Locus 1428

Sequence ID 2L_DroMel_CAF1
Location 3,808,372 – 3,808,480
Length 108
Max. P 0.747765
window2324 window2325

overview

Window 4

Location 3,808,372 – 3,808,480
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.37
Mean single sequence MFE -31.11
Consensus MFE -12.71
Energy contribution -14.23
Covariance contribution 1.52
Combinations/Pair 1.12
Mean z-score -2.47
Structure conservation index 0.41
SVM decision value 0.47
SVM RNA-class probability 0.747765
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3808372 108 + 22407834
GCUGAAACUGAAACAGCAUUCGGAGGAUAACCAGAGUGUCUAGGGGCAGCUAGUAA------AACCCCUAGAUUAUGCAAGCGAGCAGUUUCA-----GGAUUCAG-AUUCAAGCGCAAA
.(((((.(((((((.((((((...((....)).))))))(((((((..........------..)))))))....(((......)))))))))-----)..)))))-............. ( -33.80)
>DroSec_CAF1 17674 105 + 1
GCUGAAACUGAAACAGCAUUCGGAGGAUAACCAGAGUGUCUAGGGG---CUAGUAA------AACCCUUAGAUUAUGUGAGCGAGCAGUUUCA-----GGAUUCAG-AUUCAAGCGCAAA
.(((((.(((((((.((((((...((....)).))))(((((((((---.......------..)))))))))...........)).))))))-----)..)))))-............. ( -30.30)
>DroSim_CAF1 17665 105 + 1
GCUGAAACUGAAACAGCAUUCGGAGGAUAACCAGAGUGUCUAGGGG---CUAGUAA------AAACCCUAGAUUAUGUGAGCGAGCAGUUUCA-----GGAUUCAG-AUUCAAGCGCAAA
.(((((.(((((((.((((((...((....)).))))((((((((.---.......------...))))))))...........)).))))))-----)..)))))-............. ( -30.80)
>DroEre_CAF1 19148 108 + 1
GCUGAAACUGAAACAGCAUGCGGCGGAUAAGCAGAGUUUCUAGGGG---CUGGUAAAAGAAAAACACCCAGUUUCUGG----GAGCAGUUUCA-----UGAUUCAGAUUUCAAGGACAAA
.(((((.(((((((........((......))...((((((((..(---((((..............)))))..))))----)))).))))))-----.).))))).............. ( -34.34)
>DroYak_CAF1 19516 106 + 1
GCUGAAACUGAAACAGCAUGCGGAGGAUAACCAGAGAUAUAAGGGG---CUGGUAA------AACACCCAGAUUCUGG----UAGCAGUUUUAACGAUUGAUUCAG-UUUCGAGGAUAAA
.(((((((((((.(((....((..(((..(((((((.......(((---.((....------..)))))...))))))----)......)))..)).))).)))))-)))).))...... ( -26.30)
>consensus
GCUGAAACUGAAACAGCAUUCGGAGGAUAACCAGAGUGUCUAGGGG___CUAGUAA______AACCCCUAGAUUAUGG_AGCGAGCAGUUUCA_____GGAUUCAG_AUUCAAGCGCAAA
.(((((.(((((((.((.......((....)).....((((((((....................))))))))...........)).))))))......).))))).............. (-12.71 = -14.23 +   1.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,808,372 – 3,808,480
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.37
Mean single sequence MFE -26.65
Consensus MFE -12.79
Energy contribution -14.55
Covariance contribution 1.76
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.48
SVM decision value 0.16
SVM RNA-class probability 0.613589
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3808372 108 - 22407834
UUUGCGCUUGAAU-CUGAAUCC-----UGAAACUGCUCGCUUGCAUAAUCUAGGGGUU------UUACUAGCUGCCCCUAGACACUCUGGUUAUCCUCCGAAUGCUGUUUCAGUUUCAGC
.............-(((((..(-----((((((.(((((.........(((((((((.------.........)))))))))......((....))..)))..)).))))))).))))). ( -32.00)
>DroSec_CAF1 17674 105 - 1
UUUGCGCUUGAAU-CUGAAUCC-----UGAAACUGCUCGCUCACAUAAUCUAAGGGUU------UUACUAG---CCCCUAGACACUCUGGUUAUCCUCCGAAUGCUGUUUCAGUUUCAGC
.............-(((((..(-----((((((.(((((.........((((.(((((------.....))---))).))))......((....))..)))..)).))))))).))))). ( -27.00)
>DroSim_CAF1 17665 105 - 1
UUUGCGCUUGAAU-CUGAAUCC-----UGAAACUGCUCGCUCACAUAAUCUAGGGUUU------UUACUAG---CCCCUAGACACUCUGGUUAUCCUCCGAAUGCUGUUUCAGUUUCAGC
.............-(((((..(-----((((((.(((((.........(((((((((.------.....))---.)))))))......((....))..)))..)).))))))).))))). ( -26.60)
>DroEre_CAF1 19148 108 - 1
UUUGUCCUUGAAAUCUGAAUCA-----UGAAACUGCUC----CCAGAAACUGGGUGUUUUUCUUUUACCAG---CCCCUAGAAACUCUGCUUAUCCGCCGCAUGCUGUUUCAGUUUCAGC
.......((((((.(((((...-----.((((..((.(----((((...))))).)).))))......(((---(....((.....))((......)).....)))).))))))))))). ( -23.00)
>DroYak_CAF1 19516 106 - 1
UUUAUCCUCGAAA-CUGAAUCAAUCGUUAAAACUGCUA----CCAGAAUCUGGGUGUU------UUACCAG---CCCCUUAUAUCUCUGGUUAUCCUCCGCAUGCUGUUUCAGUUUCAGC
.........((((-(((((.((..(((..........(----(((((((..(((.(((------.....))---))))..))...))))))..........))).)).)))))))))... ( -24.65)
>consensus
UUUGCGCUUGAAU_CUGAAUCC_____UGAAACUGCUCGCU_ACAUAAUCUAGGGGUU______UUACUAG___CCCCUAGACACUCUGGUUAUCCUCCGAAUGCUGUUUCAGUUUCAGC
..............(((((........((((((.((............((((((((..................))))))))......((.......))....)).))))))..))))). (-12.79 = -14.55 +   1.76)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:22 2006