Locus 863

Sequence ID 2R_DroMel_CAF1
Location 4,018,468 – 4,018,628
Length 160
Max. P 0.998600
window1493 window1494 window1495

overview

Window 3

Location 4,018,468 – 4,018,588
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.45
Mean single sequence MFE -37.70
Consensus MFE -28.25
Energy contribution -30.06
Covariance contribution 1.81
Combinations/Pair 1.10
Mean z-score -1.99
Structure conservation index 0.75
SVM decision value 0.51
SVM RNA-class probability 0.764440
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4018468 120 - 20766785
GGCAAGCCGAUUAGGGCUUGGGUCCGUCAAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGAAAAUGGCCUAUAAAUUUUACAUUUAACGCGGCCCGAGGAUGACUCUUUUC
((((((((......))))))...))((((..(((..((((((.....)))))).(((((..(((((.......)))))..(((((.....))))).)))))...)))..))))....... ( -37.40)
>DroSec_CAF1 1323 119 - 1
GGCAAGCCGAUUAGGGCUCGGGUCCGCCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUAUAAAUUUUACAUUUAACGCGGCCCGAGGAUGACUCUUUUC
((....))((..((((((((((.((((.........((((((.....))))))........(((((....-..)))))...................)))))))))).....))))..)) ( -39.30)
>DroSim_CAF1 3375 119 - 1
GGCAAGCCGAUUAGGGCUCGGGUCCGCCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCGACGG-AAUGGCCUAUAAAUUUUACAUUUAACGCGGCCCGAGGAUGACUCUUUUC
((....))((..((((((((((.((((.........((((((.....))))))........(((((....-..)))))...................)))))))))).....))))..)) ( -38.10)
>DroEre_CAF1 1316 104 - 1
GGCAAGCCGAUUAG-GC-CGGGUCCGUCCAGCUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUAUAAAUUUUACAUUUC-------------AUGACUCUUUUC
((....))...(((-((-((..((((((((((....((((((.....)))))).....)))))...))))-).)))))))...............-------------............ ( -36.10)
>DroYak_CAF1 3210 118 - 1
GGCAAGCCGAUUAGGGC-CGGGUCCGUCAGACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUAUAAAUUUUACAUUUAACGCGGCCCGAGGAUGACUCUUUUC
((....)).....((((-((((((.....)))....((((((.....)))))).))(((..(((((....-..)))))..(((((.....))))).))))))))(((.....)))..... ( -37.60)
>consensus
GGCAAGCCGAUUAGGGCUCGGGUCCGUCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG_AAUGGCCUAUAAAUUUUACAUUUAACGCGGCCCGAGGAUGACUCUUUUC
((....))((..((((((((((.((((.........((((((.....))))))........(((((.......)))))...................)))))))))).....))))..)) (-28.25 = -30.06 +   1.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,018,508 – 4,018,628
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.81
Mean single sequence MFE -39.12
Consensus MFE -33.78
Energy contribution -34.46
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -2.70
Structure conservation index 0.86
SVM decision value 3.16
SVM RNA-class probability 0.998600
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4018508 120 + 20766785
UAGGCCAUUUUCGUUGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGUUUGACGGACCCAAGCCCUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUUCAAUGUA
..(((((.......)))))((((.((((((((..(((..(((((....(((.....)))..))))).)))..)))))))).))))........(((((((....)))))))......... ( -37.70)
>DroSec_CAF1 1363 119 + 1
UAGGCCAUU-CCGUUGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGUUGGGCGGACCCGAGCCCUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUUCAAUGUA
..(((((..-....)))))((((.((((((((..(((..(((((.......(((....)))))))).)))..)))))))).))))........(((((((....)))))))......... ( -40.81)
>DroSim_CAF1 3415 119 + 1
UAGGCCAUU-CCGUCGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGUUGGGCGGACCCGAGCCCUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUUCAAUGUA
..((((...-.....))))((((.((((((((..(((..(((((.......(((....)))))))).)))..)))))))).))))........(((((((....)))))))......... ( -38.91)
>DroEre_CAF1 1343 117 + 1
UAGGCCAUU-CCGUUGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGCUGGACGGACCCG-GC-CUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUCCAAUGUA
..(((((..-....)))))((((.((((((((..(((..((((....))))((.((....))-.)-))))..)))))))).))))..(((.(.(((((((....))))))).)...))). ( -39.30)
>DroYak_CAF1 3250 118 + 1
UAGGCCAUU-CCGUUGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGUCUGACGGACCCG-GCCCUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUUCAAUGUA
..(((((..-....)))))((((.((((((((..(((..((((.....(((.....)))..)-))).)))..)))))))).))))........(((((((....)))))))......... ( -38.90)
>consensus
UAGGCCAUU_CCGUUGGCCAGCACGGUAAGCCUUUUAAAGGCUUUAAAGUUGGACGGACCCGAGCCCUAAUCGGCUUGCCAUGCUAAACACGCUUUUUUGUCUACGGAAAAUUCAAUGUA
..(((((.......)))))((((.((((((((..(((..(((((....(((.....)))..))))).)))..)))))))).))))........(((((((....)))))))......... (-33.78 = -34.46 +   0.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,018,508 – 4,018,628
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.81
Mean single sequence MFE -39.42
Consensus MFE -34.58
Energy contribution -34.86
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -2.46
Structure conservation index 0.88
SVM decision value 3.10
SVM RNA-class probability 0.998441
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4018508 120 - 20766785
UACAUUGAAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAGGGCUUGGGUCCGUCAAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGAAAAUGGCCUA
................((((((........))))))((((((.(((((....(((((((.(((.......)))...))))))).....))))).)))))).(((((.......))))).. ( -38.20)
>DroSec_CAF1 1363 119 - 1
UACAUUGAAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAGGGCUCGGGUCCGCCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUA
................((((((........))))))((((((.(((((....((((((.(((....)))........)))))).....))))).)))))).(((((....-..))))).. ( -39.30)
>DroSim_CAF1 3415 119 - 1
UACAUUGAAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAGGGCUCGGGUCCGCCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCGACGG-AAUGGCCUA
...........((((((.((((........))))((((((((.(((((....((((((.(((....)))........)))))).....))))).))))))))....))))-))....... ( -38.30)
>DroEre_CAF1 1343 117 - 1
UACAUUGGAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAG-GC-CGGGUCCGUCCAGCUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUA
...(((((.(((.(((((((((........)))))...)))).))))))))(((-((-((..((((((((((....((((((.....)))))).....)))))...))))-).))))))) ( -42.60)
>DroYak_CAF1 3250 118 - 1
UACAUUGAAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAGGGC-CGGGUCCGUCAGACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG-AAUGGCCUA
................((((((........))))))((((((.(((((....(((((-.(((((.....)))))....))))).....))))).)))))).(((((....-..))))).. ( -38.70)
>consensus
UACAUUGAAUUUUCCGUAGACAAAAAAGCGUGUUUAGCAUGGCAAGCCGAUUAGGGCUCGGGUCCGUCCAACUUUAAAGCCUUUAAAAGGCUUACCGUGCUGGCCAACGG_AAUGGCCUA
................((((((........))))))((((((.(((((....((((((.((((.......))))...)))))).....))))).)))))).(((((.......))))).. (-34.58 = -34.86 +   0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:14 2006