Locus 1012

Sequence ID 2R_DroMel_CAF1
Location 4,215,408 – 4,215,568
Length 160
Max. P 0.924803
window1792 window1793 window1794

overview

Window 2

Location 4,215,408 – 4,215,528
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -39.65
Consensus MFE -31.94
Energy contribution -34.00
Covariance contribution 2.06
Combinations/Pair 1.11
Mean z-score -2.19
Structure conservation index 0.81
SVM decision value 1.16
SVM RNA-class probability 0.924803
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4215408 120 + 20766785
UCCUCCCAUAGCUUUGCUAUCAUCUAGGGGCAACUCGCUGUGGUACGUUGCCAUGGGCGAGGAAGCCAUUUAUGCUAUGUAUUCCCUGCCCAUAACCGUGCCGAUAGCGGUCUUUAUGUU
......(((((..((((((((.....(((....))).....((((((.....(((((((.((((..(((.......)))..)))).)))))))...))))))))))))))...))))).. ( -44.00)
>DroSec_CAF1 26970 120 + 1
UCUUCCCAUAGCUUUGCUCAGCUCUAGGGGCAACUCGCUGUGGUACGUUGCCAUGGCCGAGGAAUCCAUUUAUGCUGUGUAUUCCCUGCCUAUAACCAUGCCGAUAGCAGUCUUUAUGUU
...((((..((((......))))...))))..(((.(((((((((.((((....(((.(.(((((.(((.......))).)))))).)))..))))..)))).))))))))......... ( -32.00)
>DroEre_CAF1 28745 119 + 1
-CCUCCGAUAGCUUUGUUGAGCUCUAGGGGCGAUUCGCUGUGGUACGUUGCCAUGGGCGAGGAAUUCAUGUAUGCAGUGUAUUCCCUGCCCAUAACCGUGCCAAUAGCGGUUUUUAUGUU
-.((((...(((((....)))))...))))....(((((((((((((.....(((((((.(((((.(((.......))).))))).)))))))...)))))).))))))).......... ( -46.40)
>DroYak_CAF1 29607 120 + 1
UCCUCCGAUAGCUUUGUUAAGCUCUAGGGGCACAUCGCUGUGGUACGUUGCCAUGACCGAGGAAUACAUUUAUGCAGUGUAUUCCCUGCCCAUAACCAUGCCAAUAGCGGUUUUUAUGUU
..((((...(((((....)))))...))))...((((((((((((.(((...(((..((.((((((((((.....)))))))))).))..))))))..)))).))))))))......... ( -36.20)
>consensus
UCCUCCCAUAGCUUUGCUAAGCUCUAGGGGCAACUCGCUGUGGUACGUUGCCAUGGCCGAGGAAUCCAUUUAUGCAGUGUAUUCCCUGCCCAUAACCAUGCCAAUAGCGGUCUUUAUGUU
..((((...(((((....)))))...))))....(((((((((((((.....(((((((.(((((.(((.......))).))))).)))))))...)))))).))))))).......... (-31.94 = -34.00 +   2.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,215,408 – 4,215,528
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.61
Mean single sequence MFE -38.30
Consensus MFE -28.45
Energy contribution -30.33
Covariance contribution 1.87
Combinations/Pair 1.09
Mean z-score -2.44
Structure conservation index 0.74
SVM decision value 1.04
SVM RNA-class probability 0.905283
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4215408 120 - 20766785
AACAUAAAGACCGCUAUCGGCACGGUUAUGGGCAGGGAAUACAUAGCAUAAAUGGCUUCCUCGCCCAUGGCAACGUACCACAGCGAGUUGCCCCUAGAUGAUAGCAAAGCUAUGGGAGGA
........(((((((...((.((((((((((((..((((..(((.......)))..))))..)))))))))..))).))..)))).)))...(((...(.(((((...))))).).))). ( -41.80)
>DroSec_CAF1 26970 120 - 1
AACAUAAAGACUGCUAUCGGCAUGGUUAUAGGCAGGGAAUACACAGCAUAAAUGGAUUCCUCGGCCAUGGCAACGUACCACAGCGAGUUGCCCCUAGAGCUGAGCAAAGCUAUGGGAAGA
........(((((((...((.((((((((.(((.((((((...((.......)).))))))..))))))))..))).))..))).))))..(((...((((......))))..))).... ( -33.10)
>DroEre_CAF1 28745 119 - 1
AACAUAAAAACCGCUAUUGGCACGGUUAUGGGCAGGGAAUACACUGCAUACAUGAAUUCCUCGCCCAUGGCAACGUACCACAGCGAAUCGCCCCUAGAGCUCAACAAAGCUAUCGGAGG-
...........((((..(((.((((((((((((..(((((.((.((....)))).)))))..)))))))))..))).))).)))).....((((...((((......))))...)).))- ( -40.70)
>DroYak_CAF1 29607 120 - 1
AACAUAAAAACCGCUAUUGGCAUGGUUAUGGGCAGGGAAUACACUGCAUAAAUGUAUUCCUCGGUCAUGGCAACGUACCACAGCGAUGUGCCCCUAGAGCUUAACAAAGCUAUCGGAGGA
..........((((((..(((((.(((((((.(..((((((((.(.....).))))))))..).)))))))..(((......)))..)))))..)))(((((....)))))..))).... ( -37.60)
>consensus
AACAUAAAAACCGCUAUCGGCACGGUUAUGGGCAGGGAAUACACAGCAUAAAUGGAUUCCUCGCCCAUGGCAACGUACCACAGCGAGUUGCCCCUAGAGCUUAACAAAGCUAUCGGAGGA
...........((((...((.((((((((((((..(((((.((.........)).)))))..)))))))))..))).))..)))).....((((((.((((......)))).)))).)). (-28.45 = -30.33 +   1.87)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,215,448 – 4,215,568
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.08
Mean single sequence MFE -31.93
Consensus MFE -27.06
Energy contribution -26.75
Covariance contribution -0.31
Combinations/Pair 1.16
Mean z-score -1.41
Structure conservation index 0.85
SVM decision value -0.03
SVM RNA-class probability 0.520210
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4215448 120 + 20766785
UGGUACGUUGCCAUGGGCGAGGAAGCCAUUUAUGCUAUGUAUUCCCUGCCCAUAACCGUGCCGAUAGCGGUCUUUAUGUUUAUCCAAUCUCGAACCGAUGUGCCACCAUUUUACCAUUCG
((((((((((..(((((((.((((..(((.......)))..)))).))))))).(((((.......)))))........................))))))))))............... ( -35.90)
>DroSec_CAF1 27010 120 + 1
UGGUACGUUGCCAUGGCCGAGGAAUCCAUUUAUGCUGUGUAUUCCCUGCCUAUAACCAUGCCGAUAGCAGUCUUUAUGUUUAUCCAAUCUCGAACCGAUGUGCCACCAUUUUACCAUUCG
((((((((((....(((.(.(((((.(((.......))).)))))).))).((((.((((..(((....)))..)))).))))............))))))))))............... ( -27.80)
>DroEre_CAF1 28784 120 + 1
UGGUACGUUGCCAUGGGCGAGGAAUUCAUGUAUGCAGUGUAUUCCCUGCCCAUAACCGUGCCAAUAGCGGUUUUUAUGUUUUUCCAAUCGCGAACUGAUGUGCCACCAUUUUACCACUCG
(((((((((...(((((((.(((((.(((.......))).))))).)))))))((((((.......))))))........................)))))))))............... ( -36.00)
>DroYak_CAF1 29647 120 + 1
UGGUACGUUGCCAUGACCGAGGAAUACAUUUAUGCAGUGUAUUCCCUGCCCAUAACCAUGCCAAUAGCGGUUUUUAUGUUUAUCCAAUCCCGAACCGAUGUGCCACCAUUUUACCAUUCG
((((((((((..........((((((((((.....)))))))))).....(((((....(((......)))..))))).................))))))))))............... ( -28.00)
>consensus
UGGUACGUUGCCAUGGCCGAGGAAUCCAUUUAUGCAGUGUAUUCCCUGCCCAUAACCAUGCCAAUAGCGGUCUUUAUGUUUAUCCAAUCUCGAACCGAUGUGCCACCAUUUUACCAUUCG
((((((((((..(((((((.(((((.(((.......))).))))).)))))))...((((..(((....)))..)))).................))))))))))............... (-27.06 = -26.75 +  -0.31)

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 09:54:08 2006