Locus 1406

Sequence ID 3L_DroMel_CAF1
Location 4,092,351 – 4,092,545
Length 194
Max. P 0.999122
window2182 window2183 window2184 window2185 window2186

overview

Window 2

Location 4,092,351 – 4,092,467
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.09
Mean single sequence MFE -39.22
Consensus MFE -33.90
Energy contribution -34.50
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.86
SVM decision value 0.75
SVM RNA-class probability 0.840224
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4092351 116 - 23771897
----CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGUAAGCGAACAGGUUGUCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
----.((((((......))))))((((...)))).....(((((...........)))))...(((((.((((((..((.((((..((((....))))....)))))).))))))))))) ( -36.60)
>DroSec_CAF1 36417 116 - 1
----CGACGUCAACGCGAACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCGAACAGGUUGGCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
----...((((..(((.((((((((((...))))..((((((((.((((.(........)...(((((.....)))))....))))))))))))......)))))))))...)))).... ( -37.00)
>DroSim_CAF1 36739 116 - 1
----CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCGAACAGGUUGGCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
----(((((((......)))))))..((((((((...(((((((.((((.(........)...(((((.....)))))....)))))))))))((((.....))))))))).)))..... ( -38.60)
>DroEre_CAF1 37180 120 - 1
CCUUCGACUUCGACGCGGACGUCGCAGUCGCUGCACUUGGCGCAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCGAACAGGUUGGCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
((.((((((.(((((....))))).))))(((((...((((.(((((((.(........)...(((((.....)))))....)))))))))))((((.....))))))))).)).))... ( -45.10)
>DroYak_CAF1 37874 116 - 1
----CGACGUCGACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCGAACAGGUUGGCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
----(((((((......)))))))..((((((((...(((((((.((((.(........)...(((((.....)))))....)))))))))))((((.....))))))))).)))..... ( -38.80)
>consensus
____CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCGAACAGGUUGGCCAGACAAAAGAUGUUGCGGCAGAUGGAAG
....(((((((......)))))))..(((((.(((((..(......)..))....(((((......(((((.((....)).)))))...)))))........))).)))))......... (-33.90 = -34.50 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,092,391 – 4,092,505
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.81
Mean single sequence MFE -47.82
Consensus MFE -40.18
Energy contribution -40.82
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.61
Structure conservation index 0.84
SVM decision value 2.87
SVM RNA-class probability 0.997492
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4092391 114 + 23771897
CGCUUACAGACAGGAAGUUUGCCAAUUUUCUCAAGUUUAGCCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG------ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGU
.(((...((((((((((((....))))))))...))))......(((((((..((((((((((......))))))(------(((((........))))))))))..))))))))))... ( -46.60)
>DroSec_CAF1 36457 114 + 1
CGCUUCCAGACAGGAAGUUUGCCAAUUUUCUCAAGUUUAGCCAAGUGCAGCGACUGCGACGUUCGCGUUGACGUCG------ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCAGU
.((((((.....))))))((((.(((((....))))).......(((((((..((((((((((.((((((....))------)))).........))))))))))..))))))).)))). ( -46.30)
>DroSim_CAF1 36779 114 + 1
CGCUUCCAGACAGGAAGUUUGCCAAUUUUCUCAAGUUUAGCCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG------GCGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGU
.((((((.....))))))...................((((...(((((((..((((((((((......))))))(------(((((........))))))))))..))))))).)))). ( -48.80)
>DroEre_CAF1 37220 120 + 1
CGCUUCCAGACAGGAAGUUUGCCAAUUUUCUCAAGUUGCGCCAAGUGCAGCGACUGCGACGUCCGCGUCGAAGUCGAAGGCGAAGCUCCUCUGCUAGCGUCGCAGCAGCUGCGCAGCUGU
.((((((.....))))))..((((((((....)))))).))...(((((((..(((((((((.(((.(((....)))..))).(((......))).)))))))))..)))))))...... ( -52.60)
>DroYak_CAF1 37914 114 + 1
CGCUUCCAGACAGGAAGUUUGCCAAUUUUCUCAAGUUUAGCCAAGUGCAGCGACUGCGACGUCCGCGUCGACGUCG------AAGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGU
.((((((.....))))))...................((((...(((((((..(((((((((..((.(((....))------).........))..)))))))))..))))))).)))). ( -44.80)
>consensus
CGCUUCCAGACAGGAAGUUUGCCAAUUUUCUCAAGUUUAGCCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG______ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGU
.((((((.....)))))).....................((...(((((((..(((((((((..(((..(((((........))).))..).))..)))))))))..))))))).))... (-40.18 = -40.82 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,092,391 – 4,092,505
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.81
Mean single sequence MFE -45.82
Consensus MFE -39.22
Energy contribution -39.82
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.86
SVM decision value 1.08
SVM RNA-class probability 0.911230
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4092391 114 - 23771897
ACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU------CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGUAAGCG
...((((((((((.(((((((((((........)))))------)((((((......))))))))))).))))).((..(......)..))......((((.......)))).)).))). ( -45.70)
>DroSec_CAF1 36457 114 - 1
ACUGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU------CGACGUCAACGCGAACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCG
..((((..(((((.(((((((((((........)))))------)(((((........)))))))))).))))).((..(......)..))......))))..(((((.....))))).. ( -46.00)
>DroSim_CAF1 36779 114 - 1
ACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGC------CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCG
...(((..(((((.(((((((((...(((....))).(------((.((....))))).))))))))).))))).((..(......)..))......)))...(((((.....))))).. ( -45.90)
>DroEre_CAF1 37220 120 - 1
ACAGCUGCGCAGCUGCUGCGACGCUAGCAGAGGAGCUUCGCCUUCGACUUCGACGCGGACGUCGCAGUCGCUGCACUUGGCGCAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCG
...(((..(((((.(((((((((...((......))(((((..(((....))).)))))))))))))).))))).((..(......)..))......)))...(((((.....))))).. ( -46.20)
>DroYak_CAF1 37914 114 - 1
ACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCUU------CGACGUCGACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCG
...(((..(((((.(((((((((((((((....))).(------((....)))..))).))))))))).))))).((..(......)..))......)))...(((((.....))))).. ( -45.30)
>consensus
ACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU______CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGGCUAAACUUGAGAAAAUUGGCAAACUUCCUGUCUGGAAGCG
...(((..(((((.(((((((((...(((....)))........((.((....))))..))))))))).))))).((..(......)..))......)))...(((((.....))))).. (-39.22 = -39.82 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,092,431 – 4,092,545
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.81
Mean single sequence MFE -44.08
Consensus MFE -37.46
Energy contribution -38.10
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.86
Structure conservation index 0.85
SVM decision value 3.38
SVM RNA-class probability 0.999122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4092431 114 + 23771897
CCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG------ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGUUUAAUAUUCGGUGAGUAUUUCGAAAAACAAAGAAAAACCC
....(((((((..((((((((((......))))))(------(((((........))))))))))..)))))))...(((((....(((((........))))))))))........... ( -44.80)
>DroSec_CAF1 36497 114 + 1
CCAAGUGCAGCGACUGCGACGUUCGCGUUGACGUCG------ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCAGUUUAAUAUUCGGUGAGUAUUUCCAAAAACAAAGGAAAACCC
((..(((((((..((((((((((.((((((....))------)))).........))))))))))..)))))))....(((((((((((...))))))).....))))...))....... ( -42.90)
>DroSim_CAF1 36819 114 + 1
CCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG------GCGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGUUUAAUAUUCGGUGAGUAUUUCCAAAAACAAAGGAAAACCC
((..(((((((..((((((((((......))))))(------(((((........))))))))))..)))))))...((((((((((((...))))))).....)))))..))....... ( -44.80)
>DroEre_CAF1 37260 120 + 1
CCAAGUGCAGCGACUGCGACGUCCGCGUCGAAGUCGAAGGCGAAGCUCCUCUGCUAGCGUCGCAGCAGCUGCGCAGCUGUUUAAUAUUCGGUGAGUAUUUCCAAAAACAAAGGAAAACCC
((..(((((((..(((((((((.(((.(((....)))..))).(((......))).)))))))))..)))))))...((((((((((((...))))))).....)))))..))....... ( -46.70)
>DroYak_CAF1 37954 114 + 1
CCAAGUGCAGCGACUGCGACGUCCGCGUCGACGUCG------AAGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGUUUAAUAUUCGGUGAGUAUUUCCAAAAACAAAGGAAAGCCC
....(((((((..(((((((((..((.(((....))------).........))..)))))))))..))))))).(((.....((((((...))))))((((.........))))))).. ( -41.20)
>consensus
CCAAGUGCAGCGACUGCGACGUCCGCGUUGACGUCG______ACGCUCCUCAGCCAGCGUCGCAGCAGCUGCGCAGCUGUUUAAUAUUCGGUGAGUAUUUCCAAAAACAAAGGAAAACCC
((..(((((((..(((((((((..(((..(((((........))).))..).))..)))))))))..)))))))....(((((((((((...))))))).....))))...))....... (-37.46 = -38.10 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,092,431 – 4,092,545
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.81
Mean single sequence MFE -42.56
Consensus MFE -35.56
Energy contribution -36.20
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.41
Structure conservation index 0.84
SVM decision value 0.31
SVM RNA-class probability 0.682927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4092431 114 - 23771897
GGGUUUUUCUUUGUUUUUCGAAAUACUCACCGAAUAUUAAACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU------CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGG
((((.((((..........)))).))))....................(((((.(((((((((((........)))))------)((((((......))))))))))).)))))...... ( -43.70)
>DroSec_CAF1 36497 114 - 1
GGGUUUUCCUUUGUUUUUGGAAAUACUCACCGAAUAUUAAACUGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU------CGACGUCAACGCGAACGUCGCAGUCGCUGCACUUGG
(((((((((.........))))).))))....................(((((.(((((((((((........)))))------)(((((........)))))))))).)))))...... ( -42.50)
>DroSim_CAF1 36819 114 - 1
GGGUUUUCCUUUGUUUUUGGAAAUACUCACCGAAUAUUAAACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGC------CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGG
(((((((((.........))))).))))....................(((((.(((((((((...(((....))).(------((.((....))))).))))))))).)))))...... ( -43.00)
>DroEre_CAF1 37260 120 - 1
GGGUUUUCCUUUGUUUUUGGAAAUACUCACCGAAUAUUAAACAGCUGCGCAGCUGCUGCGACGCUAGCAGAGGAGCUUCGCCUUCGACUUCGACGCGGACGUCGCAGUCGCUGCACUUGG
(((((((((.........))))).))))....................(((((.(((((((((...((......))(((((..(((....))).)))))))))))))).)))))...... ( -43.30)
>DroYak_CAF1 37954 114 - 1
GGGCUUUCCUUUGUUUUUGGAAAUACUCACCGAAUAUUAAACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCUU------CGACGUCGACGCGGACGUCGCAGUCGCUGCACUUGG
.((((....((((..(((((.........)))))...)))).))))..(((((.(((((((((((((((....))).(------((....)))..))).))))))))).)))))...... ( -40.30)
>consensus
GGGUUUUCCUUUGUUUUUGGAAAUACUCACCGAAUAUUAAACAGCUGCGCAGCUGCUGCGACGCUGGCUGAGGAGCGU______CGACGUCAACGCGGACGUCGCAGUCGCUGCACUUGG
(((((((((.........))))).))))....................(((((.(((((((((...(((....)))........((.((....))))..))))))))).)))))...... (-35.56 = -36.20 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:42 2006