Locus 2262

Sequence ID X_DroMel_CAF1
Location 6,124,534 – 6,124,962
Length 428
Max. P 0.993279
window3658 window3659 window3660 window3661 window3662 window3663

overview

Window 8

Location 6,124,534 – 6,124,652
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.12
Mean single sequence MFE -35.11
Consensus MFE -22.38
Energy contribution -25.94
Covariance contribution 3.56
Combinations/Pair 1.21
Mean z-score -1.68
Structure conservation index 0.64
SVM decision value -0.00
SVM RNA-class probability 0.531983
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124534 118 + 22224390
AUAGGCA-GCUGACUGGAAAGUCGUCGCCUGCUCUCUCGCUCACUCUCGGGCGGUAGGUUACUUUGUUU-UCGCUCUCUGCCACUUAAAGUGACCGUUUCUUUUGUCUAGUCUAUUGGAA
.(((((.-((.((((....)))))).))))).....((((((......))))))..((((((((((...-..((.....))....))))))))))..........(((((....))))). ( -36.30)
>DroSec_CAF1 25805 119 + 1
AUAGGCAAGCUGACUGGAAAGUCGCCGCCUGCUCUCUCGCUCACUCUCGGGCGGUAGGUUACUUUGUUU-UCGCUCUCUGCCACCUAAAGUGACCGUUUCUUUUGUCUAGUCUAUUGGAA
.((((((((..((((....))))((((((((................)))))))).((((((((((...-..((.....))....))))))))))......))))))))........... ( -37.89)
>DroEre_CAF1 22919 119 + 1
AUAGGCAAGCUGGCUGGAAAGUCGCCGCCUGCUCUCUCGCUCACUCUCGGGCAGCUCUU-ACUUUGUUUGACAUUGUGUGCCUCUUAAUGUGGCCAUUUCUUUUGUCAAACCAAUUGAGA
.(((((..((.((((....)))))).))))).......((((......))))...((((-(.((.((((((((..(((.(((.(.....).))))))......)))))))).)).))))) ( -37.70)
>DroYak_CAF1 20592 120 + 1
AUAGGCAAGCUGACUGGAAAGUCGUCGCCUGCUCUCUCGCUCACUCUCGGGCAGCAGUUCACUUUGCUUGACAAUUUUUACCUCUUAAUGUGGCCAUUUCUUUUGUCUAACCUAUUGAGA
.(((((..((.((((....)))))).)))))...((((((((......))))(((((......))))).(((((......((.(.....).)).........))))).........)))) ( -28.56)
>consensus
AUAGGCAAGCUGACUGGAAAGUCGCCGCCUGCUCUCUCGCUCACUCUCGGGCAGCAGGUUACUUUGUUU_ACACUCUCUGCCACUUAAAGUGACCAUUUCUUUUGUCUAACCUAUUGAAA
.((((((((..((((....))))((((((((................)))))))).((((((((((...((.((.....)).)).))))))))))......))))))))........... (-22.38 = -25.94 +   3.56)

alignment

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secondary structure

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Window 9

Location 6,124,652 – 6,124,771
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 91.46
Mean single sequence MFE -30.40
Consensus MFE -26.20
Energy contribution -25.20
Covariance contribution -1.00
Combinations/Pair 1.21
Mean z-score -2.05
Structure conservation index 0.86
SVM decision value 1.18
SVM RNA-class probability 0.926505
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124652 119 + 22224390
AUGAGAUUUCGCAUUGACAAGAGUAUUUAACACAUGAAGGCCAAUCAAUUGGCUAGCUGCAAUACGCAAAAUUGGGCAUUGAAAACAAAAUGCGUAGUGCAUAUGUGCACUGCUUUUAU
..................(((((((.....((((((..((((((....))))))...((((.((((((...(((...........)))..)))))).))))))))))...))))))).. ( -29.00)
>DroSec_CAF1 25924 119 + 1
AUGAGAUUUCGCAUUGGCAAGAGUAUUUAACACAUGAAGGCCAAUCAAUUGGCUAGCUGCAAUACGCAUAAUUGGGCAUUGAAAACAAAAUGCGUAGUGUAUUGGUGCACUGCUUUCAU
((((((....((((((((....((.....)).......((((((....)))))).))).((((.(.((....)).).)))).......)))))((((((((....)))))))))))))) ( -30.70)
>DroEre_CAF1 23038 119 + 1
AUGAGAUUUUGCAUUGUCAAGAGUAUUUAACACAUGAAGGCCAAUCAAUUGGCUAGCUGCAAUGUGCAUAAUUAGGCAUUGAAAAUAAAAUGCGUAGUGCAUAGGUGCAAUGCUUUUAU
....(((........)))(((((((((...........((((((....))))))....(((.(((((((...((.(((((........))))).)))))))))..)))))))))))).. ( -32.20)
>DroYak_CAF1 20712 119 + 1
AUGAGAUUUUGCAUUGGCAAGAGUAUUUAACAAAUGAAGACCAAUCAAUUGGUUAGCUGCAAUACGCAAAAUUAGGCAUUGAAAACAAAGUGCGUAGUGCAUUUGUGCAGUGUUUUCAU
((((((((((((....))))))................((((((....)))))).((((((....(((...(((.(((((........))))).)))))).....))))))..)))))) ( -29.70)
>consensus
AUGAGAUUUCGCAUUGGCAAGAGUAUUUAACACAUGAAGGCCAAUCAAUUGGCUAGCUGCAAUACGCAAAAUUAGGCAUUGAAAACAAAAUGCGUAGUGCAUAGGUGCACUGCUUUCAU
((((((....((((((.((...................((((((....)))))).(((((.....)))..((((.(((((........))))).)))))).....)))))))))))))) (-26.20 = -25.20 +  -1.00)

alignment

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secondary structure

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Window 0

Location 6,124,692 – 6,124,811
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 87.82
Mean single sequence MFE -40.27
Consensus MFE -33.26
Energy contribution -34.45
Covariance contribution 1.19
Combinations/Pair 1.17
Mean z-score -3.30
Structure conservation index 0.83
SVM decision value 2.39
SVM RNA-class probability 0.993279
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124692 119 + 22224390
CCAAUCAAUUGGCUAGCUGCAAUACGCAAAAUUGGGCAUUGAAAACAAAAUGCGUAGUGCAUAUGUGCACUGCUUUUAUCUCGCUCGCUCUCGUGAGCGAGAGAGCGGAGUUAUCGAUA
.......(((((.(((((((((((.(((...(((.(((((........))))).)))))).))).))).((((((...((((((((((....)))))))))))))))))))))))))). ( -43.30)
>DroSec_CAF1 25964 119 + 1
CCAAUCAAUUGGCUAGCUGCAAUACGCAUAAUUGGGCAUUGAAAACAAAAUGCGUAGUGUAUUGGUGCACUGCUUUCAUCUCGCUCGCUCUCAUGAGCGAGAGAGCGGAGUUAUCGAUA
...(((...(((((.((..((((((((.....((.(((((........))))).))))))))))..)).((((((...(((((((((......))))))))))))))))))))..))). ( -41.20)
>DroEre_CAF1 23078 119 + 1
CCAAUCAAUUGGCUAGCUGCAAUGUGCAUAAUUAGGCAUUGAAAAUAAAAUGCGUAGUGCAUAGGUGCAAUGCUUUUAUCUCGCUCGCUCUCAUGGGCGAGAGAGUACAGUUAUCGAUA
...(((...((((((((((((.(((((((...((.(((((........))))).)))))))))..))))..))).....(((.(((((((....))))))).)))...)))))..))). ( -39.80)
>DroYak_CAF1 20752 115 + 1
CCAAUCAAUUGGUUAGCUGCAAUACGCAAAAUUAGGCAUUGAAAACAAAGUGCGUAGUGCAUUUGUGCAGUGUUUUCAUCUCGCUUGCUCUCAUG----AGAGAGGGCGGCUAUCGAUU
......(((((((.((((((............(((((..((((((((..(..((.........))..)..))))))))....)))))(((((...----.))))).))))))))))))) ( -36.80)
>consensus
CCAAUCAAUUGGCUAGCUGCAAUACGCAAAAUUAGGCAUUGAAAACAAAAUGCGUAGUGCAUAGGUGCACUGCUUUCAUCUCGCUCGCUCUCAUGAGCGAGAGAGCGCAGUUAUCGAUA
.......(((((.(((((((...............(((((........)))))((((((((....))))))))......(((.(((((((....))))))).))).)))))))))))). (-33.26 = -34.45 +   1.19)

alignment

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secondary structure

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Window 1

Location 6,124,692 – 6,124,811
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 87.82
Mean single sequence MFE -30.60
Consensus MFE -24.48
Energy contribution -25.73
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -1.52
Structure conservation index 0.80
SVM decision value 0.18
SVM RNA-class probability 0.623327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124692 119 - 22224390
UAUCGAUAACUCCGCUCUCUCGCUCACGAGAGCGAGCGAGAUAAAAGCAGUGCACAUAUGCACUACGCAUUUUGUUUUCAAUGCCCAAUUUUGCGUAUUGCAGCUAGCCAAUUGAUUGG
.((((((......(((.((((((((.(....).))))))))....))).(.((.....((((.((((((..(((..(.....)..)))...)))))).))))....))).))))))... ( -36.90)
>DroSec_CAF1 25964 119 - 1
UAUCGAUAACUCCGCUCUCUCGCUCAUGAGAGCGAGCGAGAUGAAAGCAGUGCACCAAUACACUACGCAUUUUGUUUUCAAUGCCCAAUUAUGCGUAUUGCAGCUAGCCAAUUGAUUGG
.((((((...((..(((.(((((((....))))))).)))..)).(((((((........))))((((((.(((..(.....)..)))..))))))......))).....))))))... ( -32.20)
>DroEre_CAF1 23078 119 - 1
UAUCGAUAACUGUACUCUCUCGCCCAUGAGAGCGAGCGAGAUAAAAGCAUUGCACCUAUGCACUACGCAUUUUAUUUUCAAUGCCUAAUUAUGCACAUUGCAGCUAGCCAAUUGAUUGG
.........((((((((.(((((.(....).))))).)))......((((((((....))))....(((((........)))))......))))....)))))....((((....)))) ( -26.50)
>DroYak_CAF1 20752 115 - 1
AAUCGAUAGCCGCCCUCUCU----CAUGAGAGCAAGCGAGAUGAAAACACUGCACAAAUGCACUACGCACUUUGUUUUCAAUGCCUAAUUUUGCGUAUUGCAGCUAACCAAUUGAUUGG
((((((((((.((.(((((.----...)))))...(((((((.....((.((.((((((((.....))).)))))...)).))....))))))).....)).)))).....)))))).. ( -26.80)
>consensus
UAUCGAUAACUCCGCUCUCUCGCUCAUGAGAGCGAGCGAGAUAAAAGCAGUGCACAAAUGCACUACGCAUUUUGUUUUCAAUGCCCAAUUAUGCGUAUUGCAGCUAGCCAAUUGAUUGG
.((((((.....(((((((........)))))))((((((((((((((((((((....))))))..)).)))))))))((((((.((....)).))))))..))).....))))))... (-24.48 = -25.73 +   1.25)

alignment

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secondary structure

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Window 2

Location 6,124,732 – 6,124,851
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 84.73
Mean single sequence MFE -34.22
Consensus MFE -22.62
Energy contribution -22.88
Covariance contribution 0.25
Combinations/Pair 1.27
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value -0.00
SVM RNA-class probability 0.532204
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124732 119 + 22224390
GAAAACAAAAUGCGUAGUGCAUAUGUGCACUGCUUUUAUCUCGCUCGCUCUCGUGAGCGAGAGAGCGGAGUUAUCGAUAAGUUGCCUGACCCUCUUUCCAACACUAAUCUCAGCUGUUG
((((.......((((((((((....)))))))).....((((((((((....))))))))))..))((.((((.(((....)))..))))))..))))(((((((......)).))))) ( -39.10)
>DroSec_CAF1 26004 119 + 1
GAAAACAAAAUGCGUAGUGUAUUGGUGCACUGCUUUCAUCUCGCUCGCUCUCAUGAGCGAGAGAGCGGAGUUAUCGAUAAGUUGACGUACCCUCUUUCCAACACUGAUCUCAGCUGUGG
..........(((((....(((((((((.((((((...(((((((((......))))))))))))))).).)))))))).....)))))........(((.(((((....))).))))) ( -38.10)
>DroEre_CAF1 23118 119 + 1
GAAAAUAAAAUGCGUAGUGCAUAGGUGCAAUGCUUUUAUCUCGCUCGCUCUCAUGGGCGAGAGAGUACAGUUAUCGAUAAAUUCCCUGUCCCUCUUUCCAACACUAAUCGCAGCUGUUC
....((((((.((((.(..(....)..).))))))))))(((.(((((((....))))))).))).((((((..((((............................)))).)))))).. ( -29.79)
>DroYak_CAF1 20792 115 + 1
GAAAACAAAGUGCGUAGUGCAUUUGUGCAGUGUUUUCAUCUCGCUUGCUCUCAUG----AGAGAGGGCGGCUAUCGAUUAAUUCCCUGCCCCUCUUUUCAACACUAAUCGCAGCUGUUC
...((((...((((((((((((..(.((((((.........))).))).)..)))----((((.((((((.....((.....)).))))))))))......)))))..))))..)))). ( -29.90)
>consensus
GAAAACAAAAUGCGUAGUGCAUAGGUGCACUGCUUUCAUCUCGCUCGCUCUCAUGAGCGAGAGAGCGCAGUUAUCGAUAAAUUCCCUGACCCUCUUUCCAACACUAAUCGCAGCUGUUC
...........((((((((((....)))))))).((((((..((((((((((........))))))).)))....))))))...............................))..... (-22.62 = -22.88 +   0.25)

alignment

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secondary structure

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Window 3

Location 6,124,851 – 6,124,962
Length 111
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 74.70
Mean single sequence MFE -29.10
Consensus MFE -16.92
Energy contribution -17.17
Covariance contribution 0.24
Combinations/Pair 1.34
Mean z-score -2.18
Structure conservation index 0.58
SVM decision value 1.59
SVM RNA-class probability 0.965792
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6124851 111 + 22224390
-AAGUGUAUGCGUUUGUGUGUGUAUUCUAACAGAGGGAGGUGUAUAAAUUUGUAUAUACAUACAUAUGUAUGCAUGUAGACGCACAGACAUCUUCUUGUGACGUUCUUUGUU
-..((((((((((.(((((((((((....(((((...(......)...)))))))))))))))).))))))))))...(((((((((........))))).))))....... ( -32.60)
>DroSec_CAF1 26123 99 + 1
-AGGUGCGUGCGUGUGU-UGUGUAUUCCAACAGAGGGAGGUGUGUAAAUUUGUAUGUACAU--------AUGCAUGUAUACGCACAGACAUC---UUGUGAAGUUCUUUGUU
-((((((((((((((..-((((((((((......)))).(((..((......))..))).)--------)))))...)))))))).).))))---)................ ( -25.40)
>DroYak_CAF1 20907 104 + 1
C---UGCAAGUGC--GUGUGUGUAUUCUAACAGAUGGAGGUGUGUAAAUUUGUAUGUACAAAUGGAUGUACAUACAAACAAGCACGGACAUA---UUGUGACGUUCUUUGUU
.---.(((((.((--((((((((.(((((.....))))).(((((...((((((((((((......))))))))))))...))))).)))))---)....))))..))))). ( -29.30)
>consensus
_A_GUGCAUGCGU_UGUGUGUGUAUUCUAACAGAGGGAGGUGUGUAAAUUUGUAUGUACAUA___AUGUAUGCAUGUACACGCACAGACAUC___UUGUGACGUUCUUUGUU
.........(((((((((((((((((((.......))))(((((((......))))))).........)))))))))))))))....(((......)))............. (-16.92 = -17.17 +   0.24)

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 10:30:03 2006