((((.....).))))((((....))))))))).(((((........------..........)))))...........--............ ( -20.87)
>DroSec_CAF1 293827 117 + 1
UACAUCUUG-CCACUAUAUACAUUUGGUACUCCUCUUCAUGUCGCCCAAGUGGGCGUGGCCAGCGCCAAAGCAAAAGCACAAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAA
....((((.-...........((((((((((.....((.((((((((....)))))((((....))))..((....))))).)).....)))))))))).......--....)))).... ( -28.00)
>DroSim_CAF1 315420 117 + 1
UACAUCUUG-CCACUAUAUAUAUUUGGUACACCUCUUCAUGUCGCCCAAGUGGGCGUGGCCAGCGCCAAAGCAAAAGCACAAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAA
....(((((-((((...........((....))..........((((....)))))))))..((......))...(((((..........)))))...........--....)))).... ( -26.60)
>DroYak_CAF1 306121 114 + 1
UACACUCUGCCCACUAUAUAUAUUUGGUAAGCCUCUUCAUGUCGCCCAAGUGGGCGUGGCUGGCGUAAUGGCAA------AAGAUUCCAAGUGCUAAAUCAACAAAGAGCAAAAGAACAA
....(((((((.((((........)))).((((.........(((((....))))).)))))))....(((((.------..(....)...))))).........))))........... ( -26.60)
>consensus
UACACCUUG_CCACUAUAUAUAUUUGGUACACCUCUUCAUGUCGCCCAAGUGGGCGUGGCCAGCGCAAAAGCAA______AAGAUCCCAAGUGCUAAAUCAACAAA__ACAAAAGAACAA
.....................(((((((((............(((((....)))))......((......))..................)))))))))..................... (-17.42 = -17.93 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,100,788 – 5,100,900
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.38
Mean single sequence MFE -36.37
Consensus MFE -30.68
Energy contribution -30.12
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -3.34
Structure conservation index 0.84
SVM decision value 2.04
SVM RNA-class probability 0.986303
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100788 112 + 23771897
GUCGCCCAAGUGGGCGUGGCCAGCGCAAAAGCAA------AAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAACGACCGAUACAAAUUUGUUCGCUGCUGCGCUGCCUUUAAU
..(((((....))))).(((.((((((..(((..------..........((.........))...--......((((((..............)))))))))..)))))))))...... ( -33.04)
>DroSec_CAF1 293866 118 + 1
GUCGCCCAAGUGGGCGUGGCCAGCGCCAAAGCAAAAGCACAAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAAAGACCGAUACAAAUUUGUUCGCUGCUGCGCUGCCUUUAAU
..(((((....))))).(((.(((((...(((...(((((..........)))))...........--......(((((((............))))))))))...))))))))...... ( -39.10)
>DroSim_CAF1 315459 118 + 1
GUCGCCCAAGUGGGCGUGGCCAGCGCCAAAGCAAAAGCACAAGAUCCCAAGUGCUAAAUCAACAAA--ACAAAAGAACAACGACCGAUACAAAUUUGUUCGCUGCUGCGCUGCCUUUAAU
..(((((....))))).(((.(((((...(((...(((((..........)))))...........--......((((((..............)))))))))...))))))))...... ( -37.14)
>DroYak_CAF1 306161 114 + 1
GUCGCCCAAGUGGGCGUGGCUGGCGUAAUGGCAA------AAGAUUCCAAGUGCUAAAUCAACAAAGAGCAAAAGAACAACGAGCGAUACAAAUUUGUUCGCUGCUGCGCUGCCUUUAAU
..(((((....))))).(((.((((((..(((..------....(((....((((............))))...)))....((((((.......)))))))))..)))))))))...... ( -36.20)
>consensus
GUCGCCCAAGUGGGCGUGGCCAGCGCAAAAGCAA______AAGAUCCCAAGUGCUAAAUCAACAAA__ACAAAAGAACAACGACCGAUACAAAUUUGUUCGCUGCUGCGCUGCCUUUAAU
..(((((....))))).(((.(((((...(((..................((.........))...........((((((..............)))))))))...))))))))...... (-30.68 = -30.12 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,100,788 – 5,100,900
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.38
Mean single sequence MFE -37.42
Consensus MFE -31.84
Energy contribution -33.15
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.85
SVM decision value 1.15
SVM RNA-class probability 0.922433
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100788 112 - 23771897
AUUAAAGGCAGCGCAGCAGCGAACAAAUUUGUAUCGGUCGUUGUUCUUUUGU--UUUGUUGAUUUAGCACUUGGGAUCUU------UUGCUUUUGCGCUGGCCACGCCCACUUGGGCGAC
......((((((((((.(((((((((..(((...)))...))))))......--......(((((........)))))..------..))).))))))).))).(((((....))))).. ( -37.80)
>DroSec_CAF1 293866 118 - 1
AUUAAAGGCAGCGCAGCAGCGAACAAAUUUGUAUCGGUCUUUGUUCUUUUGU--UUUGUUGAUUUAGCACUUGGGAUCUUGUGCUUUUGCUUUGGCGCUGGCCACGCCCACUUGGGCGAC
......((((((((...((((((((((............)))))))......--...........(((((..(....)..)))))...)))...))))).))).(((((....))))).. ( -39.50)
>DroSim_CAF1 315459 118 - 1
AUUAAAGGCAGCGCAGCAGCGAACAAAUUUGUAUCGGUCGUUGUUCUUUUGU--UUUGUUGAUUUAGCACUUGGGAUCUUGUGCUUUUGCUUUGGCGCUGGCCACGCCCACUUGGGCGAC
......((((((((...(((((((((..(((...)))...))))))......--...........(((((..(....)..)))))...)))...))))).))).(((((....))))).. ( -39.30)
>DroYak_CAF1 306161 114 - 1
AUUAAAGGCAGCGCAGCAGCGAACAAAUUUGUAUCGCUCGUUGUUCUUUUGCUCUUUGUUGAUUUAGCACUUGGAAUCUU------UUGCCAUUACGCCAGCCACGCCCACUUGGGCGAC
......(((.(((((((((((((((....))).))))).))))((((..((((............))))...))))....------.........)))..))).(((((....))))).. ( -33.10)
>consensus
AUUAAAGGCAGCGCAGCAGCGAACAAAUUUGUAUCGGUCGUUGUUCUUUUGU__UUUGUUGAUUUAGCACUUGGGAUCUU______UUGCUUUGGCGCUGGCCACGCCCACUUGGGCGAC
......((((((((((.(((((((((..(((...)))...))))))..............(((((........)))))..........))).))))))).))).(((((....))))).. (-31.84 = -33.15 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:28 2006