Locus 890

Sequence ID 2R_DroMel_CAF1
Location 4,040,603 – 4,040,801
Length 198
Max. P 0.625254
window1552 window1553

overview

Window 2

Location 4,040,603 – 4,040,721
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.18
Mean single sequence MFE -41.96
Consensus MFE -31.75
Energy contribution -31.80
Covariance contribution 0.05
Combinations/Pair 1.30
Mean z-score -1.57
Structure conservation index 0.76
SVM decision value 0.07
SVM RNA-class probability 0.567197
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4040603 118 - 20766785
ACUCCCCCGA--UAUUGUGUGUUAGGCAAGUCAGGCCCUUGGGCCCCAUUUAAUUAGCUUGCUGGCGGUCAAGCUGGGCAUCUAUUGAAUGGCUGAUAAGCCUAGCCAACAGUGCAGCCA
........(.--((((((..(((((((..((((((((....))))(((((((((.((..(((..((......))..).)).))))))))))).))))..)))))))..)))))))..... ( -43.20)
>DroSec_CAF1 23226 118 - 1
ACUCCCCCGA--UAUUGUGGGUUUGGCAAGUCGGGCCCUUGGGCCCCAUUUAAUUAGCUUGCUGGAGGUCAAGCUGGGCAUCUAUUGAAUGGUUGAUAAGCCUGGCCAACAGUGCAGCCA
.....((((.--.....))))..((((((((.(((((....))))).)))).....((..((((..(((((.(((...((.((((...)))).))...))).)))))..)))))).)))) ( -43.90)
>DroSim_CAF1 25377 118 - 1
ACUCCCCCGA--UACUGUGGGUUUGGCAAGUCGGGCCCUUGGGCCCCAUUUAAUUAGCUUGCUGGCGGUCAAGCUGGGCAUCUAUUGAAUGGCUGAUAAGCCUGGCCAACAGUGCAGCCA
........(.--((((((.(((..(((..((((((((....)))))((((((((.((..(((..((......))..).)).))))))))))...)))..)))..))).)))))))..... ( -45.70)
>DroEre_CAF1 22671 106 - 1
ACUCCUGCAA--UACUGUGGGUCAGUCAAGUCGGACCCUUGGGUCCCCUUUAAUUAGCUAGC------------UGGGCAUCAAUUGAAUGGCCAAUAAGCCGGGCCAGUAGUGCAGCCU
....(((((.--(((((..((..(((.(((..(((((....)))))..))).)))..)).((------------(.(((....((((......))))..))).)))))))).)))))... ( -35.50)
>DroYak_CAF1 26274 120 - 1
ACUCCCCCGAUGUAUUGUGGGUAAGGCAAGUCGGGCCCCAGGGCCCCGUUUAAUUAGCUAGCUGGCGGUCAGGCUGGGCAUCAAUUGAAUUGCUGAUAAGCCUAACCAGUAGUGCAGCCU
..........(((((((..(((.((((..((((((((....))))).((((((((.(((((((........)))).)))...))))))))....)))..)))).)))..))))))).... ( -41.50)
>consensus
ACUCCCCCGA__UAUUGUGGGUUAGGCAAGUCGGGCCCUUGGGCCCCAUUUAAUUAGCUUGCUGGCGGUCAAGCUGGGCAUCUAUUGAAUGGCUGAUAAGCCUGGCCAACAGUGCAGCCA
............((((((.((((.(((..((((((((....))))(((((((((..(((((((........))).))))....))))))))).))))..))).)))).))))))...... (-31.75 = -31.80 +   0.05)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 4,040,683 – 4,040,801
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.01
Mean single sequence MFE -27.43
Consensus MFE -23.67
Energy contribution -23.95
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.26
Structure conservation index 0.86
SVM decision value 0.19
SVM RNA-class probability 0.625254
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4040683 118 + 20766785
AAGGGCCUGACUUGCCUAACACACAAUA--UCGGGGGAGUCGCUCAUCUGCCCAUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCACUCCACACACGUCCUCAAUAAAUA
..((((.((((((.(((...........--..))).)))))).......)))).((((((.............)))))).((((((.(((..((...........))..))).)))))). ( -26.24)
>DroSec_CAF1 23306 118 + 1
AAGGGCCCGACUUGCCAAACCCACAAUA--UCGGGGGAGUCGCUCAUCUGCCCAUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCACUCCACACACGUCCUCAAUAAAUA
..((((.((((((.((............--...)).)))))).......)))).((((((.............)))))).((((((.(((..((...........))..))).)))))). ( -26.78)
>DroSim_CAF1 25457 118 + 1
AAGGGCCCGACUUGCCAAACCCACAGUA--UCGGGGGAGUCGCUCAUCUGCCCAUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCACUCCACACACGUCCUCAAUAAAUA
..((((.((((((.((..((.....)).--...)).)))))).......)))).((((((.............)))))).((((((.(((..((...........))..))).)))))). ( -27.32)
>DroEre_CAF1 22739 117 + 1
AAGGGUCCGACUUGACUGACCCACAGUA--UUGCAGGAGUCGCUCAUCUGCCCAUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCAC-CCACACACGUCCUCCAUAAUUA
..((((.((((((((..(((........--..((((..(.....)..))))...((((((.............)))))).)))..)))))).)).))-)).................... ( -25.72)
>DroYak_CAF1 26354 120 + 1
UGGGGCCCGACUUGCCUUACCCACAAUACAUCGGGGGAGUCGCUCAUCUGCCCCUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCGCUCCACACACGUCCUCAAUAAAUA
.(((((.((((((.(((...............))).)))))).......)))))((((((.............)))))).((((((.(((..((.(.......).))..))).)))))). ( -31.08)
>consensus
AAGGGCCCGACUUGCCUAACCCACAAUA__UCGGGGGAGUCGCUCAUCUGCCCAUGAAUAUAAUUAACCGCAUUAUUCAAGUUUAUCGAGUGCGCACUCCACACACGUCCUCAAUAAAUA
..((((.((((((.((.................)).)))))).......)))).((((((.............)))))).((((((.(((..((...........))..))).)))))). (-23.67 = -23.95 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:12 2006