Locus 3428

Sequence ID 2R_DroMel_CAF1
Location 11,582,276 – 11,582,415
Length 139
Max. P 0.996605
window5595 window5596

overview

Window 5

Location 11,582,276 – 11,582,379
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.45
Mean single sequence MFE -29.76
Consensus MFE -11.05
Energy contribution -12.77
Covariance contribution 1.72
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.37
SVM decision value 0.18
SVM RNA-class probability 0.621133
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11582276 103 - 20766785
CU---------UCUGUUAGCCAACUUGAGUGGAAUUCCCAA-UG-GAAUUCUAUGGGGCAAUCAAAGUGGGCAGCU------AACCCAUCGCAUCGACAGGGGUAAAUAUUUUAGGAAAU
((---------((((((.(((.......((((((((((...-.)-)))))))))..))).......(((((.....------..)))))......))))))))................. ( -29.40)
>DroSec_CAF1 16012 112 - 1
CUCC-------UCUGUUGGCCAACUUGAGUGGAAUUCCCAUGUG-GAAUUCUAUGGGGCAAUCAAAGUGGGCAACUGCUACUAACCCAACGCAUCGACAGGGGUAAAUAUUUUAGGAAAA
..((-------((((((((((.......((((((((((.....)-)))))))))..)))......((..(....)..))...............)))))))))................. ( -35.50)
>DroSim_CAF1 16815 113 - 1
CUCC-------UCUGUUGGCCAACUUGAGUGGAAUUCCUAUGUGGGAAUUCUAUGGGGCAAUCAAAGUGGGCAACUACUACCAACCCAACGCAUCGACAGGGGUAAAUAUUUUAGGAAAU
..((-------((((((((((.......(((((((((((....)))))))))))..)))......(((((....)))))...............)))))))))................. ( -38.20)
>DroEre_CAF1 16245 91 - 1
C---------UCCUAUCAGCCAACUUGAGUGGAAUUCCUU--------CUCUAUGG-GCAAUCAAAGUGGGCAUCU-----------AUCCCAUCGACGCGGGUAAAUAUUUUAGGAUAU
.---------(((((...(((.(((((((.((....))..--------)))..(((-....))))))).)))...(-----------(((((......).))))).......)))))... ( -20.90)
>DroYak_CAF1 16598 101 - 1
CUCCAAUCUAUCCCAUCAGCCAACUUGAGUGGCAUUCCUU--------CUCUAUGGGGCAAUCAAAGUGGGCACCU-----------AUCCCAUGGACAUGGGUAAAUAUUUUCGGAAAU
.(((((..((((((((..((((.(....))))).......--------.((((((((.........((((....))-----------)))))))))).)))))...)))..)).)))... ( -24.80)
>consensus
CUCC_______UCUGUUAGCCAACUUGAGUGGAAUUCCUA__UG_GAAUUCUAUGGGGCAAUCAAAGUGGGCAACU______AACCCAUCGCAUCGACAGGGGUAAAUAUUUUAGGAAAU
...........((((...(((.(((((((((((((((........))))))))).......)).)))).)))....................(((......)))........)))).... (-11.05 = -12.77 +   1.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,582,314 – 11,582,415
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.38
Mean single sequence MFE -30.58
Consensus MFE -11.61
Energy contribution -15.17
Covariance contribution 3.56
Combinations/Pair 1.09
Mean z-score -2.55
Structure conservation index 0.38
SVM decision value 2.72
SVM RNA-class probability 0.996605
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11582314 101 - 20766785
UCCUAGUGGCUUUUUAUACGCUGGCUAUAACGCCCA----CU---------UCUGUUAGCCAACUUGAGUGGAAUUCCCAA-UG-GAAUUCUAUGGGGCAAUCAAAGUGGGCAGCU----
..((((((..........)))))).......(((((----((---------(..(((.(((.......((((((((((...-.)-)))))))))..))))))..))))))))....---- ( -37.60)
>DroSec_CAF1 16052 96 - 1
UCCUAGUGGCUU-UU-----------AUAACGCCCA----CUCC-------UCUGUUGGCCAACUUGAGUGGAAUUCCCAUGUG-GAAUUCUAUGGGGCAAUCAAAGUGGGCAACUGCUA
.((....))...-..-----------.....(((((----((..-------...((((.((.......((((((((((.....)-))))))))).)).))))...)))))))........ ( -30.60)
>DroSim_CAF1 16855 98 - 1
UCCUAGUGGCUUUUU-----------AUAACGCCCA----CUCC-------UCUGUUGGCCAACUUGAGUGGAAUUCCUAUGUGGGAAUUCUAUGGGGCAAUCAAAGUGGGCAACUACUA
...((((((..((..-----------..)).(((((----((..-------...((((.((.......(((((((((((....))))))))))).)).))))...)))))))..)))))) ( -33.10)
>DroEre_CAF1 16278 91 - 1
UCCCCAUGGCCUUUUAUAC---GGCUAUAACGGCCA----C---------UCCUAUCAGCCAACUUGAGUGGAAUUCCUU--------CUCUAUGG-GCAAUCAAAGUGGGCAUCU----
.....((((((........---))))))...(.(((----(---------(.......(((.....(((.((....))..--------)))....)-))......))))).)....---- ( -25.72)
>DroYak_CAF1 16631 105 - 1
UCCUCGUGGCCUUUUAUGC---GGCUAUAACGCCCAACCACUCCAAUCUAUCCCAUCAGCCAACUUGAGUGGCAUUCCUU--------CUCUAUGGGGCAAUCAAAGUGGGCACCU----
.....((((((........---))))))...(((((.((((((.......................))))))...((((.--------......)))).........)))))....---- ( -25.90)
>consensus
UCCUAGUGGCUUUUUAU_C___GGCUAUAACGCCCA____CUCC_______UCUGUUAGCCAACUUGAGUGGAAUUCCUA__UG_GAAUUCUAUGGGGCAAUCAAAGUGGGCAACU____
.....((((((...........))))))...(((((......................(((.......(((((((((........)))))))))..)))........)))))........ (-11.61 = -15.17 +   3.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:17 2006