Locus 7958

Sequence ID 3L_DroMel_CAF1
Location 21,091,927 – 21,092,125
Length 198
Max. P 0.999940
window12981 window12982 window12983 window12984

overview

Window 1

Location 21,091,927 – 21,092,047
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -34.56
Consensus MFE -27.40
Energy contribution -27.52
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value 0.23
SVM RNA-class probability 0.645135
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21091927 120 + 23771897
AUAUUCGGCACAGGUCGGGAAAUGGCAAUCAUCAGAAUGACAGCUCGGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACUGCAAAGACAUCGUCCAUUUCUGUCAUGGAUAUGGCC
...((((((....))))))....(((....(((...(((((((...(((.(((((...(..........).)))))......((....))......)))....))))))).)))...))) ( -29.70)
>DroSec_CAF1 142138 120 + 1
AUAUCCGGCACAGGUCAGGAAAUGGCAAUCAUCAGAAUGACAGCUCCGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCC
(((((((.....((((.(((..((.((.((....)).)).))..)))...)))).........((((.(((((((((((((........)).)))))))))))))))..))))))).... ( -38.40)
>DroSim_CAF1 49194 120 + 1
AUAUCCGGCACAGGUCAGGAAAUGGCAAUCAUCAGAAUGACAGCUCCUAAGGCCAAAACCAACGCAGCAGGUGGCUAAUUCACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCC
((((((((....((((((((..((.((.((....)).)).))..))))..))))....))...((((.(((((((((((((........)).)))))))))))))))...)))))).... ( -37.30)
>DroEre_CAF1 64394 120 + 1
AUAUCCGGCACAGGUCAGGGAACGGCAAUCAUCAGAAUGACAACUCAGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCC
(((((((((....(((.(....))))..((((....))))...........))).........((((.((((((((.((((........)).)).))))))))))))...)))))).... ( -30.60)
>DroYak_CAF1 36270 120 + 1
AUAUCCGGCACAGGUCGGGAAAUGGCAAUAAUCAGAAUGACAGCUCAGAAGGCCAAUACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCC
...((((((....))))))....(((....(((...(((((((...(((.((((............((.(((((.....)))))))...(....))))).)))))))))).)))...))) ( -36.80)
>consensus
AUAUCCGGCACAGGUCAGGAAAUGGCAAUCAUCAGAAUGACAGCUCAGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCC
(((((((((....))).(((((((((.....((.........(((.....))).............((.(((((.....)))))))...)).....))))))))).....)))))).... (-27.40 = -27.52 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 21,091,967 – 21,092,087
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -42.84
Consensus MFE -38.94
Energy contribution -39.78
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -3.45
Structure conservation index 0.91
SVM decision value 4.70
SVM RNA-class probability 0.999940
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21091967 120 + 23771897
CAGCUCGGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACUGCAAAGACAUCGUCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCA
..........((((((.((...(((.....)))(((((.....(((((((((((.(.((((.(((.....))).))))).)))))))).))).......))))).....)).)))))).. ( -38.40)
>DroSec_CAF1 142178 120 + 1
CAGCUCCGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCA
.......((((((((((......((((.(((((((((((((........)).)))))))))))))))((((((....))))))..))))))..))))....(((((((...))))))).. ( -44.90)
>DroSim_CAF1 49234 120 + 1
CAGCUCCUAAGGCCAAAACCAACGCAGCAGGUGGCUAAUUCACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCCAUGUCUUUGGCUACUUCAUUUGGCUAAGAGUCUUGGCCCA
..........(((((((......((((.(((((((((((((........)).)))))))))))))))((((((....))))))..))))))).........(((((((...))))))).. ( -40.60)
>DroEre_CAF1 64434 120 + 1
CAACUCAGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUGGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCA
.......(((((((............((.(((((.....))))))).(((((((.((((((.(((.....))).))))))))))))).)))..))))....(((((((...))))))).. ( -44.70)
>DroYak_CAF1 36310 120 + 1
CAGCUCAGAAGGCCAAUACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCA
.......(((((((............((.(((((.....)))))))((((((((.((((((.(((.....))).)))))))))))))))))..))))....(((((((...))))))).. ( -45.60)
>consensus
CAGCUCAGAAGGCCAAAACAAACGCAGCAGGUGGCCAAUUCACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCA
.......(((((((............((.(((((.....)))))))((((((((.((((((.(((.....))).)))))))))))))))))..))))....(((((((...))))))).. (-38.94 = -39.78 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,091,967 – 21,092,087
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -41.32
Consensus MFE -39.04
Energy contribution -40.24
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.94
SVM decision value 3.43
SVM RNA-class probability 0.999205
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21091967 120 - 23771897
UGGGCCAAGACUCUUAGCCAAAUGAAGUUGCCAAAGACAUGGCCAUAUCCAUGACAGAAAUGGACGAUGUCUUUGCAGUGAAUUGGCCACCUGCUGCGUUUGUUUUGGCCUUCCGAGCUG
.((((((((((.(.((((..........(((.((((((((.(((((.((.......)).)))).).)))))))))))(((.......)))..)))).)...))))))))))......... ( -39.10)
>DroSec_CAF1 142178 120 - 1
UGGGCCAAGACUCUUAGCCAAAUGAAGUUGCCAAAGACAUGGACAUAUCCAUGACAGAAAUGGCCAAUGUCUUUGCGGUGAAUUGGCCACCUGCUGCGUUUGUUUUGGCCUUCGGAGCUG
.((((((((((.(.((((...........((.((((((((((.(((.((.......)).))).)).))))))))))((((.......)))).)))).)...))))))))))......... ( -39.30)
>DroSim_CAF1 49234 120 - 1
UGGGCCAAGACUCUUAGCCAAAUGAAGUAGCCAAAGACAUGGACAUAUCCAUGACAGAAAUGGCCAAUGUCUUUGCGGUGAAUUAGCCACCUGCUGCGUUGGUUUUGGCCUUAGGAGCUG
.(((((((((((.(((......))).((((((((((((((((.(((.((.......)).))).)).))))))))).((((.......)))).)))))...)))))))))))......... ( -41.20)
>DroEre_CAF1 64434 120 - 1
UGGGCCAAGACUCUUAGCCAAAUGAAGUUGCCCAAGACAUGGCCAUAUCCAUGACAGAAAUGGCCGAUGUCUUUGCGGUGAAUUGGCCACCUGCUGCGUUUGUUUUGGCCUUCUGAGUUG
.((((((((((.(.((((...........((..(((((((((((((.((.......)).)))))).))))))).))((((.......)))).)))).)...))))))))))......... ( -44.20)
>DroYak_CAF1 36310 120 - 1
UGGGCCAAGACUCUUAGCCAAAUGAAGUUGCCAAAGACAUGGCCAUAUCCAUGACAGAAAUGGCCGAUGUCUUUGCGGUGAAUUGGCCACCUGCUGCGUUUGUAUUGGCCUUCUGAGCUG
.(((((((.((.(.((((...........((.((((((((((((((.((.......)).)))))).))))))))))((((.......)))).)))).)...)).)))))))......... ( -42.80)
>consensus
UGGGCCAAGACUCUUAGCCAAAUGAAGUUGCCAAAGACAUGGCCAUAUCCAUGACAGAAAUGGCCGAUGUCUUUGCGGUGAAUUGGCCACCUGCUGCGUUUGUUUUGGCCUUCGGAGCUG
.((((((((((.(.((((...........((.((((((((((((((.((.......)).)))))).))))))))))((((.......)))).)))).)...))))))))))......... (-39.04 = -40.24 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 21,092,007 – 21,092,125
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.93
Mean single sequence MFE -33.39
Consensus MFE -27.88
Energy contribution -28.72
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.59
Structure conservation index 0.84
SVM decision value 2.81
SVM RNA-class probability 0.997187
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21092007 118 + 23771897
CACUGCAAAGACAUCGUCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAGGACGUUUCUUCCAGACAGAC--ACCCAUCCACCUA
..(((..((((...(((((.....(((((.((((((....)))))).))))).........(((((((...)))))))......)))))..)))).)))......--............. ( -31.90)
>DroSec_CAF1 142218 118 + 1
CACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAGUCCGCUUCUUCCAGACAGAC--ACCCAUCCACCUA
....((.(((((.(((((((....(((((.((((((....)))))).)))))........)))))))..))))).)).......(((.(((......)).).)))--............. ( -29.20)
>DroSim_CAF1 49274 118 + 1
CACCGCAAAGACAUUGGCCAUUUCUGUCAUGGAUAUGUCCAUGUCUUUGGCUACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAGUCCGCUUCUUCCAGACAGAC--ACCCAUCCACCUA
....((.(((((.(((((((.....((((.((((((....)))))).)))).........)))))))..))))).)).......(((.(((......)).).)))--............. ( -28.34)
>DroEre_CAF1 64474 120 + 1
CACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUGGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAGGACGCUUCUUCUAGACAGCCAGAAGCAUUCACCUA
..((((.(((((((.((((((.(((.....))).)))))))))))))..))..........(((((((...)))))))......))..((((((.((....))..))))))......... ( -41.40)
>DroYak_CAF1 36350 117 + 1
CACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAAGACGCUUCUUCCAG-CAGAC--AACCAUUCACCUA
....((((((((((.((((((.(((.....))).))))))))))))))(((..(((.....(((((((...))))))).....)))..))).......)-)....--............. ( -36.10)
>consensus
CACCGCAAAGACAUCGGCCAUUUCUGUCAUGGAUAUGGCCAUGUCUUUGGCAACUUCAUUUGGCUAAGAGUCUUGGCCCAUAAAGGACGCUUCUUCCAGACAGAC__ACCCAUCCACCUA
.....(((((((((.((((((.(((.....))).)))))))))))))))((..(((.((..(((((((...))))))).)).)))...)).............................. (-27.88 = -28.72 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:04 2006