Locus 7343

Sequence ID 2L_DroMel_CAF1
Location 20,483,733 – 20,483,904
Length 171
Max. P 0.929058
window11780 window11781 window11782

overview

Window 0

Location 20,483,733 – 20,483,833
Length 100
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 87.97
Mean single sequence MFE -32.86
Consensus MFE -23.80
Energy contribution -23.82
Covariance contribution 0.02
Combinations/Pair 1.15
Mean z-score -1.67
Structure conservation index 0.72
SVM decision value 0.06
SVM RNA-class probability 0.562076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20483733 100 + 22407834
CAGCAAACAGCGCCGGGAAAAUC----------------GGAAAACCUCAGUGCAAACCGAGGGACGAGUGACAGUGUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAAAUG
..((.....)).((((.....))----------------)).........((((((((((((((((.((..((.....))..)))))).))).).))))))))............. ( -30.50)
>DroSec_CAF1 885 100 + 1
CAGCAAACAGCGCCGGGAAAAUC----------------GGAAAACCUCAGUGCAAACCGAGGGACGAGUGACAGCGUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAGAUG
..((((((.((.((((.....))----------------))....((((.((....)).))))...((((((((((.....))))).))))).)))))))).((((......)))) ( -34.70)
>DroSim_CAF1 6267 100 + 1
CAGCAAACAGCGCCGGGAAAAUC----------------GGAAAACCUCAGUGCAAACCGAGGGACGAGUGACAGCGUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAGAUG
..((((((.((.((((.....))----------------))....((((.((....)).))))...((((((((((.....))))).))))).)))))))).((((......)))) ( -34.70)
>DroEre_CAF1 825 116 + 1
CAGCAAACAGCGUCGGGAAAAUCGUCGGGAAACUCGCUGGGAAAACCUCAGUGCCAACCGAGGGACGACUGACAGCGUGUUGUUGACCGCCCUGCGUUUGCACAUCAAAUCAAAUG
..((((((.(((((((.....((.((((......(((((((.....)))))))....)))).))....))))).(((.(((...))))))...))))))))............... ( -37.50)
>DroYak_CAF1 100 100 + 1
CAGCAAACAGCGUCGGAAAAAUC----------------GGAAAACCUCAGUGAAAACCAAGGGUCGAGUGACAGCGCGUUGUUGACCGACCUGCGCUUGCACAUCAAAUCAAAUG
..((((.(((.(((((.....((----------------((....(((..((....))..))).))))..(((((....)))))..))))))))...))))............... ( -26.90)
>consensus
CAGCAAACAGCGCCGGGAAAAUC________________GGAAAACCUCAGUGCAAACCGAGGGACGAGUGACAGCGUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAAAUG
..((((...((((.(((.............................(((.((....)).)))((((((.((((.....)))))))))).))).))))))))............... (-23.80 = -23.82 +   0.02)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,483,793 – 20,483,904
Length 111
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 73.63
Mean single sequence MFE -30.28
Consensus MFE -10.60
Energy contribution -11.74
Covariance contribution 1.14
Combinations/Pair 1.17
Mean z-score -2.45
Structure conservation index 0.35
SVM decision value 1.20
SVM RNA-class probability 0.929058
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20483793 111 + 22407834
GUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAAAUGUAUUUGCUGCGGCAGCUUUGUGAA---ACAAAAACCAGCAAAAAGUGGAGCAGC-----CGGACAAACAACAACUAACA
.((((((((((((..((((.((..(((((........)))).(((((((.(.....((((....---.))))..))))))))..)..)))))).-----))))).)))))))....... ( -34.70)
>DroSec_CAF1 945 111 + 1
GUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAGAUGUAUUUGCUGCGGCAGCUUUGUGAA---ACAAAAACCAGCAAAAAGUGGAGCAGC-----CGGACAACCAACAACUCACA
.((((((((((((..((((.((..((((((......))))).(((((((.(.....((((....---.))))..))))))))..)..)))))).-----))))))).)))))....... ( -38.60)
>DroSim_CAF1 6327 111 + 1
GUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAGAUGUAUUUGCUGCGGCAGCUUUGUGAA---ACAAAAACCAGCAAAAAGUGGAGCAGC-----CGGACAAACAACAACUCACA
.((((((((((((..((((.((..((((((......))))).(((((((.(.....((((....---.))))..))))))))..)..)))))).-----))))).)))))))....... ( -38.60)
>DroEre_CAF1 901 108 + 1
GUGUUGUUGACCGCCCUGCGUUUGCACAUCAAAUCAAAUGUAUUUGCUGCGGCAGCUUUUUGAA---ACAAAACCCGGCAAAAAGCGGAGCAGC-----CAGGCAA---ACAACUAACA
..((((((....(((.((((((((..........))))))))...(((((....((((((((..---.(.......).))))))))...)))))-----..))).)---)))))..... ( -31.70)
>DroYak_CAF1 160 112 + 1
GCGUUGUUGACCGACCUGCGCUUGCACAUCAAAUCAAAUGUAUUUGCUGCGGCAGCUUUGUGAA---ACAAAAACCAGCAAAAAGUGGAGCAGCAGCC-AAGGCAA---ACAACUAAUA
..((((((..((...(((((((..(((((........)))).(((((((.(.....((((....---.))))..))))))))..)..).)).))))..-..))..)---)))))..... ( -28.80)
>DroPer_CAF1 43244 102 + 1
AUGUC-----------------CGUGCAUCAAAUCAAAUGUAUUUGCUGCCGCAGCUUUGCAGACCUACAAAAGACCCAAAAAACUANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
..(((-----------------.(.(((.((((((....).))))).))))((......)).)))...................................................... (  -9.30)
>consensus
GUGUUGUUGUCCGCUCUGCGUUUGCACAUCAAAUCAAAUGUAUUUGCUGCGGCAGCUUUGUGAA___ACAAAAACCAGCAAAAAGUGGAGCAGC_____CGGACAA___ACAACUAACA
..(((((.......((((.......((((........))))....(((((....(((((......................)))))...))))).....))))......)))))..... (-10.60 = -11.74 +   1.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,483,793 – 20,483,904
Length 111
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 73.63
Mean single sequence MFE -32.37
Consensus MFE -14.88
Energy contribution -16.45
Covariance contribution 1.57
Combinations/Pair 1.17
Mean z-score -1.98
Structure conservation index 0.46
SVM decision value 0.73
SVM RNA-class probability 0.836031
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20483793 111 - 22407834
UGUUAGUUGUUGUUUGUCCG-----GCUGCUCCACUUUUUGCUGGUUUUUGU---UUCACAAAGCUGCCGCAGCAAAUACAUUUGAUUUGAUGUGCAAACGCAGAGCGGACAACAACAC
.......(((((((.(((((-----.((((.......((((((((((((((.---....)))))..)))..))))))((((((......)))))).....))))..)))))))))))). ( -35.50)
>DroSec_CAF1 945 111 - 1
UGUGAGUUGUUGGUUGUCCG-----GCUGCUCCACUUUUUGCUGGUUUUUGU---UUCACAAAGCUGCCGCAGCAAAUACAUCUGAUUUGAUGUGCAAACGCAGAGCGGACAACAACAC
.......(((((.(((((((-----.((((.......((((((((((((((.---....)))))..)))..))))))((((((......)))))).....))))..)))))))))))). ( -37.80)
>DroSim_CAF1 6327 111 - 1
UGUGAGUUGUUGUUUGUCCG-----GCUGCUCCACUUUUUGCUGGUUUUUGU---UUCACAAAGCUGCCGCAGCAAAUACAUCUGAUUUGAUGUGCAAACGCAGAGCGGACAACAACAC
.......(((((((.(((((-----.((((.......((((((((((((((.---....)))))..)))..))))))((((((......)))))).....))))..)))))))))))). ( -37.80)
>DroEre_CAF1 901 108 - 1
UGUUAGUUGU---UUGCCUG-----GCUGCUCCGCUUUUUGCCGGGUUUUGU---UUCAAAAAGCUGCCGCAGCAAAUACAUUUGAUUUGAUGUGCAAACGCAGGGCGGUCAACAACAC
.....(((((---.....((-----(((((((.((..(((((.((((...((---((....)))).))).).)))))((((((......)))))).....)).)))))))))))))).. ( -33.30)
>DroYak_CAF1 160 112 - 1
UAUUAGUUGU---UUGCCUU-GGCUGCUGCUCCACUUUUUGCUGGUUUUUGU---UUCACAAAGCUGCCGCAGCAAAUACAUUUGAUUUGAUGUGCAAGCGCAGGUCGGUCAACAACGC
.....(((((---(.(((..-.(((((.((.((((.....).))).(((((.---....)))))..)).)))))...............(((.(((....))).)))))).)))))).. ( -32.70)
>DroPer_CAF1 43244 102 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNUAGUUUUUUGGGUCUUUUGUAGGUCUGCAAAGCUGCGGCAGCAAAUACAUUUGAUUUGAUGCACG-----------------GACAU
................................(((((((.(((..((.....))..))).)))))))(((((.(((((.(....)))))).))).))-----------------..... ( -17.10)
>consensus
UGUUAGUUGU___UUGUCCG_____GCUGCUCCACUUUUUGCUGGUUUUUGU___UUCACAAAGCUGCCGCAGCAAAUACAUUUGAUUUGAUGUGCAAACGCAGAGCGGACAACAACAC
.....(((((....((.(((......((((.......(((((((((((((((......))))))..))))..)))))((((((......)))))).....))))..))).))))))).. (-14.88 = -16.45 +   1.57)

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 12:34:14 2006