Locus 6640

Sequence ID 2R_DroMel_CAF1
Location 20,730,469 – 20,730,621
Length 152
Max. P 0.998480
window10572 window10573 window10574 window10575

overview

Window 2

Location 20,730,469 – 20,730,589
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -33.78
Consensus MFE -32.06
Energy contribution -32.06
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.95
SVM decision value 2.63
SVM RNA-class probability 0.995911
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20730469 120 + 20766785
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGUGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((.......(((((....))))).........((.((((((.....)))))).))..)))))).))))))))).))...... ( -32.00)
>DroSec_CAF1 163967 120 + 1
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGCGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((.......(((((....))))).........((.((((((.....)))))).))..)))))).))))))))).))...... ( -31.70)
>DroSim_CAF1 169389 120 + 1
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGCGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((.......(((((....))))).........((.((((((.....)))))).))..)))))).))))))))).))...... ( -31.70)
>DroEre_CAF1 204888 120 + 1
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGUGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCGCUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((((.....(((((....))))).........((.((((((.....)))))).)))))))))).))))))))).))...... ( -39.00)
>DroYak_CAF1 170549 120 + 1
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGUGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCGGUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((.(.....(((((....))))).........((.((((((.....)))))).))).)))))).))))))))).))...... ( -34.50)
>consensus
UUUUUCAGACAAAUAAUCCAGCCUUAAGCAUGGUGAUUAAGCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACG
....................((.((((((.(((.((((((.......(((((....))))).........((.((((((.....)))))).))..)))))).))))))))).))...... (-32.06 = -32.06 +  -0.00)

alignment

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secondary structure

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Window 3

Location 20,730,469 – 20,730,589
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -36.96
Consensus MFE -35.30
Energy contribution -35.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.96
SVM decision value 2.77
SVM RNA-class probability 0.996931
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20730469 120 - 20766785
CGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCACCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.(((((((.((.((((((.....)))))).)).........(((((....))))).....).)))))).))..)))))..)).((((.....))))...... ( -35.20)
>DroSec_CAF1 163967 120 - 1
CGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCGCCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.(((((((.((.((((((.....)))))).)).........(((((....))))).....).)))))).))..)))))..)).((((.....))))...... ( -35.70)
>DroSim_CAF1 169389 120 - 1
CGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCGCCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.(((((((.((.((((((.....)))))).)).........(((((....))))).....).)))))).))..)))))..)).((((.....))))...... ( -35.70)
>DroEre_CAF1 204888 120 - 1
CGUCGCGCUCUAAGCCGGAGAUUAAGCGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCACCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.((((((((((.((((((.....)))))).)).........(((((....))))).....)))))))).))..)))))..)).((((.....))))...... ( -42.40)
>DroYak_CAF1 170549 120 - 1
CGUCGCGCUCUAAGCCGGAGAUUAACCGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCACCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.((((((.(((.((((((.....)))))).)).........(((((....))))).....).)))))).))..)))))..)).((((.....))))...... ( -35.80)
>consensus
CGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGCUUAAUCACCAUGCUUAAGGCUGGAUUAUUUGUCUGAAAAA
......((..(((((.((.((((((..((.((((((.....)))))).)).........(((((....))))).......)))))).))..)))))..)).((((.....))))...... (-35.30 = -35.30 +   0.00)

alignment

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secondary structure

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Window 4

Location 20,730,509 – 20,730,621
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.29
Mean single sequence MFE -29.22
Consensus MFE -26.68
Energy contribution -26.84
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.09
Structure conservation index 0.91
SVM decision value -0.03
SVM RNA-class probability 0.516862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20730509 112 + 20766785
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACGCGUUU-UUUCGCGACUCCGCCUGCAUUGUUUUU-------
((..((((((((....)))))..(((((..((.((((((.....)))))).))))))))))...(((...((((((((.......-..))))).))).))).)).........------- ( -30.00)
>DroSec_CAF1 164007 112 + 1
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACGCGUUU-UUUCGCGACUCCGCCUGCAUUGUUUUU-------
((..((((((((....)))))..(((((..((.((((((.....)))))).))))))))))...(((...((((((((.......-..))))).))).))).)).........------- ( -30.00)
>DroSim_CAF1 169429 112 + 1
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACGCGUUU-UUUCGCGACUCCGCCUGCAUUGUUUUU-------
((..((((((((....)))))..(((((..((.((((((.....)))))).))))))))))...(((...((((((((.......-..))))).))).))).)).........------- ( -30.00)
>DroEre_CAF1 204928 120 + 1
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCGCUUAAUCUCCGGCUUAGAGCGCGACGCGUUUUUUUCGCGACACCGUCUGCAUUGUUUUUUUUUUUU
((..(((.((((....))))((((......((.((((((.....)))))).))(((........))).....))))..((((.......)))).....))).))................ ( -27.40)
>DroYak_CAF1 170589 111 + 1
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCGGUUAAUCUCCGGCUUAGAGCGCGACGCGUUUUUUUCGCGACUCCUUCUGCAUUGUUU---------
(((.((.(((((....))))).(....(((((.((((((.....)))))).)))))....))).)))...((((((((..........))))).)))..............--------- ( -28.70)
>consensus
GCUUGAUCCCCUACCAAGGGGCGUAAUAUUGACGGAUUUUCCUUAAAUCCCUCUGUUAAUCUCCGGCUUAGAGCGCGACGCGUUU_UUUCGCGACUCCGCCUGCAUUGUUUUU_______
((..((((((((....))))).........((.((((((.....)))))).)).....)))...(((...((((((((..........))))).))).))).))................ (-26.68 = -26.84 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,730,509 – 20,730,621
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.29
Mean single sequence MFE -33.36
Consensus MFE -30.26
Energy contribution -31.06
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.91
SVM decision value 3.12
SVM RNA-class probability 0.998480
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20730509 112 - 20766785
-------AAAAACAAUGCAGGCGGAGUCGCGAAA-AAACGCGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
-------.........((.(((((((.(((((..-.......)))))))))..)))...(((.....((.((((((.....)))))).)).........(((((....))))))))..)) ( -34.80)
>DroSec_CAF1 164007 112 - 1
-------AAAAACAAUGCAGGCGGAGUCGCGAAA-AAACGCGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
-------.........((.(((((((.(((((..-.......)))))))))..)))...(((.....((.((((((.....)))))).)).........(((((....))))))))..)) ( -34.80)
>DroSim_CAF1 169429 112 - 1
-------AAAAACAAUGCAGGCGGAGUCGCGAAA-AAACGCGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
-------.........((.(((((((.(((((..-.......)))))))))..)))...(((.....((.((((((.....)))))).)).........(((((....))))))))..)) ( -34.80)
>DroEre_CAF1 204928 120 - 1
AAAAAAAAAAAACAAUGCAGACGGUGUCGCGAAAAAAACGCGUCGCGCUCUAAGCCGGAGAUUAAGCGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
................((.....(((.((((.......)))).))).((((.....)))).....))((.((((((.....)))))).)).........(((((....)))))....... ( -32.10)
>DroYak_CAF1 170589 111 - 1
---------AAACAAUGCAGAAGGAGUCGCGAAAAAAACGCGUCGCGCUCUAAGCCGGAGAUUAACCGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
---------.............((((.(((((..........)))))))))..((..((........((.((((((.....)))))).)).........(((((....))))).))..)) ( -30.30)
>consensus
_______AAAAACAAUGCAGGCGGAGUCGCGAAA_AAACGCGUCGCGCUCUAAGCCGGAGAUUAACAGAGGGAUUUAAGGAAAAUCCGUCAAUAUUACGCCCCUUGGUAGGGGAUCAAGC
................((.(((((((.(((((..........)))))))))..)))...(((.....((.((((((.....)))))).)).........(((((....))))))))..)) (-30.26 = -31.06 +   0.80)

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 12:15:56 2006