Locus 5177

Sequence ID 2L_DroMel_CAF1
Location 14,663,389 – 14,663,487
Length 98
Max. P 0.984653
window8242 window8243

overview

Window 2

Location 14,663,389 – 14,663,487
Length 98
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.73
Mean single sequence MFE -34.52
Consensus MFE -26.35
Energy contribution -27.45
Covariance contribution 1.10
Combinations/Pair 1.18
Mean z-score -3.46
Structure conservation index 0.76
SVM decision value 1.79
SVM RNA-class probability 0.977293
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14663389 98 + 22407834
GAAAACAGAUGACGCAUCGUCUGCGUCUGCAAUGAAUGCACUUUUUCUGCAAUUUGACUUUU------------C-CGAAGACAAAGCAGACGAGCUGUCUUCUCGUCUGC
((((((((((((((((.....))))))((((..(((......)))..)))))))))..))))------------)-..........(((((((((.......))))))))) ( -30.00)
>DroSec_CAF1 18024 110 + 1
GAAAACAGAUGACGCAUCGUCUGCGUCUGCAAUGAAUGCACUUUUUCUGCAAUUUGACUUUCGUCUAAAGGCAGA-CGAAGACAAAGCAGACGAGCUGUCUUCUCGUCUAC
....(((((.(((((.((((((((...((((.....))))((((.(((((.....(((....))).....)))))-.)))).....)))))))))).))).))).)).... ( -39.30)
>DroEre_CAF1 18032 111 + 1
GAAAACAGAUGACGCAUCGUCUGCGUCUGCAAUGAAUGCACUUUUUCUGCAAUUUGACUUUCGUCUAAAGGCAGACCGAAGACAAAGCAGACGAGCUGUCUUCUCGUCUGC
.....((((((((((.((((((((...((((.....))))((((.(((((.....(((....))).....)))))..)))).....)))))))))).))).....))))). ( -37.90)
>DroYak_CAF1 18420 111 + 1
GAAAACAGAUGACGCAUCGUCUGCGUCUGCAAUGAAUGCACUUUUUCUGCAAUUUGACUUUCGUCUAAAGGCAGACCGAAGACAAAGCAGACGAGCUGUCUUCUCGUCUGC
.....((((((((((.((((((((...((((.....))))((((.(((((.....(((....))).....)))))..)))).....)))))))))).))).....))))). ( -37.90)
>DroMoj_CAF1 18880 77 + 1
GAAAAACGAUGACGCAUCGUCUGCGUCUGCAUUAAAUAUUCAU-UUCUGCAUUU--------------------------------GCAGACGAACUGUCUUCGAGCAUG-
......(((.((((..(((((((((..((((..((((....))-)).))))..)--------------------------------))))))))..)))).)))......- ( -26.70)
>DroAna_CAF1 17501 111 + 1
AAAAUCCGAUGACGCAUCGUCUGCGUCUGCAUUGAAUGCACUUUUUCUGCAAUUUGACUUUCGUCUGCAGUCGGGCCAAAACCAAUGCAGACGAACUGUCUUUUCGUCUAC
......(((.((((((.....))))))((((..(((......)))..))))....(((.((((((((((...((.......))..))))))))))..)))...)))..... ( -35.30)
>consensus
GAAAACAGAUGACGCAUCGUCUGCGUCUGCAAUGAAUGCACUUUUUCUGCAAUUUGACUUUCGUCUAAAGGCAGA_CGAAGACAAAGCAGACGAGCUGUCUUCUCGUCUGC
......(((.((((..((((((((...((((..(((......)))..)))).((((.((((.((((......)))).)))).))))))))))))..)))).)))....... (-26.35 = -27.45 +   1.10)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,663,389 – 14,663,487
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.73
Mean single sequence MFE -39.47
Consensus MFE -27.07
Energy contribution -28.50
Covariance contribution 1.43
Combinations/Pair 1.19
Mean z-score -4.34
Structure conservation index 0.69
SVM decision value 1.98
SVM RNA-class probability 0.984653
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14663389 98 - 22407834
GCAGACGAGAAGACAGCUCGUCUGCUUUGUCUUCG-G------------AAAAGUCAAAUUGCAGAAAAAGUGCAUUCAUUGCAGACGCAGACGAUGCGUCAUCUGUUUUC
(((((((((.......)))))))))((((.(((..-.------------..))).))))..(((((.....((((.....))))((((((.....)))))).))))).... ( -36.50)
>DroSec_CAF1 18024 110 - 1
GUAGACGAGAAGACAGCUCGUCUGCUUUGUCUUCG-UCUGCCUUUAGACGAAAGUCAAAUUGCAGAAAAAGUGCAUUCAUUGCAGACGCAGACGAUGCGUCAUCUGUUUUC
..((((.(((.(((.((((((((((.....(((..-(((((..((.(((....))).))..)))))..)))((((.....))))...)))))))).))))).))))))).. ( -43.60)
>DroEre_CAF1 18032 111 - 1
GCAGACGAGAAGACAGCUCGUCUGCUUUGUCUUCGGUCUGCCUUUAGACGAAAGUCAAAUUGCAGAAAAAGUGCAUUCAUUGCAGACGCAGACGAUGCGUCAUCUGUUUUC
((((((..(((((((((......))..))))))).)))))).....(((....))).....(((((.....((((.....))))((((((.....)))))).))))).... ( -45.50)
>DroYak_CAF1 18420 111 - 1
GCAGACGAGAAGACAGCUCGUCUGCUUUGUCUUCGGUCUGCCUUUAGACGAAAGUCAAAUUGCAGAAAAAGUGCAUUCAUUGCAGACGCAGACGAUGCGUCAUCUGUUUUC
((((((..(((((((((......))..))))))).)))))).....(((....))).....(((((.....((((.....))))((((((.....)))))).))))).... ( -45.50)
>DroMoj_CAF1 18880 77 - 1
-CAUGCUCGAAGACAGUUCGUCUGC--------------------------------AAAUGCAGAA-AUGAAUAUUUAAUGCAGACGCAGACGAUGCGUCAUCGUUUUUC
-......(((.(((...((((((((--------------------------------...((((..(-(.......))..))))...))))))))...))).)))...... ( -24.60)
>DroAna_CAF1 17501 111 - 1
GUAGACGAAAAGACAGUUCGUCUGCAUUGGUUUUGGCCCGACUGCAGACGAAAGUCAAAUUGCAGAAAAAGUGCAUUCAAUGCAGACGCAGACGAUGCGUCAUCGGAUUUU
(((((((((.......)))))))))............((((((((((((....)))....)))))......(((((...)))))((((((.....)))))).))))..... ( -41.10)
>consensus
GCAGACGAGAAGACAGCUCGUCUGCUUUGUCUUCG_UCUGCCUUUAGACGAAAGUCAAAUUGCAGAAAAAGUGCAUUCAUUGCAGACGCAGACGAUGCGUCAUCUGUUUUC
(((((((((.......))))))))).....................(((....))).....(((((.....((((.....))))((((((.....)))))).))))).... (-27.07 = -28.50 +   1.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:56 2006