Locus 3923

Sequence ID 2R_DroMel_CAF1
Location 12,922,243 – 12,922,393
Length 150
Max. P 0.990044
window6335 window6336 window6337 window6338

overview

Window 5

Location 12,922,243 – 12,922,363
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.11
Mean single sequence MFE -32.72
Consensus MFE -24.70
Energy contribution -26.08
Covariance contribution 1.37
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.76
SVM decision value 0.61
SVM RNA-class probability 0.799176
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12922243 120 + 20766785
AGCGAAAUGAGUUACUCUGGUUUGGCCAAAAAUAAUUCUAUAACUGAGCUGCCAGAUCGCAUGCAGACUUAACAGUACACUGCUAACAGUUACUGUUAAAAGUACGCGCCAAUUUUGAAA
..((((((..((...((((((..(((((...(((....)))...)).)))))))))..((.(((....(((((((((.((((....)))))))))))))..))).))))..))))))... ( -29.70)
>DroSec_CAF1 45564 120 + 1
AGCGAAAUGAGUUACCCUGGUUUGGGCAAAACUAAUUCUAUAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGGAA
.(((....(((((((((......)))......))))))....(((...(((((........)))))..(((((((((.((((....))))))))))))).))).))).(((....))).. ( -35.70)
>DroSim_CAF1 33790 120 + 1
AGCAAAAUGAGUUACCCUGGUUUGGCCAAAACUAAUUCUAUAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGAAA
..((((((..........((((((((........................))))))))...(((.((((((((((((.((((....))))))))))))..))).)..))).))))))... ( -32.36)
>DroYak_CAF1 48109 119 + 1
AGCGAAAAGAGUUACUCUAGUUUUG-CACAAAUAUUUCUACAACUGAGCUGCCAGAUCGUCGGCAGAUUUAACAGUGGCCUGCUAACAGUCACUGUUAAAAGUACGCGGCAAUUUUGAAA
.((((((..((.....))..)))))-).((((.(((.(..(.......(((((........))))).((((((((((((.((....)))))))))))))).....)..).)))))))... ( -33.10)
>consensus
AGCGAAAUGAGUUACCCUGGUUUGGCCAAAAAUAAUUCUAUAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGAAA
.(((....((((((...(((.....)))....))))))....(((...(((((........)))))..(((((((((.((((....))))))))))))).))).)))............. (-24.70 = -26.08 +   1.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,922,243 – 12,922,363
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -34.68
Consensus MFE -25.99
Energy contribution -26.80
Covariance contribution 0.81
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.75
SVM decision value 0.52
SVM RNA-class probability 0.769038
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12922243 120 - 20766785
UUUCAAAAUUGGCGCGUACUUUUAACAGUAACUGUUAGCAGUGUACUGUUAAGUCUGCAUGCGAUCUGGCAGCUCAGUUAUAGAAUUAUUUUUGGCCAAACCAGAGUAACUCAUUUCGCU
......((((((.(((((..((((((((((((((....)))).))))))))))..))).(((......)))))))))))...((.(((((((.((.....))))))))).))........ ( -31.90)
>DroSec_CAF1 45564 120 - 1
UUCCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUAUAGAAUUAGUUUUGCCCAAACCAGGGUAACUCAUUUCGCU
......((((((.((.....((((((((((((((....)))).))))))))))..((((((....))))))))))))))...(((...(..((((((......))))))..)..)))... ( -39.10)
>DroSim_CAF1 33790 120 - 1
UUUCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUAUAGAAUUAGUUUUGGCCAAACCAGGGUAACUCAUUUUGCU
......((((((.((.....((((((((((((((....)))).))))))))))..((((((....)))))))))))))).((((((.((((((((.....))))...)))).)))))).. ( -35.90)
>DroYak_CAF1 48109 119 - 1
UUUCAAAAUUGCCGCGUACUUUUAACAGUGACUGUUAGCAGGCCACUGUUAAAUCUGCCGACGAUCUGGCAGCUCAGUUGUAGAAAUAUUUGUG-CAAAACUAGAGUAACUCUUUUCGCU
.............(((....((((((((((.(((....)))..)))))))))).((((((......))))))((((((((((.((....)).))-))..))).)))..........))). ( -31.80)
>consensus
UUUCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUAUAGAAUUAGUUUUGGCCAAACCAGAGUAACUCAUUUCGCU
.............(((....((((((((((((((....)))).)))))))))).(((((((....)))))))..........((.(((.((((((.....))))))))).))....))). (-25.99 = -26.80 +   0.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,922,283 – 12,922,393
Length 110
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 90.39
Mean single sequence MFE -33.00
Consensus MFE -27.83
Energy contribution -27.20
Covariance contribution -0.63
Combinations/Pair 1.16
Mean z-score -3.64
Structure conservation index 0.84
SVM decision value 2.19
SVM RNA-class probability 0.990044
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12922283 110 + 20766785
UAACUGAGCUGCCAGAUCGCAUGCAGACUUAACAGUACACUGCUAACAGUUACUGUUAAAAGUACGCGCCAAUUUUGAAAGCUCGAAAGCCAAAGCUUACAAAAU-UAACU
.....(((((..((((.(((.(((....(((((((((.((((....)))))))))))))..))).))).....))))..)))))(.((((....)))).).....-..... ( -30.10)
>DroSec_CAF1 45604 111 + 1
UAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGGAAGCUCGAAAGCCAAAGCUUACAAAAUUUAACC
.....(((((.(((((.....(((.((((((((((((.((((....))))))))))))..))).)..)))...))))).)))))(.((((....)))).)........... ( -35.90)
>DroSim_CAF1 33830 111 + 1
UAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGAAAGCUCGAAUGCCAAAGCUUACCAAAUUUAACC
....((((((..((((.....(((.((((((((((((.((((....))))))))))))..))).)..)))...))))..)))))).......................... ( -30.30)
>DroYak_CAF1 48148 111 + 1
CAACUGAGCUGCCAGAUCGUCGGCAGAUUUAACAGUGGCCUGCUAACAGUCACUGUUAAAAGUACGCGGCAAUUUUGAAAGCUCAAGAGUUAAAGCUUACAAAAUUGAAUU
...(((..(((((........))))).((((((((((((.((....))))))))))))))......)))((((((((.(((((..........))))).)))))))).... ( -35.70)
>consensus
UAACUGAGCUGCCAGAUCGCCGGCAGACUUAACAGUGCACUGCUAACAGUCACUGUUAAAAGUACGCGCCAAUUUUGAAAGCUCGAAAGCCAAAGCUUACAAAAUUUAACC
....((((((..((((......((..(((((((((((.((((....))))))))))))..)))..))......))))..)))))).((((....))))............. (-27.83 = -27.20 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,922,283 – 12,922,393
Length 110
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 90.39
Mean single sequence MFE -38.62
Consensus MFE -32.03
Energy contribution -32.02
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -3.76
Structure conservation index 0.83
SVM decision value 2.03
SVM RNA-class probability 0.986033
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12922283 110 - 20766785
AGUUA-AUUUUGUAAGCUUUGGCUUUCGAGCUUUCAAAAUUGGCGCGUACUUUUAACAGUAACUGUUAGCAGUGUACUGUUAAGUCUGCAUGCGAUCUGGCAGCUCAGUUA
.((((-((((((.((((((........)))))).))))))))))(((((..((((((((((((((....)))).))))))))))..))).(((......)))))....... ( -38.20)
>DroSec_CAF1 45604 111 - 1
GGUUAAAUUUUGUAAGCUUUGGCUUUCGAGCUUCCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUA
...........(.((((....)))).)(((((.(((..((((.((.(((..((((((((((((((....)))).))))))))))..))))).)))).))).)))))..... ( -41.60)
>DroSim_CAF1 33830 111 - 1
GGUUAAAUUUGGUAAGCUUUGGCAUUCGAGCUUUCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUA
.(((((.(((((.((((((........))))))))))).)))))........(((((((((((((....)))).)))))))))(.(((((((....))))))))....... ( -38.30)
>DroYak_CAF1 48148 111 - 1
AAUUCAAUUUUGUAAGCUUUAACUCUUGAGCUUUCAAAAUUGCCGCGUACUUUUAACAGUGACUGUUAGCAGGCCACUGUUAAAUCUGCCGACGAUCUGGCAGCUCAGUUG
....((((((((.((((((........)))))).)))))))).........((((((((((.(((....)))..)))))))))).((((((......))))))........ ( -36.40)
>consensus
AGUUAAAUUUUGUAAGCUUUGGCUUUCGAGCUUUCAAAAUUGGCGCGUACUUUUAACAGUGACUGUUAGCAGUGCACUGUUAAGUCUGCCGGCGAUCUGGCAGCUCAGUUA
...........................(((((.(((..((((.((.(((..((((((((((((((....)))).))))))))))..))))).)))).))).)))))..... (-32.03 = -32.02 +  -0.00)

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 11:07:28 2006