Locus 5167

Sequence ID 3R_DroMel_CAF1
Location 13,563,602 – 13,563,737
Length 135
Max. P 0.984203
window8442 window8443

overview

Window 2

Location 13,563,602 – 13,563,706
Length 104
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 76.15
Mean single sequence MFE -27.95
Consensus MFE -18.77
Energy contribution -18.27
Covariance contribution -0.50
Combinations/Pair 1.21
Mean z-score -2.19
Structure conservation index 0.67
SVM decision value 1.97
SVM RNA-class probability 0.984203
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13563602 104 - 27905053
UCUUUC--------------GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGGUAUUGCAAAAUAGAUUCGAAAAGUAGUGAGACAUUUUUGAGUGUGUUUAAAGGUGUAUUUCG
..((((--------------(((((((((..((((.(((((((.((....))))))))).)))))))))))))))))......((.(((((((((((....)))))))))))...)). ( -30.00)
>DroSec_CAF1 5749 100 - 1
UAUUUC--------------GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGUUAUUGCAAAAAAGAUUCGAAAAGUUGGGAGACAUUUUUGGG----UCUAAAGGUGCAUUUCG
..((((--------------((((((....(((((...(((((........)))))....)))))..))))))))))....(..(..((((((((..----..))))))))..)..). ( -24.50)
>DroSim_CAF1 3707 100 - 1
UGUUUC--------------GGAUUUGUUAUUUGCUAUACUCUGCUAUCAAGGGGUUAUGGCAAAAAAGAUUCCAAAAGUAGGGAGACAUUUUUGGG----CCUAAAGGUGCAUUUCG
......--------------.((..(((..(((((((((((((........)))).))))))))).......((((((((..(....)))))))))(----((....))))))..)). ( -26.10)
>DroEre_CAF1 4603 105 - 1
UCUUUCGCCUCACACCGUACGGAUUUAUUAUUUGCUAUGCUCUGCUUUUGUGAGGGUAUUGCAAA-GAGAUUCGAAAAGGUGCUCGACACUUUUGGG----CUUAAAGGU--------
(((((.((((.........(((((((....(((((.(((((((((....)).))))))).)))))-.))))))).(((((((.....))))))))))----)..))))).-------- ( -31.20)
>consensus
UCUUUC______________GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGGUAUUGCAAAAAAGAUUCGAAAAGUAGGGAGACAUUUUUGGG____CCUAAAGGUGCAUUUCG
....................((((((....(((((.(((((((.(......)))))))).)))))..))))))..............((((((((((....))))))))))....... (-18.77 = -18.27 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,563,642 – 13,563,737
Length 95
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 84.97
Mean single sequence MFE -19.27
Consensus MFE -12.20
Energy contribution -12.32
Covariance contribution 0.13
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.63
SVM decision value 0.10
SVM RNA-class probability 0.581325
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13563642 95 - 27905053
AAAAUUCUUUCAAUGCCUUACAUUUUUUAUUUCUUUC--------------GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGGUAUUGCAAAAUAGAUUCGAAAA
.................................((((--------------(((((((((..((((.(((((((.((....))))))))).))))))))))))))))). ( -22.60)
>DroSec_CAF1 5785 95 - 1
AAAAUUCUUCCAAUGCCUUAUAUUUUUUAUUUAUUUC--------------GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGUUAUUGCAAAAAAGAUUCGAAAA
.................................((((--------------((((((....(((((...(((((........)))))....)))))..)))))))))). ( -17.00)
>DroSim_CAF1 3743 95 - 1
AAAAUUCUUCCAAUGCCUUACAUUUUUUAUUUGUUUC--------------GGAUUUGUUAUUUGCUAUACUCUGCUAUCAAGGGGUUAUGGCAAAAAAGAUUCCAAAA
.....................................--------------(((.((....(((((((((((((........)))).)))))))))...)).))).... ( -16.90)
>DroEre_CAF1 4631 108 - 1
AAAAUUCUUCCAAUGCCUUACAUUUUUUAUUUCUUUCGCCUCACACCGUACGGAUUUAUUAUUUGCUAUGCUCUGCUUUUGUGAGGGUAUUGCAAA-GAGAUUCGAAAA
.................................(((((.(((...((....))........(((((.(((((((((....)).))))))).)))))-)))...))))). ( -20.60)
>consensus
AAAAUUCUUCCAAUGCCUUACAUUUUUUAUUUCUUUC______________GGAUUUAUUAUUUGCUAUACUCUGCUAUCAAGGGGGUAUUGCAAAAAAGAUUCGAAAA
...................................................((((((....(((((.(((((((.(......)))))))).)))))..))))))..... (-12.20 = -12.32 +   0.13)

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 11:48:11 2006