Locus 8409

Sequence ID X_DroMel_CAF1
Location 20,882,360 – 20,882,598
Length 238
Max. P 0.875033
window13809 window13810 window13811

overview

Window 9

Location 20,882,360 – 20,882,478
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.10
Mean single sequence MFE -35.11
Consensus MFE -22.35
Energy contribution -23.73
Covariance contribution 1.37
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.64
SVM decision value 0.89
SVM RNA-class probability 0.875033
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20882360 118 + 22224390
AAAGUGGCGAAAAACUUCUAGAGAGUGGGAGAGAAAACUCCGCUGCAGUUCAGUCGG--UUGUUAUCAGCAGCAGUUGCUUGUUGACGACAAUCGAUUCUGAUUCUGAUUCUGCUUCCAA
..(((((.(.....((((((.....))))))......).)))))((((.((((((((--((((..((((((((....)).))))))..))))))))........))))..))))...... ( -38.30)
>DroSec_CAF1 2246 100 + 1
AAAGGGGCGGAAAACUUCCAGAGAGUGGGAGAGAAAACUCCG--------------------UUAUCAGCAGCAGUUGCUUGUUGACGGCAAUCGAUUCAGAUUCUGAUUCUGAUUCCAA
...((((.......((((((.....))))))......))))(--------------------(..((((((((....)).))))))..))....((.(((((.......))))).))... ( -29.32)
>DroSim_CAF1 3034 117 + 1
AGAGGGGCGGAAAACUUCCAGAGAGUGGGAGAGAAAACUCCGCUGCAGUUUAGUCGG---UGUUAUCAGCAGCAGUUGCUUGUUGACGGCAAUCGAUUCAGAUUCUGAUUCUGAUUCCAA
...(.((((((...((((((.....)))))).......)))))).)......(((((---(((..((((((((....)).))))))..)).))))))(((((.......)))))...... ( -38.40)
>DroYak_CAF1 3196 105 + 1
AAAGUGGCGGAAAACUUCCAGAGAGUGGGAGAUGGAACUCCGCUGCAGUUUGGUCAGUGUUGUUAUCAGCAGCAGUUGCUUGUUGACGGCAAUCGAUUUUGAUUU---------------
...(..(((((...((((((.....)))))).......)))))..).....((((((.(((((..((((((((....)).))))))..))))).....)))))).--------------- ( -34.40)
>consensus
AAAGGGGCGGAAAACUUCCAGAGAGUGGGAGAGAAAACUCCGCUGCAGUUUAGUCGG___UGUUAUCAGCAGCAGUUGCUUGUUGACGGCAAUCGAUUCAGAUUCUGAUUCUGAUUCCAA
...((((((((...((((((.....)))))).......))))))))...............((..((((((((....)).))))))..))((((......))))................ (-22.35 = -23.73 +   1.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,882,438 – 20,882,558
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.67
Mean single sequence MFE -24.45
Consensus MFE -16.88
Energy contribution -17.62
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.69
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20882438 120 - 22224390
AACAAAAACAAAAAAGCAAACAAAUGUCGAUGGUUGCACACGACUGCGUUGUGUGAACAAUGGAGAGCUGGUUAACAGUAUUGGAAGCAGAAUCAGAAUCAGAAUCGAUUGUCGUCAACA
........................(((.((((....((((((((...)))))))).(((((.((...((((((....((.(((....))).))...))))))..)).))))))))).))) ( -27.60)
>DroSec_CAF1 2306 117 - 1
AACAAAAA-AAAAAAGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUUG--AGCUGGUAAACAGUAUUGGAAUCAGAAUCAGAAUCUGAAUCGAUUGCCGUCAACA
........-...............(((.(((.((..((((((((...))))))))...(((((--(((((.....)))).......(((((.......))))).)))))))).))).))) ( -26.40)
>DroSim_CAF1 3111 117 - 1
AACAAAAA-AAAAACGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG--AGCUGGUAAACAGUAUUGGAAUCAGAAUCAGAAUCUGAAUCGAUUGCCGUCAACA
........-.....((((....(((((((.(((.......)))))))))).))))....((((--.((((.....))))....((.(((((.......))))).)).....))))..... ( -26.10)
>DroYak_CAF1 3276 99 - 1
AAAAACAA-AUAAACGCUAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG--AGCUGGUAAACA------------------AAAUCAAAAUCGAUUGCCGUCAACA
........-...............(((.(((.((..((((((((...))))))))...(((.(--(..((((.....------------------..))))...)).))))).))).))) ( -17.70)
>consensus
AACAAAAA_AAAAAAGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG__AGCUGGUAAACAGUAUUGGAAUCAGAAUCAGAAUCAGAAUCGAUUGCCGUCAACA
.......................(((.((((((...((((((((...))))))))...........((((.....))))..........................)))))).)))..... (-16.88 = -17.62 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,882,478 – 20,882,598
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.22
Mean single sequence MFE -29.34
Consensus MFE -23.14
Energy contribution -23.08
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.79
SVM decision value -0.02
SVM RNA-class probability 0.523093
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20882478 120 - 22224390
GCAGAAGUAACGGGCAGUCGGCAACAGUGGGCCGUUCGAAAACAAAAACAAAAAAGCAAACAAAUGUCGAUGGUUGCACACGACUGCGUUGUGUGAACAAUGGAGAGCUGGUUAACAGUA
((((..((..(((((.(((.((....)).))).))))).................((((.((........)).))))..))..))))(((((....))))).....((((.....)))). ( -30.00)
>DroSec_CAF1 2346 115 - 1
GCAGAAGUAACGGGCAGUCGGCAACAGUGGGCAGUUG--AAACAAAAA-AAAAAAGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUUG--AGCUGGUAAACAGUA
.(((..((....(((.(((((((...((..((..((.--.........-..))..))..))...))))))).))).((((((((...)))))))).))..)))--.((((.....)))). ( -28.20)
>DroSim_CAF1 3151 115 - 1
GCAGAAGUAACGGGCAGUCGGCAACAGUGGGCAGUUG--AAACAAAAA-AAAAACGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG--AGCUGGUAAACAGUA
............(((.(((((((...((..((.(((.--.........-...)))))..))...))))))).))).((((((((...))))))))........--.((((.....)))). ( -29.62)
>DroYak_CAF1 3301 110 - 1
GCAGAAGUAACGGCCGGUCGGCAACAGUGGGUCGU----AAAAAACAA-AUAAACGCUAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG--AGCUGGUAAACA---
.(((......((((.((((((((...((.((.(((----.........-....))))).))...))))))))))))((((((((...))))))))........--..))).......--- ( -29.52)
>consensus
GCAGAAGUAACGGGCAGUCGGCAACAGUGGGCAGUUG__AAACAAAAA_AAAAAAGCAAACAAAUGUCGAUCGCUGCACACGACGGCGUUGUGUGAACAAUGG__AGCUGGUAAACAGUA
.(((........(((.(((((((...((..((.......................))..))...))))))).))).((((((((...))))))))............))).......... (-23.14 = -23.08 +  -0.06)

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 13:03:15 2006