Locus 5125

Sequence ID 3R_DroMel_CAF1
Location 13,493,871 – 13,494,007
Length 136
Max. P 0.975077
window8362 window8363 window8364

overview

Window 2

Location 13,493,871 – 13,493,985
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.87
Mean single sequence MFE -40.42
Consensus MFE -33.02
Energy contribution -33.02
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.82
SVM decision value 0.31
SVM RNA-class probability 0.682824
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13493871 114 + 27905053
AC------UUUGUAAGGGCCACUAUAAGAGUGACAUUCAUGACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAGG
.(------((((...(.((((((((..((((.((((((.......)))))).))))..))))).).)).)((((.......))))(((((.(((((.......))))).)))))))))). ( -40.20)
>DroVir_CAF1 47104 113 + 1
AG------CUUGUAUGGGCCAAUAAAUGCUGGGCAUGUACAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGA-
.(------.((((((((.(((........))).).))))))))((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))....- ( -41.70)
>DroGri_CAF1 56390 114 + 1
AG------UUUAUGUGGCCCAAUAAAAUGCAGUCGGAUACAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGAU
.(------(((((.((((.((......))..)))).))).)))((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..... ( -38.20)
>DroWil_CAF1 45249 114 + 1
AC------UUUGUAAGGGCCAAGAAAUCACAGCAAAUCAUCACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGGA
.(------((((..............(((((((..((((((...(((......))).)))))).((((....)))).)).)))))(((((.(((((.......))))).)))))))))). ( -37.60)
>DroMoj_CAF1 47111 114 + 1
CG------CUUUUGUGGGCCAAUAAAUGCCCAGGAGAUACAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCAGGAU
..------.((((.(((((........))))).))))......((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..... ( -44.00)
>DroPer_CAF1 54752 120 + 1
AGCACGCACUUUUUAGGGCCAAUAUAUUGGGCUUAUCCACAAGGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAAG
........(((((((((.((((....)))).))))........((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))))))) ( -40.80)
>consensus
AG______CUUGUAAGGGCCAAUAAAUGACAGGCAUACACAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGAG
...........................................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..... (-33.02 = -33.02 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,493,905 – 13,494,007
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.84
Mean single sequence MFE -36.75
Consensus MFE -32.92
Energy contribution -32.92
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.90
SVM decision value 1.74
SVM RNA-class probability 0.975077
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13493905 102 + 27905053
GACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAGG------------------AUUUUUUCCAUAUAUUUUACUU
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...((------------------(.....)))............. ( -36.20)
>DroVir_CAF1 47138 104 + 1
AACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGA---------------GUA-AUAUAAUAACUUUUUGUUGUUU
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))....---------------...-....((((((.....)))))). ( -35.70)
>DroPse_CAF1 57782 116 + 1
AACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAAG----GACUACAGGUCCAUAUUUUUGUUAAAUUUCUUUCCU
(((((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))....(----(((.....))))........)))............. ( -39.50)
>DroEre_CAF1 40851 93 + 1
GACGGGGAUGUAGCUCAGAUGGUAGAGCCCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAUUG------------------GUUUUUU---------UAGUUU
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).....------------------.......---------...... ( -32.00)
>DroWil_CAF1 45283 110 + 1
CACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGGAAGAGGACU--UGGUCCUUUUUUUUGACAAUUU--------
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))((((((((((((.--..))))))))))))........-------- ( -44.00)
>DroYak_CAF1 49857 87 + 1
GACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAGG------------------AUUUUUU---------------
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).....------------------.......--------------- ( -33.10)
>consensus
GACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAGG__________________AUUUUUU__A__UU__UU__UU
...((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))............................................. (-32.92 = -32.92 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,493,905 – 13,494,007
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.84
Mean single sequence MFE -26.53
Consensus MFE -22.55
Energy contribution -22.72
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.85
SVM decision value 1.12
SVM RNA-class probability 0.917888
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13493905 102 - 27905053
AAGUAAAAUAUAUGGAAAAAAU------------------CCUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUC
...........((((.......------------------.....((((.(((((((.......))))))).)))).....(((.....)))((((........)))).......)))). ( -26.00)
>DroVir_CAF1 47138 104 - 1
AAACAACAAAAAGUUAUUAUAU-UAC---------------UCCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUU
......................-...---------------....((((.(((((((.......))))))).)))).....(((.....)))((((........))))............ ( -23.70)
>DroPse_CAF1 57782 116 - 1
AGGAAAGAAAUUUAACAAAAAUAUGGACCUGUAGUC----CUUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUU
.(((..((.......(((((....((((.....)))----))))))(((.(((((((.......))))))).)))))....(((.....)))((((........))))....)))..... ( -31.20)
>DroEre_CAF1 40851 93 - 1
AAACUA---------AAAAAAC------------------CAAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGGGCUCUACCAUCUGAGCUACAUCCCCGUC
......---------.......------------------.....((.(((((((((.......)))))..((((.(.........).))))((((........))))..)))).))... ( -24.10)
>DroWil_CAF1 45283 110 - 1
--------AAAUUGUCAAAAAAAAGGACCA--AGUCCUCUUCCUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUG
--------.......(((..((.(((((..--.))))).))..)))(((.(((((((.......))))))).))).(((..(((.....)))((((........)))).........))) ( -30.50)
>DroYak_CAF1 49857 87 - 1
---------------AAAAAAU------------------CCUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUC
---------------.......------------------.....((((.(((((((.......))))))).)))).....(((.....)))((((........))))............ ( -23.70)
>consensus
AA__AA__AA__U__AAAAAAU__________________CCUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUC
.............................................((((.(((((((.......))))))).)))).....(((.....)))((((........))))............ (-22.55 = -22.72 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:57 2006