Locus 2716

Sequence ID 2R_DroMel_CAF1
Location 9,522,048 – 9,522,326
Length 278
Max. P 0.970155
window4501 window4502 window4503 window4504 window4505

overview

Window 1

Location 9,522,048 – 9,522,166
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.87
Mean single sequence MFE -42.95
Consensus MFE -39.01
Energy contribution -39.33
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.91
SVM decision value 1.65
SVM RNA-class probability 0.970155
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9522048 118 + 20766785
GGUUGUUGGUUGUUAGUUACUUGGCUAGUUA--GUUGGCUUGUCGCUUUCGUCACUGGAGGCGGCACCAUUUUGUUUGGCGUCGUUUUCUCAUGGGCCAACAGACGUUUCAGCCAGCCGA
....((((((((.(((((....)))))(((.--(((((((..(.(((((((....)))))))(((.(((.......))).)))........)..))))))).)))....))))))))... ( -42.50)
>DroSec_CAF1 18647 120 + 1
CGUUGUUGCUUGUUAGUAACUUGGCUAGUUAGAGUUGGCUUGUCGCUUUCGUCAACGGAGGCGGCACCAUUUUGUUUGGCGUCGUUUUCUCAUGGGCCAACAGACGUUUCAGCCAGCCGA
....((((((....))))))((((((.(((.(((.(((..(((((((((((....)))))))))))))).((((((.(((.((((......)))))))))))))...)))))).)))))) ( -43.30)
>DroSim_CAF1 19012 120 + 1
CGUUGUUGGCUGUUAGUAACUUGGCUAGUUAGAGUUGGCUUGUCGCUUUCGUCACCGGAGGCGGCACCAUUUUGUUUGGCGUCGUUUUCUCAUGGGCCAACAGACGUUUCAGCCAGCCGA
....((((((((...((...((((((.((.((((.((((.(((((((((((....)))))))))))(((.......))).))))..)))).)).))))))...))....))))))))... ( -47.30)
>DroYak_CAF1 18389 112 + 1
------UGGUUGUUAGUAACUUGGCUAGUUA--GUUGGCUUGUCGCUUUCGUCACUGGAGGCGGCACCAUUUUGUUUGGCGUCGUUUUCUCAUGGGCCAACAGACGUUUCAGCCAGCCGA
------((((((.((((......))))(((.--(((((((..(.(((((((....)))))))(((.(((.......))).)))........)..))))))).)))....))))))..... ( -38.70)
>consensus
CGUUGUUGGUUGUUAGUAACUUGGCUAGUUA__GUUGGCUUGUCGCUUUCGUCACCGGAGGCGGCACCAUUUUGUUUGGCGUCGUUUUCUCAUGGGCCAACAGACGUUUCAGCCAGCCGA
....(((((((((((((......))))).....(((((((..(.(((((((....)))))))(((.(((.......))).)))........)..)))))))........))))))))... (-39.01 = -39.33 +   0.31)

alignment

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secondary structure

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Window 2

Location 9,522,048 – 9,522,166
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.87
Mean single sequence MFE -31.27
Consensus MFE -26.20
Energy contribution -26.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.01
SVM RNA-class probability 0.539819
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9522048 118 - 20766785
UCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACAAGCCAAC--UAACUAGCCAAGUAACUAACAACCAACAACC
...((((((((....((..((((((....(((....((.(((((.......))))).)).)))..((..(....)..))..))))))--..))))))).))).................. ( -29.20)
>DroSec_CAF1 18647 120 - 1
UCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCGUUGACGAAAGCGACAAGCCAACUCUAACUAGCCAAGUUACUAACAAGCAACAACG
..((((((..((....)).((((((....(((....((.(((((.......))))).)).))).((((.(....)))))..)))))).....))))))..(((.((....)).))).... ( -32.70)
>DroSim_CAF1 19012 120 - 1
UCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCGGUGACGAAAGCGACAAGCCAACUCUAACUAGCCAAGUUACUAACAGCCAACAACG
...(.((((((........((((((..............(((((.......))))).(((...((....))...)))....))))))..(((((.....)))))....)))))).).... ( -33.60)
>DroYak_CAF1 18389 112 - 1
UCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACAAGCCAAC--UAACUAGCCAAGUUACUAACAACCA------
..(((((((((....((..((((((....(((....((.(((((.......))))).)).)))..((..(....)..))..))))))--..))))))).))))...........------ ( -29.60)
>consensus
UCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACAAGCCAAC__UAACUAGCCAAGUUACUAACAACCAACAACG
..((((((..((....)).((((((....(((....((.(((((.......))))).)).)))...((.(....)))....)))))).....))))))...................... (-26.20 = -26.20 +  -0.00)

alignment

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secondary structure

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Window 3

Location 9,522,086 – 9,522,206
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.92
Mean single sequence MFE -39.70
Consensus MFE -37.67
Energy contribution -37.67
Covariance contribution 0.00
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.95
SVM decision value 0.45
SVM RNA-class probability 0.739750
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9522086 120 - 20766785
UUAUUGCAAAUGGAGAAGCGGCGAAGAAGGCUGAAAGUCGUCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACA
..........(((((..(((((..............(((((.(((..((.((....)).))..))).........)))))((((.......))))))))))))))((..(....)..)). ( -36.90)
>DroSec_CAF1 18687 120 - 1
UUAUUGCAAACGGAGAAGCGGCGAAGAAGGCUGAAAGUCGUCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCGUUGACGAAAGCGACA
...........((((..(((((..............(((((.(((..((.((....)).))..))).........)))))((((.......)))))))))))))((((.(....))))). ( -39.80)
>DroSim_CAF1 19052 120 - 1
UUAUUGCAAACGGAGAAGCGGCGAAGAUGGCUGAAAGUCGUCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCGGUGACGAAAGCGACA
...((((....((((..(((((...((((((.....))))))(((..((.((....)).))..)))..............((((.......)))))))))))))(....)....)))).. ( -42.20)
>DroYak_CAF1 18421 120 - 1
UUAUUGCAAAUGGAGAAGCGGCGAAGAUGGCUGAAAGUCGUCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACA
..........(((((..(((((...((((((.....))))))(((..((.((....)).))..)))..............((((.......))))))))))))))((..(....)..)). ( -39.90)
>consensus
UUAUUGCAAACGGAGAAGCGGCGAAGAAGGCUGAAAGUCGUCGGCUGGCUGAAACGUCUGUUGGCCCAUGAGAAAACGACGCCAAACAAAAUGGUGCCGCCUCCAGUGACGAAAGCGACA
..........(((((..(((((...((((((.....))))))(((..((.((....)).))..)))..............((((.......)))))))))))))).((.(....)))... (-37.67 = -37.67 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,522,206 – 9,522,326
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.25
Mean single sequence MFE -33.22
Consensus MFE -31.94
Energy contribution -32.25
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.88
Structure conservation index 0.96
SVM decision value 0.95
SVM RNA-class probability 0.888219
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9522206 120 + 20766785
AAUGUAUCUUCUCGCCGGUCGCGUUUAAAACCGCAUUUUUUUCGCCUUGCGUUUGGAAACGCGAGCGGUUUUUGCAGCUAUCUAAUAAAUUCAUUAAUUCCAAUGCUGACGGGCGUUUUA
............((((.((((((((.......(((......((((.(((((((....)))))))))))....))).......((((......)))).....))))).))).))))..... ( -31.30)
>DroSec_CAF1 18807 120 + 1
AAUGUAUGUUCUCGCCGGUCGCGUUUAAAACCGCAUUUUUUUCGCCUUGCGUUUGGAAACGCGAGCGGUUUUUGCAGCUACCAAAUUAAUUCAUUAAUUCCCAUGCUGACGGGCGUUUUA
.....((((((..((((.((((((((..((.((((............)))).))..)))))))).)))).....((((.....((((((....)))))).....))))..)))))).... ( -35.30)
>DroSim_CAF1 19172 120 + 1
AAUGUAUCUUCUCGCCGGUCGCGUUUAAAACCGCAUUUUUUUCGCCUUGCGUUUGGAAACGCGAGCGGUUUUUGCAGCUAACAAAUUAAUUCAUUAAUUCCCAUGCUGACGGGCGUUUUA
(((((........((((.((((((((..((.((((............)))).))..)))))))).))))..(((((((.....((((((....)))))).....)))).))))))))... ( -33.80)
>DroYak_CAF1 18541 120 + 1
AAUGUAUCUUCUCGCCGGUCGCGUUUAAAACCGCAUUUUUUUCGGCUUGCGAUUGGAAACGCAAGCGGUUUUUGCAGCUACCAAAUUAAUUCAUUAAUUCCAAUGCUGACGGGCGUUUUA
............((((.((((((...((((((((.......(((.....)))..(....)....)))))))))))(((.....((((((....)))))).....)))))).))))..... ( -32.50)
>consensus
AAUGUAUCUUCUCGCCGGUCGCGUUUAAAACCGCAUUUUUUUCGCCUUGCGUUUGGAAACGCGAGCGGUUUUUGCAGCUACCAAAUUAAUUCAUUAAUUCCAAUGCUGACGGGCGUUUUA
............((((.((((((...((((((((............(((((((....))))))))))))))))))(((.....((((((....)))))).....)))))).))))..... (-31.94 = -32.25 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,522,206 – 9,522,326
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -32.42
Consensus MFE -30.41
Energy contribution -30.85
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.94
SVM decision value 1.26
SVM RNA-class probability 0.937471
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9522206 120 - 20766785
UAAAACGCCCGUCAGCAUUGGAAUUAAUGAAUUUAUUAGAUAGCUGCAAAAACCGCUCGCGUUUCCAAACGCAAGGCGAAAAAAAUGCGGUUUUAAACGCGACCGGCGAGAAGAUACAUU
.....((((.(((((((((.(((((....)))))....))).)))((.((((((((.....((((....(....)..)))).....))))))))....))))).))))............ ( -31.30)
>DroSec_CAF1 18807 120 - 1
UAAAACGCCCGUCAGCAUGGGAAUUAAUGAAUUAAUUUGGUAGCUGCAAAAACCGCUCGCGUUUCCAAACGCAAGGCGAAAAAAAUGCGGUUUUAAACGCGACCGGCGAGAACAUACAUU
.....((((.((((((....(((((((....)))))))....)))((.((((((((.....((((....(....)..)))).....))))))))....))))).))))............ ( -32.00)
>DroSim_CAF1 19172 120 - 1
UAAAACGCCCGUCAGCAUGGGAAUUAAUGAAUUAAUUUGUUAGCUGCAAAAACCGCUCGCGUUUCCAAACGCAAGGCGAAAAAAAUGCGGUUUUAAACGCGACCGGCGAGAAGAUACAUU
.....((((.((((((..(.(((((((....))))))).)..)))((.((((((((.....((((....(....)..)))).....))))))))....))))).))))............ ( -33.20)
>DroYak_CAF1 18541 120 - 1
UAAAACGCCCGUCAGCAUUGGAAUUAAUGAAUUAAUUUGGUAGCUGCAAAAACCGCUUGCGUUUCCAAUCGCAAGCCGAAAAAAAUGCGGUUUUAAACGCGACCGGCGAGAAGAUACAUU
.....((((.((((((..(.(((((((....))))))).)..))).......(.(((((((........))))))).)........(((........)))))).))))............ ( -33.20)
>consensus
UAAAACGCCCGUCAGCAUGGGAAUUAAUGAAUUAAUUUGGUAGCUGCAAAAACCGCUCGCGUUUCCAAACGCAAGGCGAAAAAAAUGCGGUUUUAAACGCGACCGGCGAGAAGAUACAUU
.....((((.((((((..(.(((((((....))))))).)..)))((.((((((((.....((((....(....)..)))).....))))))))....))))).))))............ (-30.41 = -30.85 +   0.44)

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 10:37:42 2006