Locus 275

Sequence ID 3R_DroMel_CAF1
Location 1,072,232 – 1,072,388
Length 156
Max. P 0.805033
window473 window474 window475

overview

Window 3

Location 1,072,232 – 1,072,348
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 86.76
Mean single sequence MFE -26.81
Consensus MFE -19.61
Energy contribution -20.62
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.73
SVM decision value 0.07
SVM RNA-class probability 0.567488
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1072232 116 + 27905053
ACUGAUUUAACUAAAAAGUGCCGUUUAACUCCACUGCGCACCAUAAGCUGUAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUUCGGAACACUUUCCAUCAAUCAGCCAA
.((((((.......(((((((((............((((.(((........(((..(((.....)))..)))..))).))))........)))..)))))).....)))))).... ( -25.25)
>DroSec_CAF1 8346 116 + 1
ACUGAUUUAACUGAAAAGUGCUGUUUAACUCCCGUGCGCGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAA
.((((((....((.(((((((((....((....))((((((((.(((.(((((((((.....))))))))))))))))))))........)))..)))))).))..)))))).... ( -33.00)
>DroEre_CAF1 8824 115 + 1
AUUGAUUUAACUGAGAAGUGCUGCUUAACUCCCC-AAGCGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAA
.((((((.....(((((((((.((((........-))))((((.(((.(((((((((.....)))))))))))))))))))))).)))...((((....))))...)))))).... ( -30.10)
>DroYak_CAF1 14681 111 + 1
AUUGAUUUAACUGAGAAGCGCUUUUAAAGUCCCC-ACCCGCCAUAAGCCGUAUAUGUACUUAAUGCGUGAGUUUUGGUGCGCU----UUCCGAAACACUUUCCAUCAAUCAGCCCA
.((((((.....(..((((((.......((....-))..((((.((((((..(((.......)))..)).)))))))))))))----)..)(((.....)))....)))))).... ( -18.90)
>consensus
ACUGAUUUAACUGAAAAGUGCUGUUUAACUCCCC_ACGCGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAA
.((((((....((.((((((...............((((((((.(((.(((((((((.....)))))))))))))))))))).............)))))).))..)))))).... (-19.61 = -20.62 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,072,232 – 1,072,348
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 86.76
Mean single sequence MFE -31.38
Consensus MFE -25.27
Energy contribution -25.89
Covariance contribution 0.62
Combinations/Pair 1.18
Mean z-score -1.60
Structure conservation index 0.81
SVM decision value 0.31
SVM RNA-class probability 0.682978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1072232 116 - 27905053
UUGGCUGAUUGAUGGAAAGUGUUCCGAAAAGUAAGCGCGCCAAAAUACACACAUUAAGUACAUAUACAGCUUAUGGUGCGCAGUGGAGUUAAACGGCACUUUUUAGUUAAAUCAGU
...(((((((..(((((((((((...........((((((((............(((((.........))))))))))))).((........)))))))))))))....))))))) ( -33.20)
>DroSec_CAF1 8346 116 - 1
UUGGCUGAUUGAUGGAAAGUGUUCCGGAAAGUAAGCGCGCCAAAAUACACACAUUAAGUACAUAUGCAGCUUAUGGCGCGCACGGGAGUUAAACAGCACUUUUCAGUUAAAUCAGU
...(((((((..(((((((((((...........((((((((............(((((.........)))))))))))))((....)).....)))))))))))....))))))) ( -37.60)
>DroEre_CAF1 8824 115 - 1
UUGGCUGAUUGAUGGAAAGUGUUCCGGAAAGUAAGCGCGCCAAAAUACACACAUUAAGUACAUAUGCAGCUUAUGGCGCUU-GGGGAGUUAAGCAGCACUUCUCAGUUAAAUCAAU
...(((..((..(((((....)))))..))...)))((((((............(((((.........)))))))))))((-(((((((........))))))))).......... ( -27.80)
>DroYak_CAF1 14681 111 - 1
UGGGCUGAUUGAUGGAAAGUGUUUCGGAA----AGCGCACCAAAACUCACGCAUUAAGUACAUAUACGGCUUAUGGCGGGU-GGGGACUUUAAAAGCGCUUCUCAGUUAAAUCAAU
.....(((((..((..((((((((...((----(((.((((........(((..(((((.........)))))..))))))-).)..))))..))))))))..))....))))).. ( -26.90)
>consensus
UUGGCUGAUUGAUGGAAAGUGUUCCGGAAAGUAAGCGCGCCAAAAUACACACAUUAAGUACAUAUACAGCUUAUGGCGCGC_GGGGAGUUAAACAGCACUUCUCAGUUAAAUCAAU
...(((((((..(((((((((((...((......((((((((............(((((.........))))))))))))).......))....)))))))))))....))))))) (-25.27 = -25.89 +   0.62) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,072,270 – 1,072,388
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 90.59
Mean single sequence MFE -27.33
Consensus MFE -24.52
Energy contribution -23.84
Covariance contribution -0.68
Combinations/Pair 1.21
Mean z-score -1.38
Structure conservation index 0.90
SVM decision value 0.63
SVM RNA-class probability 0.805033
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1072270 118 + 27905053
CACCAUAAGCUGUAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUUCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACG
.............(((..(((.....)))..))).((((((((..........((((....))))........(((.((((.......))))...)))........)))))))).... ( -27.30)
>DroSec_CAF1 8384 118 + 1
CGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACC
.((.....))(((((((((.....)))))))))..((((((((..........((((....))))........(((.((((.......))))...)))........)))))))).... ( -29.30)
>DroSim_CAF1 8522 113 + 1
-----AAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACC
-----.....(((((((((.....)))))))))..((((((((..........((((....))))........(((.((((.......))))...)))........)))))))).... ( -29.00)
>DroEre_CAF1 8861 118 + 1
CGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUUGAAUUCCCCGAUCUGGGCAAACACAACGCGCCAACGCC
........(((((((((((.....)))))))))..((((((((..........((((....))))........(((.((((.......))))...)))........)))))))).)). ( -30.20)
>DroYak_CAF1 14718 113 + 1
CGCCAUAAGCCGUAUAUGUACUUAAUGCGUGAGUUUUGGUGCGCU----UUCCGAAACACUUUCCAUCAAUCAGCCCAUUGAAUUCCCUGAUCUGGGCA-ACACAUCGUGCCAACACC
.((..((((...........))))..))(((.(((((((......----..)))))))...............(((((...............))))).-.)))...(((....))). ( -20.86)
>consensus
CGCCAUAAGCUGCAUAUGUACUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACC
..........(((((((((.....)))))))))..((((((((..........((((....))))........(((.((((.......))))...)))........)))))))).... (-24.52 = -23.84 +  -0.68) 

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 09:39:16 2006