Locus 6031

Sequence ID 3R_DroMel_CAF1
Location 15,898,462 – 15,898,618
Length 156
Max. P 0.968673
window9837 window9838

overview

Window 7

Location 15,898,462 – 15,898,568
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 86.37
Mean single sequence MFE -35.30
Consensus MFE -26.82
Energy contribution -30.42
Covariance contribution 3.60
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.76
SVM decision value 1.63
SVM RNA-class probability 0.968673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15898462 106 - 27905053
GCCGCCAUACAAGAAGAUGCGGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACCACUGGGGGCACCAAAAGUGGCAGGAAGUCGCGUUUUUCAAACCG
............(((((((((((((((((((((((((......))))..)))))).....(((((.((....))...)))))..)))))))))))))))....... ( -40.80)
>DroSec_CAF1 5715 103 - 1
GCCGCCAUA---GAAGACGCGGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACUACUGGGGGCACCAAAAGUGGCAGGAAGUCGCUUUUUUCUAACCU
.......((---(((((.(((((((((((((((((((......))))..)))))).....(((((.((....))...)))))..)))))))))..))))))).... ( -37.90)
>DroSim_CAF1 5731 103 - 1
GCCGCCAUA---GAAGACGCGGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACCACUGGGGGCACCAAAAGUGGCAGGAAGUCGCUUUUUUCUAACCU
.......((---(((((.(((((((((((((((((((......))))..)))))).....(((((.((....))...)))))..)))))))))..))))))).... ( -40.20)
>DroEre_CAF1 5451 84 - 1
GCCGCCACA---CAAGACGCAGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACCACUAGGGGCAC------------------GCGUU-UUCUAACCU
.........---.(((((((.(((..(((((((((((......))))..)))))))....((....)))))..------------------)))))-))....... ( -20.90)
>DroYak_CAF1 6587 103 - 1
GCCGCCAUA---GAAGACGCAGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACCACUGGGGGCACAAAAAGUGGGAGGAAGUCGCGUUUUUCUAUUCU
......(((---((((((((.((((((((((((((((......))))..)))))).....(((((..(....)....)))))..)))))).))).))))))))... ( -36.70)
>consensus
GCCGCCAUA___GAAGACGCGGCUUCCGUUUCAGACACACGCCUGUCAAUGAAGCGACAACCACUGGGGGCACCAAAAGUGGCAGGAAGUCGCGUUUUUCUAACCU
............(((((((((((((((((((((((((......))))..)))))).....(((((.((....))...)))))..)))))))))))))))....... (-26.82 = -30.42 +   3.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,898,528 – 15,898,618
Length 90
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -25.54
Consensus MFE -16.72
Energy contribution -17.58
Covariance contribution 0.86
Combinations/Pair 1.10
Mean z-score -1.42
Structure conservation index 0.65
SVM decision value -0.03
SVM RNA-class probability 0.516998
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15898528 90 - 27905053
ACUGG--------------GGUUUCCACAGCCUGCGAAACAAAGGCGACAUAUCAACAAAUGUUGCCGCCAUACAAGAAGAUGCGGCUUCCGUUUCAGACACAC
....(--------------((((.....)))))..(((((...((((((((........))))))))(((..............)))....)))))........ ( -23.84)
>DroSec_CAF1 5781 87 - 1
ACUGG--------------GGUUUCCACAGCCUGCGAAACAAAGGAGACAUAUCAACAAAUGUUGCCGCCAUA---GAAGACGCGGCUUCCGUUUCAGACACAC
.((((--------------((((((((.....)).)))))...((((((((........)))))(((((....---......))))).)))..)))))...... ( -21.70)
>DroSim_CAF1 5797 87 - 1
ACUGG--------------GGUUUCCACAGCCUGCGAAACAAAGGCGACAUAUCAACAAAUGUUGCCGCCAUA---GAAGACGCGGCUUCCGUUUCAGACACAC
.((((--------------((((((((.....)).)))))...((((((((........)))))))).)).))---)..((.((((...)))).))........ ( -24.20)
>DroEre_CAF1 5498 87 - 1
ACUGG--------------GGCUUCCAUAGCCUGCGAAACAAAGGCGACAUAUCAACAAAUGUUGCCGCCACA---CAAGACGCAGCUUCCGUUUCAGACACAC
.(((.--------------.((......(((.((((.......((((((((........))))))))(.....---)....)))))))...))..)))...... ( -25.70)
>DroYak_CAF1 6653 97 - 1
ACAGGCGGCA--AUCGU--GGCACUGGUAGCCUGCGAAACAAAGGCGACAUAUCAACAAAUGUUGCCGCCAUA---GAAGACGCAGCUUCCGUUUCAGACACAC
..(((((((.--.((((--(((.......))).))))......((((((((........)))))))))))...---((((......)))).))))......... ( -28.70)
>DroPer_CAF1 12566 100 - 1
GCAGGCUGGAGGAUAGUGGGGGGGCUGGAG-UGGGGAAACAAAAGCGACAUAUCAACAAAUGUUGCCGGCAUA---GAAGACGCAGCUUCCGUGGCAGCCACAC
...(((((..(((.(((.(.(...(((..(-(.((....)....(((((((........)))))))).)).))---)....).).))))))....))))).... ( -29.10)
>consensus
ACUGG______________GGUUUCCACAGCCUGCGAAACAAAGGCGACAUAUCAACAAAUGUUGCCGCCAUA___GAAGACGCAGCUUCCGUUUCAGACACAC
...................(((.......)))...(((((...((((((((........)))))))).........((((......)))).)))))........ (-16.72 = -17.58 +   0.86)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:52 2006