Locus 1044

Sequence ID 3L_DroMel_CAF1
Location 3,080,120 – 3,080,228
Length 108
Max. P 0.900615
window1617 window1618

overview

Window 7

Location 3,080,120 – 3,080,228
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.61
Mean single sequence MFE -34.88
Consensus MFE -30.78
Energy contribution -30.66
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.27
Structure conservation index 0.88
SVM decision value 0.53
SVM RNA-class probability 0.771106
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3080120 108 + 23771897
--CACUUGCCUGACACAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAUUAUUUUU---UAGUUCACA-----C--
--.....(((..((...((((.....((((........)))).(((((.......))))))))).(((((.......)))))))..)))((((((.....---))))))...-----.-- ( -39.40)
>DroSec_CAF1 13094 102 + 1
GCCCCUUCAAUAACCCGGCCCGGUUAGCUCAGUGGGUAGGGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUAGGCGUUUUACUUUU---UU---------------
(((.........((((.((((.....(((.....))).)))).(((((.......)))))))))((((((.......))))))...)))...........---..--------------- ( -32.50)
>DroSim_CAF1 13050 100 + 1
--CGCUCGCCUCACAUAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAUUAUAUUU---UA---------------
--...((((((.((...((((.....((((........)))).(((((.......))))))))).(((((.......))))))).)))))).........---..--------------- ( -35.70)
>DroEre_CAF1 17202 107 + 1
--CGCUCAUUCUUCACAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAUG--CUUUU---UUGUUUACU------UU
--((((((.........((((.....((((........)))).(((((.......)))))))))((((((.......)))))).))))))...--.....---.........------.. ( -33.20)
>DroYak_CAF1 13739 116 + 1
--CACUAUUCUUGCACAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAA--CUUUUUUUUUGUAUACUUUACGUUU
--...............(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))....--..........(((.....))).... ( -33.60)
>consensus
__CACUCGCCUUACACAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAUUACUUUU___UUGU__AC_________
.................(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))............................... (-30.78 = -30.66 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,080,120 – 3,080,228
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -33.57
Consensus MFE -29.44
Energy contribution -29.48
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.58
Structure conservation index 0.88
SVM decision value 1.01
SVM RNA-class probability 0.900615
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3080120 108 - 23771897
--G-----UGUGAACUA---AAAAAUAAUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUGUGUCAGGCAAGUG--
--(-----(.(((....---...........((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))....))).)).....-- ( -32.81)
>DroSec_CAF1 13094 102 - 1
---------------AA---AAAAGUAAAACGCCUAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCCCUACCCACUGAGCUAACCGGGCCGGGUUAUUGAAGGGGC
---------------..---...........((((..((((((.......))))))((((((((((.....)))))).((((.................)))).))))........)))) ( -32.93)
>DroSim_CAF1 13050 100 - 1
---------------UA---AAAUAUAAUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUAUGUGAGGCGAGCG--
---------------..---........((((((((.((((((.......)))))).(((((((((.....)))))).((((........)))).....))).....)).))))))..-- ( -36.80)
>DroEre_CAF1 17202 107 - 1
AA------AGUAAACAA---AAAAG--CAUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUGUGAAGAAUGAGCG--
..------.........---.....--(((.((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).)))...........-- ( -33.20)
>DroYak_CAF1 13739 116 - 1
AAACGUAAAGUAUACAAAAAAAAAG--UUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUGUGCAAGAAUAGUG--
....(((.....))).........(--(...((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))...))..........-- ( -32.10)
>consensus
_________GU__ACAA___AAAAGUAAUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUGUGUAAGACAAGCG__
...............................((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))................. (-29.44 = -29.48 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:40 2006