Locus 577

Sequence ID X_DroMel_CAF1
Location 1,636,516 – 1,636,676
Length 160
Max. P 0.815440
window919 window920 window921

overview

Window 9

Location 1,636,516 – 1,636,636
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.00
Mean single sequence MFE -34.92
Consensus MFE -22.53
Energy contribution -23.23
Covariance contribution 0.70
Combinations/Pair 1.45
Mean z-score -1.68
Structure conservation index 0.65
SVM decision value 0.58
SVM RNA-class probability 0.790391
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1636516 120 + 22224390
CAGCUAAGGCGGCACUUGCUUCGUUAUGCAAUAUUUCCUACAGUCCAAUGGUGGUGCCACAGAAGAACGUACCCCUGCCAAUCGACGACAAGUCGUCAUCGAUGGAGUUGCCUCAGAUAC
...((.(((((((..((((........))))............((((.(((((((((...........)))))...))))...(((((....))))).....))))))))))).)).... ( -34.90)
>DroVir_CAF1 2450 120 + 1
CCGCUAAAGCCGCGCUUGCAUCUUUGUGCAAUAUUUCUUAUAGUCCGAUGAUGGCGCCACAGAAGAAUGCGCCAUUACCAAUAGAUGAUAAGUCAUCAUCAAUGGAAUUACCGCAAAUAC
..((....)).(((.((((((....))))))............((((.(((((((((...........))))))))).)....((((((.....))))))...))).....)))...... ( -31.10)
>DroGri_CAF1 2038 120 + 1
CCGCCAAGGCAGCGCUUGCCUCGCUGUGCAAUAUCUCAUAUAGUCCAAUGAUGGCACCGCAGAAGAACGCACCGUUGCCCAUUGAUGACAAAUCGUCGUCAAUGGAAUUGCCGCAAAUAC
..((...(((((((..(((((((.((..(.((((...)))).)..)).))).)))).)))........(((....)))(((((((((((.....)))))))))))...))))))...... ( -38.40)
>DroWil_CAF1 16986 120 + 1
CUGCCAAGGCCGCACUUGCCUCGCUGUGCAAUAUCUCGUAUAGUCCAAUGAUGGCACCCCAAAAGAAUGUGCCGCUGCCCAUUGAUGAUAAGACAUCGUCAAUGGAAUUGCCACAAAUCC
.(((((((((.......)))).(((((((........))))))).......)))))...........((((..((...(((((((((((.....)))))))))))....))))))..... ( -35.40)
>DroMoj_CAF1 3328 120 + 1
CCGCGAAGGCUGCUUUAGCCUCUCUGUGCAAUAUAUCUUACAGUCCGAUGAUGGCACCACAGAAAAAUGCGCCGUUACCCAUUGACGAGAAGUCAUCGUCGAUGGAAUUACCACAAAUAC
.((((.((((((...)))))).((((((.....((((............))))....))))))....)))).......((((((((((.......))))))))))............... ( -33.30)
>DroAna_CAF1 1301 120 + 1
CUGCCAAAGCGGCUCUGGCCUCGCUCUGCAACAUCUCGUAUAGCCCGAUGGUGGUGCCACAAAAGAACGUGCCACUGCCCAUCGACGACAAGUCAUCGUCCAUGGAACUGCCCCAGAUCC
..(((.....)))(((((....(((.(((........))).)))(((((((..(((.(((........))).)))..).))))(((((.......)))))...)).......)))))... ( -36.40)
>consensus
CCGCCAAGGCCGCACUUGCCUCGCUGUGCAAUAUCUCGUAUAGUCCAAUGAUGGCACCACAGAAGAACGCGCCGCUGCCCAUUGACGACAAGUCAUCGUCAAUGGAAUUGCCACAAAUAC
..((....)).((....))........(((((................(((((((((...........))))))))).(((((((((((.....))))))))))).)))))......... (-22.53 = -23.23 +   0.70)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,636,556 – 1,636,676
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -36.88
Consensus MFE -23.68
Energy contribution -23.93
Covariance contribution 0.26
Combinations/Pair 1.52
Mean z-score -1.89
Structure conservation index 0.64
SVM decision value 0.66
SVM RNA-class probability 0.815440
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1636556 120 + 22224390
CAGUCCAAUGGUGGUGCCACAGAAGAACGUACCCCUGCCAAUCGACGACAAGUCGUCAUCGAUGGAGUUGCCUCAGAUACACGCGGAUACGAUUGGUCGGUUGGUCUUAGAAAAGUUCAU
.((.(((((((.(((((...........))))))).((((((((((((....)))))(((...((.....))...)))............)))))))..))))).))............. ( -33.30)
>DroVir_CAF1 2490 120 + 1
UAGUCCGAUGAUGGCGCCACAGAAGAAUGCGCCAUUACCAAUAGAUGAUAAGUCAUCAUCAAUGGAAUUACCGCAAAUACAUGCGGACACUAUCGGACGGUUAGUGUUGGAAAAGUUCAU
..(((((((((((((((...........)))))))).(((...((((((.....))))))..))).....(((((......))))).....)))))))...................... ( -38.20)
>DroGri_CAF1 2078 120 + 1
UAGUCCAAUGAUGGCACCGCAGAAGAACGCACCGUUGCCCAUUGAUGACAAAUCGUCGUCAAUGGAAUUGCCGCAAAUACACGCAGAUACUAUCGGACGCUUAGUGUUGGAGAAAUUCAU
..((((......((((..((((..(......)..))))(((((((((((.....)))))))))))...))))((........))..........)))).........((((....)))). ( -36.10)
>DroWil_CAF1 17026 120 + 1
UAGUCCAAUGAUGGCACCCCAAAAGAAUGUGCCGCUGCCCAUUGAUGAUAAGACAUCGUCAAUGGAAUUGCCACAAAUCCAUGCGGACACAAUUGGUCGCCUGGUAUUGGAGAAAUUCAU
...(((((((..(((...((((.....((((((((...(((((((((((.....)))))))))))..(((...)))......)))).)))).))))..)))...)))))))......... ( -39.30)
>DroMoj_CAF1 3368 120 + 1
CAGUCCGAUGAUGGCACCACAGAAAAAUGCGCCGUUACCCAUUGACGAGAAGUCAUCGUCGAUGGAAUUACCACAAAUACAUGCGGAUACCAUUGGACGGUUGGUAUUGGAAAAAUUCAU
..(((((((((((((.(...........).)))))...((((((((((.......)))))))))).....((.((......)).))....))))))))...................... ( -33.70)
>DroAna_CAF1 1341 120 + 1
UAGCCCGAUGGUGGUGCCACAAAAGAACGUGCCACUGCCCAUCGACGACAAGUCAUCGUCCAUGGAACUGCCCCAGAUCCAUGCGGACACCAUUGGCCGUCUGGUGUUGGAGAAGUUCAU
......(((((..(((.(((........))).)))..).))))(((((.......)))))....(((((.(.((((..(((.((((.((....)).)))).)))..)))).).))))).. ( -40.70)
>consensus
UAGUCCAAUGAUGGCACCACAGAAGAACGCGCCGCUGCCCAUUGACGACAAGUCAUCGUCAAUGGAAUUGCCACAAAUACAUGCGGACACCAUUGGACGGUUGGUGUUGGAAAAAUUCAU
..(.(((((((((((((...........))))))))..(((((((((((.....)))))))))))..........................))))).)...................... (-23.68 = -23.93 +   0.26)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,636,556 – 1,636,676
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -37.32
Consensus MFE -23.65
Energy contribution -22.85
Covariance contribution -0.80
Combinations/Pair 1.59
Mean z-score -1.71
Structure conservation index 0.63
SVM decision value 0.41
SVM RNA-class probability 0.726081
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1636556 120 - 22224390
AUGAACUUUUCUAAGACCAACCGACCAAUCGUAUCCGCGUGUAUCUGAGGCAACUCCAUCGAUGACGACUUGUCGUCGAUUGGCAGGGGUACGUUCUUCUGUGGCACCACCAUUGGACUG
........................((((((((((((.(.(((....(((....))).(((((((((.....)))))))))..))))))))))).......(((....))).))))).... ( -33.60)
>DroVir_CAF1 2490 120 - 1
AUGAACUUUUCCAACACUAACCGUCCGAUAGUGUCCGCAUGUAUUUGCGGUAAUUCCAUUGAUGAUGACUUAUCAUCUAUUGGUAAUGGCGCAUUCUUCUGUGGCGCCAUCAUCGGACUA
......................(((((((.....(((((......))))).....(((..(((((((...)))))))...)))..(((((((...(....)..))))))).))))))).. ( -38.30)
>DroGri_CAF1 2078 120 - 1
AUGAAUUUCUCCAACACUAAGCGUCCGAUAGUAUCUGCGUGUAUUUGCGGCAAUUCCAUUGACGACGAUUUGUCAUCAAUGGGCAACGGUGCGUUCUUCUGCGGUGCCAUCAUUGGACUA
......................(((((((.......(((......)))((((...(((((((.(((.....))).)))))))(((..((......))..)))..))))...))))))).. ( -33.10)
>DroWil_CAF1 17026 120 - 1
AUGAAUUUCUCCAAUACCAGGCGACCAAUUGUGUCCGCAUGGAUUUGUGGCAAUUCCAUUGACGAUGUCUUAUCAUCAAUGGGCAGCGGCACAUUCUUUUGGGGUGCCAUCAUUGGACUA
.........((((((....((((.((((.((((((((((......))))((...((((((((.((((...)))).))))))))..)))))))).....))))..))))...))))))... ( -38.60)
>DroMoj_CAF1 3368 120 - 1
AUGAAUUUUUCCAAUACCAACCGUCCAAUGGUAUCCGCAUGUAUUUGUGGUAAUUCCAUCGACGAUGACUUCUCGUCAAUGGGUAACGGCGCAUUUUUCUGUGGUGCCAUCAUCGGACUG
......................((((.(((((..(((((......)))))....(((((.(((((.(....)))))).)))))....(((((((......)).)))))))))).)))).. ( -34.70)
>DroAna_CAF1 1341 120 - 1
AUGAACUUCUCCAACACCAGACGGCCAAUGGUGUCCGCAUGGAUCUGGGGCAGUUCCAUGGACGAUGACUUGUCGUCGAUGGGCAGUGGCACGUUCUUUUGUGGCACCACCAUCGGGCUA
..(((((.(((((...(((..(((.((....)).)))..)))...))))).)))))....((((((.....))))))(((((...(((.((((......)))).)))..)))))...... ( -45.60)
>consensus
AUGAACUUCUCCAACACCAACCGUCCAAUAGUAUCCGCAUGUAUUUGCGGCAAUUCCAUUGACGAUGACUUGUCAUCAAUGGGCAACGGCACAUUCUUCUGUGGCGCCAUCAUCGGACUA
........................(((((.(((.(((((......((((.(...(((((.((((((.....)))))).)))))....).))))......))))))))....))))).... (-23.65 = -22.85 +  -0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:22 2006