Locus 7192

Sequence ID X_DroMel_CAF1
Location 18,009,390 – 18,009,576
Length 186
Max. P 0.934013
window11748 window11749 window11750

overview

Window 8

Location 18,009,390 – 18,009,500
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.22
Mean single sequence MFE -26.12
Consensus MFE -13.96
Energy contribution -13.40
Covariance contribution -0.56
Combinations/Pair 1.33
Mean z-score -1.73
Structure conservation index 0.53
SVM decision value 0.31
SVM RNA-class probability 0.681957
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18009390 110 - 22224390
AGAUUAAGUGCCUGGCUGGGAAAUAUUUCCAGCUCAUUUGGGCAAGAAAAUCGGACUGCUUUCCCUGAGAAUCUAAACAGCC-AAAACUAAGGAAAUUCAUUUAAAUUA---------AU
......(((...((((((((((....)))).((((....)))).(((...((((..........))))...)))...)))))-)..)))....................---------.. ( -23.70)
>DroSec_CAF1 20884 110 - 1
AGAUUAAGUGCCUGGCUGGAAAAUAUUUCCAGCUCAUUUGGGCAAGAAAAUCGCACUGCUUUCCUUGGAAAUCUUAGCAGCU-AAAACCAAGGCAAUUAAUUUAAGUUA---------AU
(((((((.(((((((((((((.....))))))))....(((((.........)).((((((((....))).....)))))..-....)))))))).)))))))......---------.. ( -31.70)
>DroEre_CAF1 21773 116 - 1
AAAUUAAAUGCCUGGCUGGGAAAAUUUUCCAGUUGAUUUGGGCAAGAAAAACCGAC----UUCCUUGGGAAUCUCAGCAGCUUGAAAGCAAGCCGUUUAAUUUACAUUUUCAACUUUUAG
((((((((((....(((((((....(((((((..((.((((..........)))).----))..)))))))))))))).(((((....)))))))))))))))................. ( -30.90)
>DroYak_CAF1 8746 100 - 1
AAACUCACAGCUGGGCUGGGAAAUAAUUUCAGUUGAUUUGGGCAAGAAAAUC-----------UGUGGGAAUCUUAGCAGUUUAAAGUCAAGCCAUUUAAUUUAGCUUU---------AU
...((((((....(((((..(.....)..)))))(((((........)))))-----------)))))).............(((((..(((........)))..))))---------). ( -18.20)
>consensus
AAAUUAAGUGCCUGGCUGGGAAAUAUUUCCAGCUCAUUUGGGCAAGAAAAUCGGAC____UUCCUUGGGAAUCUUAGCAGCU_AAAACCAAGCCAAUUAAUUUAAAUUA_________AU
.........((((((((((((.....)))))))).....))))............................................................................. (-13.96 = -13.40 +  -0.56)

alignment

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secondary structure

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Window 9

Location 18,009,460 – 18,009,576
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.62
Mean single sequence MFE -27.60
Consensus MFE -17.62
Energy contribution -19.75
Covariance contribution 2.12
Combinations/Pair 1.14
Mean z-score -2.59
Structure conservation index 0.64
SVM decision value 1.23
SVM RNA-class probability 0.934013
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18009460 116 + 22224390
CAAAUGAGCUGGAAAUAUUUCCCAGCCAGGCACUUAAUCUUUCAUAAUUUCCAUGGCUGGGCCUUUGCCACAAGUGUUGACAUUUGAUAAUUUUCAUUUAGCC----GUUUUUCACUUUU
.(((((.((((((.......((((((((((...(((........)))...)).)))))))).........((((((....))))))..........)))))))----))))......... ( -29.20)
>DroSec_CAF1 20954 116 + 1
CAAAUGAGCUGGAAAUAUUUUCCAGCCAGGCACUUAAUCUUUCAUAAUUUCCAUGGCUGUGCCUCUGCCGCAAGUGUUGACAUUUGAUAAUUUUCAUUUAGGC----GUUUUUCACUUUU
....((.(((((((.....)))))))))(((((.........................)))))...(((.((((((....)))))).(((.......))))))----............. ( -26.41)
>DroEre_CAF1 21849 120 + 1
CAAAUCAACUGGAAAAUUUUCCCAGCCAGGCAUUUAAUUUUUCAUAAAUUGCAUGGCUGGGCCGCAGCCACAAGUGUUGACAUUUGAUAAUUUUCAUUUAGAUUUAUUUUUUUUGCUUUU
.(((((.....(((((((..((((((((.(((((((........)))).))).)))))))).........((((((....))))))..))))))).....)))))............... ( -31.30)
>DroYak_CAF1 8806 116 + 1
CAAAUCAACUGAAAUUAUUUCCCAGCCCAGCUGUGAGUUUUUCAUAAUUUUCAUGGCUUGGCCAGUGCCACAAGUGUUGUCAUUUGAUCAUUUUCAUUUAGCU----GCUUUUCACUUUU
...(((((.(((............(((.(((((((((..((....))..))))))))).)))(((..(.....)..)))))).)))))...............----............. ( -23.50)
>consensus
CAAAUCAACUGGAAAUAUUUCCCAGCCAGGCACUUAAUCUUUCAUAAUUUCCAUGGCUGGGCCUCUGCCACAAGUGUUGACAUUUGAUAAUUUUCAUUUAGCC____GUUUUUCACUUUU
.........(((((((....((((((((((.(((((........))))).)).)))))))).........((((((....))))))...)))))))........................ (-17.62 = -19.75 +   2.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,009,460 – 18,009,576
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.62
Mean single sequence MFE -27.05
Consensus MFE -16.26
Energy contribution -15.70
Covariance contribution -0.56
Combinations/Pair 1.24
Mean z-score -2.26
Structure conservation index 0.60
SVM decision value 0.49
SVM RNA-class probability 0.757539
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18009460 116 - 22224390
AAAAGUGAAAAAC----GGCUAAAUGAAAAUUAUCAAAUGUCAACACUUGUGGCAAAGGCCCAGCCAUGGAAAUUAUGAAAGAUUAAGUGCCUGGCUGGGAAAUAUUUCCAGCUCAUUUG
..((((((.....----(((....(((......)))...)))........(((.(((..((((((((.((...(((........)))...)))))))))).....))))))..)))))). ( -28.90)
>DroSec_CAF1 20954 116 - 1
AAAAGUGAAAAAC----GCCUAAAUGAAAAUUAUCAAAUGUCAACACUUGCGGCAGAGGCACAGCCAUGGAAAUUAUGAAAGAUUAAGUGCCUGGCUGGAAAAUAUUUCCAGCUCAUUUG
..((((((.....----(((..(((....)))..(((.((....)).))).)))..((((((..(....).((((......))))..)))))).(((((((.....))))))))))))). ( -27.50)
>DroEre_CAF1 21849 120 - 1
AAAAGCAAAAAAAAUAAAUCUAAAUGAAAAUUAUCAAAUGUCAACACUUGUGGCUGCGGCCCAGCCAUGCAAUUUAUGAAAAAUUAAAUGCCUGGCUGGGAAAAUUUUCCAGUUGAUUUG
..............((((((.....(((((((.......((((.(....))))).....((((((((.(((.((((........))))))).))))))))..))))))).....)))))) ( -30.40)
>DroYak_CAF1 8806 116 - 1
AAAAGUGAAAAGC----AGCUAAAUGAAAAUGAUCAAAUGACAACACUUGUGGCACUGGCCAAGCCAUGAAAAUUAUGAAAAACUCACAGCUGGGCUGGGAAAUAAUUUCAGUUGAUUUG
..((.(((((...----.((((........((.((....)))).......)))).(..(((.(((..(((..............)))..))).)))..).......))))).))...... ( -21.40)
>consensus
AAAAGUGAAAAAC____AGCUAAAUGAAAAUUAUCAAAUGUCAACACUUGUGGCAGAGGCCCAGCCAUGGAAAUUAUGAAAAAUUAAGUGCCUGGCUGGGAAAUAUUUCCAGCUCAUUUG
..................................((((((...........(((...(((...)))..........(....).......))).((((((((.....)))))))))))))) (-16.26 = -15.70 +  -0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:25 2006