Locus 9602

Sequence ID 3R_DroMel_CAF1
Location 25,360,829 – 25,360,948
Length 119
Max. P 0.946757
window15350 window15351 window15352

overview

Window 0

Location 25,360,829 – 25,360,921
Length 92
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 80.75
Mean single sequence MFE -25.03
Consensus MFE -19.04
Energy contribution -19.02
Covariance contribution -0.03
Combinations/Pair 1.10
Mean z-score -1.56
Structure conservation index 0.76
SVM decision value 0.52
SVM RNA-class probability 0.768323
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25360829 92 + 27905053
------GGAACGU-----GGCCGCUUGU-UGGCUUGUUGUCUUUGUUAGUGGUAGCAGUUAGUUGACUGCACUUACCACUAAGUUAAGAUGUUUUUGUCUCCGC---
------((((((.-----(((((.....-)))))....(((((..(((((((((((((((....))))))...)))))))))...))))).....))).)))..--- ( -30.30)
>DroVir_CAF1 50782 89 + 1
------GG--CCU-----GGC-ACUGUU-UUGUUUGUUGUCUUUGUUAGUGGUAGCAGUUAGUUGGCUGCACUUACCACUAAGUUAAGAUGUUU-UGUCUUGGG--C
------.(--(((-----(((-((....-..)).....(((((..(((((((((((((((....))))))...)))))))))...)))))....-.)))..)))--) ( -26.70)
>DroPse_CAF1 48684 93 + 1
GGACCUGGAACGU-----GGCCGGUU---------GUUGUCUUUGUUAGUGGUAGCAGUUAGUUGACUUCACUUACCACUAAGUUAAGAUGUUUUUGUCUUUGCUGU
((((((((.....-----..))))..---------...(((((..((((((((((.((((....))))....))))))))))...)))))......))))....... ( -21.60)
>DroGri_CAF1 46717 95 + 1
------GG--CCUGGCCUGGC-ACUCUUUUCGUUUGUUGUCUUUGUUAGUGGUAGCAGUUAGUUGACUACACUUACCACUAAGUUAAGAUGUUU-UGUCUUCGG--U
------.(--((......)))-................(((((..(((((((((..((((((....))).))))))))))))...)))))....-.........--. ( -21.90)
>DroSec_CAF1 45477 84 + 1
------GGAACGU-----GGCCGCUU---------GUUGUCUUUGUUAGUGGUAGCAGUUAGUUGACUGCACUUACCACUAAGUUAAGAUGUUUUUGUCUCCGC---
------.....((-----((..((..---------..((((((..(((((((((((((((....))))))...)))))))))...)))))).....))..))))--- ( -27.10)
>DroMoj_CAF1 51345 89 + 1
------GG--CCU-----GGC-ACUGUU-UCGCUUGUUGUCUUUGUUAGUGGUAGCAGUUAGUUGGUUGCACUUACCACUAAGUUAAGAUGUUU-UGUCUUGGG--C
------.(--(((-----(((-......-..)))....(((((..(((((((((((((........))))...)))))))))...)))))....-......)))--) ( -22.60)
>consensus
______GG__CCU_____GGC_ACUUUU_U_G_UUGUUGUCUUUGUUAGUGGUAGCAGUUAGUUGACUGCACUUACCACUAAGUUAAGAUGUUU_UGUCUUCGC___
......................................(((((..(((((((((((((((....))))))...)))))))))...)))))................. (-19.04 = -19.02 +  -0.03)

alignment

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secondary structure

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Window 1

Location 25,360,829 – 25,360,921
Length 92
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 80.75
Mean single sequence MFE -20.35
Consensus MFE -15.34
Energy contribution -15.90
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.76
Structure conservation index 0.75
SVM decision value 1.37
SVM RNA-class probability 0.946757
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25360829 92 - 27905053
---GCGGAGACAAAAACAUCUUAACUUAGUGGUAAGUGCAGUCAACUAACUGCUACCACUAACAAAGACAACAAGCCA-ACAAGCGGCC-----ACGUUCC------
---..((((.(.......((((...(((((((((...(((((......))))))))))))))..))))......(((.-......))).-----..)))))------ ( -24.30)
>DroVir_CAF1 50782 89 - 1
G--CCCAAGACA-AAACAUCUUAACUUAGUGGUAAGUGCAGCCAACUAACUGCUACCACUAACAAAGACAACAAACAA-AACAGU-GCC-----AGG--CC------
(--((.......-.....((((...(((((((((...((((........)))))))))))))..))))......((..-....))-...-----.))--).------ ( -19.50)
>DroPse_CAF1 48684 93 - 1
ACAGCAAAGACAAAAACAUCUUAACUUAGUGGUAAGUGAAGUCAACUAACUGCUACCACUAACAAAGACAAC---------AACCGGCC-----ACGUUCCAGGUCC
..................((((...((((((((((((..((....)).)))..)))))))))..))))....---------....((((-----........)))). ( -18.10)
>DroGri_CAF1 46717 95 - 1
A--CCGAAGACA-AAACAUCUUAACUUAGUGGUAAGUGUAGUCAACUAACUGCUACCACUAACAAAGACAACAAACGAAAAGAGU-GCCAGGCCAGG--CC------
.--.........-.....((((...(((((((((...(((((......))))))))))))))..)))).................-(((......))--).------ ( -19.90)
>DroSec_CAF1 45477 84 - 1
---GCGGAGACAAAAACAUCUUAACUUAGUGGUAAGUGCAGUCAACUAACUGCUACCACUAACAAAGACAAC---------AAGCGGCC-----ACGUUCC------
---(((....).......((((...(((((((((...(((((......))))))))))))))..))))....---------..))....-----.......------ ( -22.50)
>DroMoj_CAF1 51345 89 - 1
G--CCCAAGACA-AAACAUCUUAACUUAGUGGUAAGUGCAACCAACUAACUGCUACCACUAACAAAGACAACAAGCGA-AACAGU-GCC-----AGG--CC------
(--((.......-.....((((...(((((((((...(((..........))))))))))))..))))......(((.-.....)-)).-----.))--).------ ( -17.80)
>consensus
___CCGAAGACA_AAACAUCUUAACUUAGUGGUAAGUGCAGUCAACUAACUGCUACCACUAACAAAGACAACAA_C_A_AAAAGC_GCC_____ACG__CC______
..................((((...(((((((((...(((((......))))))))))))))..))))....................................... (-15.34 = -15.90 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,360,850 – 25,360,948
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.54
Mean single sequence MFE -22.05
Consensus MFE -14.07
Energy contribution -14.98
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -2.01
Structure conservation index 0.64
SVM decision value 0.64
SVM RNA-class probability 0.809897
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25360850 98 - 27905053
UGCGCAUACACCUCGGC-CAGACAG------ACU--------GCGGAGACAAAAACAUCUUAACUUAGUGGUAAGUGCAGUCAACUAACUGCUACCACUAACAAAGACAACAA
...........(((.((-.((....------.))--------)).))).........((((...(((((((((...(((((......))))))))))))))..))))...... ( -24.90)
>DroVir_CAF1 50800 96 - 1
UGAGCAUACACCUCGCU-GAGCCUC-------------GG--CCCAAGACA-AAACAUCUUAACUUAGUGGUAAGUGCAGCCAACUAACUGCUACCACUAACAAAGACAACAA
.(((.......)))(((-(.....)-------------))--)........-.....((((...(((((((((...((((........)))))))))))))..))))...... ( -22.30)
>DroPse_CAF1 48705 105 - 1
UGCGCAUACACCUUGGCGGAGACAG------ACUCGGAGACAGCAAAGACAAAAACAUCUUAACUUAGUGGUAAGUGAAGUCAACUAACUGCUACCACUAACAAAGACAAC--
...........(((.(((....)..------....(....).)).))).........((((...((((((((((((..((....)).)))..)))))))))..))))....-- ( -21.40)
>DroGri_CAF1 46741 109 - 1
UGCGCAUACACCUAGCC-GAAGCUGGUAGAGAGCUGGAGA--CCGAAGACA-AAACAUCUUAACUUAGUGGUAAGUGUAGUCAACUAACUGCUACCACUAACAAAGACAACAA
.((...(..(((.(((.-...))))))..)..)).(....--)........-.....((((...(((((((((...(((((......))))))))))))))..))))...... ( -23.70)
>DroMoj_CAF1 51363 96 - 1
UGCGCAUACACCUCGCU-GAGCCUC-------------GG--CCCAAGACA-AAACAUCUUAACUUAGUGGUAAGUGCAACCAACUAACUGCUACCACUAACAAAGACAACAA
..............(((-(.....)-------------))--)........-.....((((...(((((((((...(((..........))))))))))))..))))...... ( -17.70)
>DroPer_CAF1 48293 102 - 1
NNNGCAUACAC-UUGGC-GAGACAG------ACUCGGAGACAGCAAAGACAAAAACAUCU-GACUUAGUGGUAAGUGAAGUCAACUAACUGCUACCACUAACAAAGACAAC--
..........(-((.((-(((....------.)))(....).)).))).........(((-...((((((((((((..((....)).)))..)))))))))...)))....-- ( -22.30)
>consensus
UGCGCAUACACCUCGCC_GAGACAG______ACU____GA__CCAAAGACA_AAACAUCUUAACUUAGUGGUAAGUGCAGUCAACUAACUGCUACCACUAACAAAGACAACAA
.........................................................((((...(((((((((...(((((......))))))))))))))..))))...... (-14.07 = -14.98 +   0.92)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:04 2006