Locus 4492

Sequence ID X_DroMel_CAF1
Location 11,880,087 – 11,880,278
Length 191
Max. P 0.998741
window7383 window7384 window7385 window7386

overview

Window 3

Location 11,880,087 – 11,880,184
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -20.27
Consensus MFE -15.41
Energy contribution -14.97
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.25
SVM RNA-class probability 0.652534
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880087 97 + 22224390
CCAAUAGCCAUUUGGGCUUGUCUUUACUUUGAUUGGAAAGCCGGCCAUGGCUAAGAUAAUCUUUCGACACGGCUUUUCACCGGAAAAUUCAAAAGAU
.....((((.....)))).((((((........((((((((((((....))...((.......))....))))))))))...((....)).)))))) ( -23.20)
>DroSec_CAF1 12096 79 + 1
AUAGUUGCCAUUUGGGCUUGUCUUUACUUUGAUUGGAAAUCCAGCCAUGGCUAGGAUAAUCUUUC------------------AAAAUUCCAAAGAU
......(((.....)))..((((((..(((((..((..(((((((....))).))))..))..))------------------))).....)))))) ( -18.80)
>DroSim_CAF1 14433 79 + 1
ACAGUUGCCAUUUGGGCUUGUCUUUACUUUGAUUGGAAAUCCAGCCAUGGCUAGGAUAAUCUUUC------------------AAAAUUCCAAAGAU
......(((.....)))..((((((..(((((..((..(((((((....))).))))..))..))------------------))).....)))))) ( -18.80)
>consensus
ACAGUUGCCAUUUGGGCUUGUCUUUACUUUGAUUGGAAAUCCAGCCAUGGCUAGGAUAAUCUUUC__________________AAAAUUCCAAAGAU
......(((.....)))(((((((..((.((..(((....)))..)).))..)))))))...................................... (-15.41 = -14.97 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,880,108 – 11,880,223
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.49
Mean single sequence MFE -28.06
Consensus MFE -10.42
Energy contribution -9.42
Covariance contribution -1.00
Combinations/Pair 1.33
Mean z-score -1.92
Structure conservation index 0.37
SVM decision value -0.02
SVM RNA-class probability 0.524403
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880108 115 + 22224390
--CUUUACUUUGAUUGGAAAGCCGGCCAUGGCUA--AGAUAAUCUUUCGACACGGCUUUUCACCGGAAAAUUCAAAAGAUUUUCCUGCAUUUUAGAUGCAUGGG-AGACUUCACCGGAUG
--............((((((((((((....))..--.((.......))....))))))))))((((.....((....))((((((((((((...)))))).)))-))).....))))... ( -33.30)
>DroSec_CAF1 12117 97 + 1
--CUUUACUUUGAUUGGAAAUCCAGCCAUGGCUA--GGAUAAUCUUUC------------------AAAAUUCCAAAGAUUUUACUGCAUUUUAGAUUCAUGGU-AGACUUCACCGGAUG
--......(((((..((..(((((((....))).--))))..))..))------------------)))..(((...((.((((........)))).))..(((-.(....))))))).. ( -19.50)
>DroSim_CAF1 14454 97 + 1
--CUUUACUUUGAUUGGAAAUCCAGCCAUGGCUA--GGAUAAUCUUUC------------------AAAAUUCCAAAGAUUUUACUGCAUUUUAGAUGCAUGGG-AGACUUCACCGGAUG
--......(((((..((..(((((((....))).--))))..))..))------------------)))..(((...........((((((...)))))).((.-...)).....))).. ( -22.30)
>DroEre_CAF1 14249 103 + 1
UACUCCACUUUGAUUGGUAAGUCGGCCAUGGCCA--AGAUAAUCUUAC---------------GCAAAAGUGCAAAAGAUUUUUCUGCAUUUUAGAUGCGUGGGUAGACUUCACCGGUUG
...........(((((((((((((((....))).--.......(((((---------------(((((((((((...((....))))))))))...))))))))..))))).))))))). ( -34.70)
>DroYak_CAF1 15756 103 + 1
UGCUUUACUUUGAUUGGAGAGUCGGCCAUGGUCGUAUGGCUAU-UUAC---------------CGGAAAAUUCAAAAGAUUUUUCUGCAUUUUAGAUGCACGGG-AGACUUUACCGGAUG
.............(((((((((((((((((....)))))))..-...(---------------(((((((.((....)).)))))((((((...))))))))).-.)))))).))))... ( -30.50)
>consensus
__CUUUACUUUGAUUGGAAAGCCGGCCAUGGCUA__AGAUAAUCUUUC__________________AAAAUUCAAAAGAUUUUACUGCAUUUUAGAUGCAUGGG_AGACUUCACCGGAUG
.......((((....((....))(((....))).........................................)))).......((((((...))))))(((..........))).... (-10.42 =  -9.42 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,880,184 – 11,880,278
Length 94
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -25.03
Consensus MFE -21.63
Energy contribution -21.35
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -1.58
Structure conservation index 0.86
SVM decision value 1.06
SVM RNA-class probability 0.908629
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880184 94 + 22224390
UUUCCUGCAUUUUAGAUGCAUGGG-AGACUUCACCGGAUGGCAAUUAGCAUUUCGGUUUUGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
(((((((((((...)))))).)))-))....((((((.((((((..(((.....(((.(((....))).))).......))))))))))))))). ( -28.70)
>DroSec_CAF1 12175 94 + 1
UUUACUGCAUUUUAGAUUCAUGGU-AGACUUCACCGGAUGGCAAUUAGCAUUUCGGUUUGGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
....((((..............))-))....((((((.((((((..(((.....((..(((((......)))))..)).))))))))))))))). ( -22.94)
>DroSim_CAF1 14512 94 + 1
UUUACUGCAUUUUAGAUGCAUGGG-AGACUUCACCGGAUGGCAAUUAGCAUUUCGGUUUGGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
.....((((((...)))))).((.-...)).((((((.((((((..(((.....((..(((((......)))))..)).))))))))))))))). ( -26.90)
>DroEre_CAF1 14312 95 + 1
UUUUCUGCAUUUUAGAUGCGUGGGUAGACUUCACCGGUUGGUAAUUAGCAUUUCGGUUUUGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
..(((((((((...)))))).))).......(((((((.(((((..(((.....(((.(((....))).))).......))))))))))))))). ( -21.30)
>DroYak_CAF1 15820 94 + 1
UUUUCUGCAUUUUAGAUGCACGGG-AGACUUUACCGGAUGGCAAUUAGCAUUUUGGUUUUGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
((..(((((((...)))))).)..-))....((((((.((((((..(((....(((..(..((......))..)..)))))))))))))))))). ( -25.30)
>consensus
UUUACUGCAUUUUAGAUGCAUGGG_AGACUUCACCGGAUGGCAAUUAGCAUUUCGGUUUUGGUUUCAGUAUUUAUUUCAGCUUUGCCGCCGGUGU
.....((((((...))))))...........((((((.((((((..(((..............................))))))))))))))). (-21.63 = -21.35 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,880,184 – 11,880,278
Length 94
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -19.95
Consensus MFE -17.79
Energy contribution -18.59
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.89
SVM decision value 3.21
SVM RNA-class probability 0.998741
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880184 94 - 22224390
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCAAAACCGAAAUGCUAAUUGCCAUCCGGUGAAGUCU-CCCAUGCAUCUAAAAUGCAGGAAA
.((((((.((((((((..............................)))..)))))..))))))......-.((.(((((.....)))))))... ( -24.71)
>DroSec_CAF1 12175 94 - 1
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCCAAACCGAAAUGCUAAUUGCCAUCCGGUGAAGUCU-ACCAUGAAUCUAAAAUGCAGUAAA
.((((((.((((((((..............................)))..)))))..))))))......-........................ ( -18.41)
>DroSim_CAF1 14512 94 - 1
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCCAAACCGAAAUGCUAAUUGCCAUCCGGUGAAGUCU-CCCAUGCAUCUAAAAUGCAGUAAA
.((((((.((((((((..............................)))..)))))..))))))......-....(((((.....)))))..... ( -22.31)
>DroEre_CAF1 14312 95 - 1
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCAAAACCGAAAUGCUAAUUACCAACCGGUGAAGUCUACCCACGCAUCUAAAAUGCAGAAAA
.((((((((((...))))..........((....))......................))))))............((((.....))))...... ( -15.30)
>DroYak_CAF1 15820 94 - 1
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCAAAACCAAAAUGCUAAUUGCCAUCCGGUAAAGUCU-CCCGUGCAUCUAAAAUGCAGAAAA
..(((((.((((((((..............................)))..)))))..))))).......-....(((((.....)))))..... ( -19.01)
>consensus
ACACCGGCGGCAAAGCUGAAAUAAAUACUGAAACCAAAACCGAAAUGCUAAUUGCCAUCCGGUGAAGUCU_CCCAUGCAUCUAAAAUGCAGAAAA
.((((((.((((((((..............................)))..)))))..))))))...........(((((.....)))))..... (-17.79 = -18.59 +   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 11:26:27 2006