Locus 8710

Sequence ID 3R_DroMel_CAF1
Location 23,286,226 – 23,286,318
Length 92
Max. P 0.948338
window13986 window13987

overview

Window 6

Location 23,286,226 – 23,286,318
Length 92
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.49
Mean single sequence MFE -25.53
Consensus MFE -18.51
Energy contribution -19.07
Covariance contribution 0.56
Combinations/Pair 1.15
Mean z-score -2.33
Structure conservation index 0.72
SVM decision value 1.38
SVM RNA-class probability 0.948338
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23286226 92 + 27905053
GAAAAGGAAUGUUAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAGGCUUGACAAGCUCUCCUGAGC-AAAAUGGAA-----------------
.....((...(((((((((((((((......)))).))))).))))))....))(((((.(((((.....))).))..)))))-.........----------------- ( -25.30)
>DroSec_CAF1 83842 90 + 1
GAAAAGGAAUGUUAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAGGCUUGACAAGCU--CCUGAGC-AAAAUGGUG-----------------
.....((...(((((((((((((((......)))).))))).))))))....))(((((..((((.....))))--..)))))-.........----------------- ( -26.80)
>DroEre_CAF1 89364 90 + 1
GAGAAGGAAUGUUAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAGGCUUGACAAGCU--CCUGAGC-AAAAUAGAA-----------------
.....((...(((((((((((((((......)))).))))).))))))....))(((((..((((.....))))--..)))))-.........----------------- ( -26.80)
>DroWil_CAF1 91510 94 + 1
---GCAGCAUAUAAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCAGCUCAAAGGCUUGACAAGCU--UCUGAGU-AUU--------GGACUAA--AAGGAA
---((((.((.((((.(((((((((......)))).))))).)))))).)))).(((((.(((((.....))))--).)))))-...--------.......--...... ( -25.10)
>DroYak_CAF1 86510 91 + 1
GAAGAGGAAUGUUAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAGGCUUGACAAGCU--CCUGAGCGAAAAUGGAA-----------------
.....((...(((((((((((((((......)))).))))).))))))....))(((((..((((.....))))--..)))))..........----------------- ( -26.80)
>DroAna_CAF1 79246 107 + 1
GCAAAAGAAUAUAAAAAGCCAGCAAUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAAGCCUGACAAGCU--CCUGAGA-AAAAUCGAAAGCGGUACGACCAGAGG
((((((.....((((.(((.(((((......)))))..))).)))).))))))..(((.............(((--..(((..-....)))..)))((.....)).))). ( -22.40)
>consensus
GAAAAGGAAUGUUAAAAGCAAGCAGUGCACUUUGCUUUGCUAUUUAAUUUUGCCGCUCAAAGGCUUGACAAGCU__CCUGAGC_AAAAUGGAA_________________
.....((...(((((((((((((((......)))).))))).))))))....))(((((..((((.....))))....)))))........................... (-18.51 = -19.07 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,286,226 – 23,286,318
Length 92
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.49
Mean single sequence MFE -22.62
Consensus MFE -15.36
Energy contribution -15.92
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.87
Structure conservation index 0.68
SVM decision value 0.88
SVM RNA-class probability 0.872934
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23286226 92 - 27905053
-----------------UUCCAUUUU-GCUCAGGAGAGCUUGUCAAGCCUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUAACAUUCCUUUUC
-----------------.........-((((((.((.(((.....)))))))))))((.((..(((((.(((((.(((........)))))))))))))..))))..... ( -21.70)
>DroSec_CAF1 83842 90 - 1
-----------------CACCAUUUU-GCUCAGG--AGCUUGUCAAGCCUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUAACAUUCCUUUUC
-----------------.........-((((((.--.(((.....)))..))))))((.((..(((((.(((((.(((........)))))))))))))..))))..... ( -22.10)
>DroEre_CAF1 89364 90 - 1
-----------------UUCUAUUUU-GCUCAGG--AGCUUGUCAAGCCUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUAACAUUCCUUCUC
-----------------.........-((((((.--.(((.....)))..))))))((.((..(((((.(((((.(((........)))))))))))))..))))..... ( -22.10)
>DroWil_CAF1 91510 94 - 1
UUCCUU--UUAGUCC--------AAU-ACUCAGA--AGCUUGUCAAGCCUUUGAGCUGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUUAUAUGCUGC---
......--.......--------...-.((((((--.(((.....))).))))))..(((....((((.(((((.(((........)))))))).))))..)))...--- ( -20.30)
>DroYak_CAF1 86510 91 - 1
-----------------UUCCAUUUUCGCUCAGG--AGCUUGUCAAGCCUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUAACAUUCCUCUUC
-----------------........((((((((.--.(((.....)))..)))))))).....(((((.(((((.(((........)))))))))))))........... ( -23.00)
>DroAna_CAF1 79246 107 - 1
CCUCUGGUCGUACCGCUUUCGAUUUU-UCUCAGG--AGCUUGUCAGGCUUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCAUUGCUGGCUUUUUAUAUUCUUUUGC
.....((((...((((....((....-))(((((--((((.....)))))))))))))...........(((((.((.....)).)))))))))................ ( -26.50)
>consensus
_________________UUCCAUUUU_GCUCAGG__AGCUUGUCAAGCCUUUGAGCGGCAAAAUUAAAUAGCAAAGCAAAGUGCACUGCUUGCUUUUAACAUUCCUUUUC
...........................(((((((...(((.....))).))))))).......(((((.(((((.(((........)))))))))))))........... (-15.36 = -15.92 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:48 2006