Locus 530

Sequence ID 3R_DroMel_CAF1
Location 1,944,332 – 1,944,429
Length 97
Max. P 0.627465
window845 window846

overview

Window 5

Location 1,944,332 – 1,944,429
Length 97
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 87.75
Mean single sequence MFE -26.05
Consensus MFE -16.89
Energy contribution -16.95
Covariance contribution 0.06
Combinations/Pair 1.19
Mean z-score -1.78
Structure conservation index 0.65
SVM decision value -0.03
SVM RNA-class probability 0.518772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1944332 97 + 27905053
AUUAACGGUUCCGCUGGCUGUUGACCG---CCACAGCCGCAACCA-------UAGCCACCGGCACUACCCGCCCUCCAGUUUCUAGCUCCAAUAAGGCCAAAACGCC
......((((..((.((((((.(....---).)))))))))))).-------..(((...(((.......)))....(((.....))).......)))......... ( -22.70)
>DroSec_CAF1 102534 97 + 1
AUUAACGGUUCCGCUGGCUGUUGGCCG---CCACAGUCGCAACCA-------UAGCCACCGGCACCACUCGCCCUCCAGUUUUUAGCCCCAAUAAGGCCAAACCGCC
......(((.(((.(((((((.((..(---(.......))..)))-------)))))).))).)))............((((...(((.......))).)))).... ( -26.20)
>DroSim_CAF1 103963 97 + 1
AUUAACGGUUCCGCUGGCUGUUGGCCG---CCACAGCCGCAACCA-------UAGCCACCGACACCACCCGCCCUCCAGUUUUUAGCCCCAAUAAGGCCAAAACGCC
......(((..((.(((((((..((.(---(....)).))....)-------)))))).))..)))............(((((..(((.......))).)))))... ( -24.80)
>DroYak_CAF1 108115 107 + 1
AUUAACGGUUCCGCUGGCUGUUGGCCACAUCCACAUCCACAACCAUAGGCCAUAGCCACCGGCUCCACCCGCUCUCCAGUUUUUUGUCCCAAUAAGGCCAAAACGCC
......((..(((.(((((((.((((.....................))))))))))).)))..))............((.(((((.((......)).))))).)). ( -30.50)
>consensus
AUUAACGGUUCCGCUGGCUGUUGGCCG___CCACAGCCGCAACCA_______UAGCCACCGGCACCACCCGCCCUCCAGUUUUUAGCCCCAAUAAGGCCAAAACGCC
......((((..(.(((((((.((......))))))))))))))..........((....(((.......))).....((((...(((.......)))..)))))). (-16.89 = -16.95 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,944,332 – 1,944,429
Length 97
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 87.75
Mean single sequence MFE -37.55
Consensus MFE -29.30
Energy contribution -29.55
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -1.54
Structure conservation index 0.78
SVM decision value 0.19
SVM RNA-class probability 0.627465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1944332 97 - 27905053
GGCGUUUUGGCCUUAUUGGAGCUAGAAACUGGAGGGCGGGUAGUGCCGGUGGCUA-------UGGUUGCGGCUGUGG---CGGUCAACAGCCAGCGGAACCGUUAAU
(((...((((((.((((((.((((....(((.....))).)))).))))))((((-------((((....)))))))---)))))))..)))((((....))))... ( -35.20)
>DroSec_CAF1 102534 97 - 1
GGCGGUUUGGCCUUAUUGGGGCUAAAAACUGGAGGGCGAGUGGUGCCGGUGGCUA-------UGGUUGCGACUGUGG---CGGCCAACAGCCAGCGGAACCGUUAAU
(((((((((((((.....))))).....((((..((((.....))))(((.((((-------((((....)))))))---).))).....))))..))))))))... ( -40.80)
>DroSim_CAF1 103963 97 - 1
GGCGUUUUGGCCUUAUUGGGGCUAAAAACUGGAGGGCGGGUGGUGUCGGUGGCUA-------UGGUUGCGGCUGUGG---CGGCCAACAGCCAGCGGAACCGUUAAU
(((...((((((.((((((.((((....(((.....))).)))).))))))((((-------((((....)))))))---)))))))..)))((((....))))... ( -38.40)
>DroYak_CAF1 108115 107 - 1
GGCGUUUUGGCCUUAUUGGGACAAAAAACUGGAGAGCGGGUGGAGCCGGUGGCUAUGGCCUAUGGUUGUGGAUGUGGAUGUGGCCAACAGCCAGCGGAACCGUUAAU
((..(((((.(((....))).)))))..))....(((((......(((.(((((.(((((.....(..(....)..)....)))))..))))).)))..)))))... ( -35.80)
>consensus
GGCGUUUUGGCCUUAUUGGGGCUAAAAACUGGAGGGCGGGUGGUGCCGGUGGCUA_______UGGUUGCGGCUGUGG___CGGCCAACAGCCAGCGGAACCGUUAAU
(((...((((((....(((.((((....(((.....))).)))).)))(..(((((.....)))))..)............))))))..)))((((....))))... (-29.30 = -29.55 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:21 2006