Locus 6440

Sequence ID 3L_DroMel_CAF1
Location 17,223,171 – 17,223,321
Length 150
Max. P 0.991565
window10329 window10330 window10331

overview

Window 9

Location 17,223,171 – 17,223,289
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.44
Mean single sequence MFE -49.06
Consensus MFE -37.34
Energy contribution -38.14
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -2.39
Structure conservation index 0.76
SVM decision value 1.22
SVM RNA-class probability 0.932732
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17223171 118 + 23771897
-CGGG-ACCCCAACAUUGCCCACAUCGCUGCGAGGAUUGGGGAAGUCUGCUUGUGGCAGGGGUUUUGGCCAGUCGGGGGCCGUGGGCUCAUUAUGUUGGGGCUUUUUAAUUAUGGCCAAA
-.(((-.(((((((((.((((((...((..((((((((.....))))..))))..)).........((((.......)))))))))).....))))))))))))................ ( -48.00)
>DroSec_CAF1 106706 119 + 1
-CGGGAACCCCAGCAUUGCCCACAUCGCUGCGGGGAUUGGGGAAGUCUGCUUGUGGCGGGGGUUUUGGCCAGUCGGGGGCCGUGGGCUCAUUAUGUUGGGGCUUUUUAAUUAUGGCCAAA
-.((((((((((((((.((((((.((((..((((((((.....))))..))))..)))).......((((.......)))))))))).....))))))))).)))))............. ( -49.70)
>DroSim_CAF1 100447 119 + 1
-CGGGAACCCCAGCAUUGCCCACAUCGCUGCGGGGAUUGGGGAAGUCUGCUUGUGGCAGGGGUUUUGGCCAGUCGGGGGCCGUGGGCUCAUUAUGUUGGGGCUUUUUAAUUAUGGCCAAA
-.((((((((((((((.(((((((((.(((((.(((((.....))))).).....)))).)))...((((.......)))))))))).....))))))))).)))))............. ( -47.40)
>DroEre_CAF1 110251 116 + 1
-UGGGA-CCCCAACAUUGCCCACAUCCCUGCG--GAUUGGGGUAUUCUGCUUUUGGCAGGGGUUUUGGCCAGUCGGGGGCGGUGGGCUCAUUAUGUUGGGGCAUUUUAAUUAUGGCCAAA
-(((..-(((((((((.((((((((((((((.--((..(.((....)).)..)).))))))))....(((.......))).)))))).....)))))))))(((.......))).))).. ( -51.60)
>DroYak_CAF1 112917 118 + 1
UUGGGAGCCCCAACUUUGCCCACAUCCCUGCG--GAUUGGGGUAGUCUGCAUUUGGCAGGGGUUUUGGCCAGUCGCUCGCUGUGAGCUCAUUAUGUUGGGGCUUUUUAAUUAUGGCCAAA
((((((((((((((...(((...((((((((.--((.((.((....)).)).)).))))))))...))).....((((.....)))).......))))))))))...........)))). ( -48.60)
>consensus
_CGGGAACCCCAACAUUGCCCACAUCGCUGCG_GGAUUGGGGAAGUCUGCUUGUGGCAGGGGUUUUGGCCAGUCGGGGGCCGUGGGCUCAUUAUGUUGGGGCUUUUUAAUUAUGGCCAAA
.......(((((((((.(((((((((.((((.(.((.((((....)))).)).).)))).)))...((((.......)))))))))).....)))))))))................... (-37.34 = -38.14 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 17,223,171 – 17,223,289
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.44
Mean single sequence MFE -36.57
Consensus MFE -30.58
Energy contribution -31.90
Covariance contribution 1.32
Combinations/Pair 1.08
Mean z-score -2.25
Structure conservation index 0.84
SVM decision value 2.27
SVM RNA-class probability 0.991565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17223171 118 - 23771897
UUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCCCCAAUCCUCGCAGCGAUGUGGGCAAUGUUGGGGU-CCCG-
..................((((((((((.....((((((((((.......)))).......((((.....)))).......................)))))).))))))))))-....- ( -38.70)
>DroSec_CAF1 106706 119 - 1
UUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCCGCCACAAGCAGACUUCCCCAAUCCCCGCAGCGAUGUGGGCAAUGCUGGGGUUCCCG-
.(((((((..........((..((......)).))...(((...)))..)))))))((((((.((...(((....)))........((((((....))))))....)).))))))....- ( -31.80)
>DroSim_CAF1 100447 119 - 1
UUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCCCCAAUCCCCGCAGCGAUGUGGGCAAUGCUGGGGUUCCCG-
.................(((((((.(((.....((((((((((.......)))).......((((.....)))).......................)))))).))).)))))))....- ( -35.10)
>DroEre_CAF1 110251 116 - 1
UUUGGCCAUAAUUAAAAUGCCCCAACAUAAUGAGCCCACCGCCCCCGACUGGCCAAAACCCCUGCCAAAAGCAGAAUACCCCAAUC--CGCAGGGAUGUGGGCAAUGUUGGGG-UCCCA-
..................((((((((((.....((((((.(((.......)))......((((((.....................--.))))))..)))))).)))))))))-)....- ( -38.25)
>DroYak_CAF1 112917 118 - 1
UUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCUCACAGCGAGCGACUGGCCAAAACCCCUGCCAAAUGCAGACUACCCCAAUC--CGCAGGGAUGUGGGCAAAGUUGGGGCUCCCAA
.................(((((((((.......((((.....))))...((.(((....((((((....((..(....)..))...--.))))))...))).))..)))))))))..... ( -39.00)
>consensus
UUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCCCCAAUCC_CGCAGCGAUGUGGGCAAUGUUGGGGUUCCCG_
..................((((((((((.....((((((((((.......)))).......((((.....)))).......................)))))).))))))))))...... (-30.58 = -31.90 +   1.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 17,223,209 – 17,223,321
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.45
Mean single sequence MFE -21.56
Consensus MFE -18.86
Energy contribution -19.06
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.87
SVM decision value 2.00
SVM RNA-class probability 0.985362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17223209 112 - 23771897
A--------AAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCC
.--------.............((((........)))).(((((((((..........((..((......)).))...(((...)))..)))))))))...((((.....))))...... ( -21.60)
>DroSec_CAF1 106745 112 - 1
A--------AAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCCGCCACAAGCAGACUUCC
.--------..................((((....((..(((((((((..........((..((......)).))...(((...)))..))))))))).....)).....))))...... ( -19.10)
>DroSim_CAF1 100486 112 - 1
A--------AAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCC
.--------.............((((........)))).(((((((((..........((..((......)).))...(((...)))..)))))))))...((((.....))))...... ( -21.60)
>DroEre_CAF1 110287 112 - 1
C--------AAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAUGCCCCAACAUAAUGAGCCCACCGCCCCCGACUGGCCAAAACCCCUGCCAAAAGCAGAAUACC
.--------.............((((........)))).(((((((((........(((......))).....((.....)).......)))))))))...((((.....))))...... ( -19.40)
>DroYak_CAF1 112955 120 - 1
AAAAGCAGAAAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCUCACAGCGAGCGACUGGCCAAAACCCCUGCCAAAUGCAGACUACC
....((..(((((...)))))..))..(((((...((..(((((((((..............((......)).((((.....))))...))))))))).....))....)))))...... ( -26.10)
>consensus
A________AAAUUUCAUUUUAAGCGACUGCAAACGCUCUUUUGGCCAUAAUUAAAAAGCCCCAACAUAAUGAGCCCACGGCCCCCGACUGGCCAAAACCCCUGCCACAAGCAGACUUCC
......................((((........)))).(((((((((..............((......)).((.....)).......)))))))))...((((.....))))...... (-18.86 = -19.06 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:47 2006