Locus 1696

Sequence ID 2L_DroMel_CAF1
Location 4,641,481 – 4,641,635
Length 154
Max. P 0.985520
window2711 window2712 window2713

overview

Window 1

Location 4,641,481 – 4,641,595
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -20.30
Consensus MFE -12.35
Energy contribution -13.23
Covariance contribution 0.87
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.61
SVM decision value 0.18
SVM RNA-class probability 0.622316
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641481 114 + 22407834
CCGUGUAACUCCCCAC------AUCCACUAACCCAAUUUUCCCAAAAGUAUCCAAACUCAGGAUACCUUUGUUAUCCUCAAAAUGAAAUUAAUAAAUACCUAUGGUACCCACCGUGGAGC
..(((........)))------.(((((..............((((.((((((.......)))))).))))................................(((....)))))))).. ( -20.70)
>DroSec_CAF1 78512 114 + 1
CCGUGUAAUCCCCCAC------AUCCAAUAAGCCAAUAUUCCCAAAAGUAUCCAAGCCCAGGAUACCUUUGUUAUCCCCAAAAUGAAAUUAAUAAAUACCUGUGGUACCCACCGUGGAGC
............((((------....................((((.((((((.......)))))).))))..............................((((...)))).))))... ( -18.70)
>DroEre_CAF1 83704 120 + 1
CCGUGUUAUUAUACAGUAUCAAGCCACAUAAACCAACAUUUCCGAAAGUAUCCAAACACAGGAUACCUGUGUUAUCCACAAAAUGAAAUUAACUCAUACCUCUGGUACCCACCGUGGAGC
..((((....))))............................(....)......((((((((...)))))))).(((((...((((.......))))......(((....)))))))).. ( -22.60)
>DroYak_CAF1 83385 120 + 1
CCGUGUUAUAAUCAUGUUUCAAACUACUUAACCCAACAAGCCCAGAACUAUCCAAACCCAGGAUUCCUUUGCUAUCCACAAAAUGAUAUUAAUAGUUAUCUCUGGUACCCACCGUGGGGU
.((((.......))))..............((((....(((..((....((((.......))))..))..)))...(((.....((((........))))...(((....)))))))))) ( -19.20)
>consensus
CCGUGUAAUUACCCAC______ACCAAAUAACCCAACAUUCCCAAAAGUAUCCAAACCCAGGAUACCUUUGUUAUCCACAAAAUGAAAUUAAUAAAUACCUCUGGUACCCACCGUGGAGC
..........................................((((.((((((.......)))))).))))............................(((((((....)))))))... (-12.35 = -13.23 +   0.87)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,641,515 – 4,641,635
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.72
Mean single sequence MFE -29.42
Consensus MFE -17.50
Energy contribution -18.00
Covariance contribution 0.50
Combinations/Pair 1.24
Mean z-score -2.64
Structure conservation index 0.59
SVM decision value 1.31
SVM RNA-class probability 0.940057
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641515 120 + 22407834
CCCAAAAGUAUCCAAACUCAGGAUACCUUUGUUAUCCUCAAAAUGAAAUUAAUAAAUACCUAUGGUACCCACCGUGGAGCCAAUGGGUAGGAUAUCAAGGAUAUCAAACAGGAAAUGGAU
.(((...((((((.......))))))(((((.(((((((.....))..........((((((((((.((......)).))).)))))))))))).)))))...............))).. ( -33.00)
>DroSec_CAF1 78546 117 + 1
CCCAAAAGUAUCCAAGCCCAGGAUACCUUUGUUAUCCCCAAAAUGAAAUUAAUAAAUACCUGUGGUACCCACCGUGGAGCCAAUGGGUAGUA---CAAGGAUAUCCAACAGGAAAUGGAU
..((((.((((((.......)))))).))))......(((..................((((((.((((((...((....)).)))))).))---).)))...(((....)))..))).. ( -32.10)
>DroEre_CAF1 83744 117 + 1
UCCGAAAGUAUCCAAACACAGGAUACCUGUGUUAUCCACAAAAUGAAAUUAACUCAUACCUCUGGUACCCACCGUGGAGCCAAUGGGUAGUU---GAAGAAUAUCCACCAGAAAAUGGGU
((...((.((((((((((((((...)))))))).(((((...((((.......))))......(((....)))))))).....)))))).))---...)).......(((.....))).. ( -31.00)
>DroYak_CAF1 83425 108 + 1
CCCAGAACUAUCCAAACCCAGGAUUCCUUUGCUAUCCACAAAAUGAUAUUAAUAGUUAUCUCUGGUACCCACCGUGGGGUCAAUGGGUAUCA---CAAGUAUAUCCAACAG---------
.(((((..............((((.........)))).......((((........)))))))))..(((.....))).....((((((((.---...).)))))))....--------- ( -21.60)
>consensus
CCCAAAAGUAUCCAAACCCAGGAUACCUUUGUUAUCCACAAAAUGAAAUUAAUAAAUACCUCUGGUACCCACCGUGGAGCCAAUGGGUAGUA___CAAGGAUAUCCAACAGGAAAUGGAU
..((((.((((((.......)))))).)))).........................(((((((((..((......))..)).)))))))............................... (-17.50 = -18.00 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,641,515 – 4,641,635
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.72
Mean single sequence MFE -35.20
Consensus MFE -24.50
Energy contribution -26.88
Covariance contribution 2.38
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.70
SVM decision value 2.01
SVM RNA-class probability 0.985520
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641515 120 - 22407834
AUCCAUUUCCUGUUUGAUAUCCUUGAUAUCCUACCCAUUGGCUCCACGGUGGGUACCAUAGGUAUUUAUUAAUUUCAUUUUGAGGAUAACAAAGGUAUCCUGAGUUUGGAUACUUUUGGG
((((....(((((..((((((...)))))).(((((((((......)))))))))..)))))............((.....))))))..(((((((((((.......))))))))))).. ( -38.00)
>DroSec_CAF1 78546 117 - 1
AUCCAUUUCCUGUUGGAUAUCCUUG---UACUACCCAUUGGCUCCACGGUGGGUACCACAGGUAUUUAUUAAUUUCAUUUUGGGGAUAACAAAGGUAUCCUGGGCUUGGAUACUUUUGGG
((((...(((....)))....((((---(..(((((((((......)))))))))..))))).....................))))..(((((((((((.......))))))))))).. ( -39.20)
>DroEre_CAF1 83744 117 - 1
ACCCAUUUUCUGGUGGAUAUUCUUC---AACUACCCAUUGGCUCCACGGUGGGUACCAGAGGUAUGAGUUAAUUUCAUUUUGUGGAUAACACAGGUAUCCUGUGUUUGGAUACUUUCGGA
........(((((.((.(((((...---...(((((((((......)))))))))(((.(((.(((((.....)))))))).)))..((((((((...)))))))).))))))).))))) ( -36.60)
>DroYak_CAF1 83425 108 - 1
---------CUGUUGGAUAUACUUG---UGAUACCCAUUGACCCCACGGUGGGUACCAGAGAUAACUAUUAAUAUCAUUUUGUGGAUAGCAAAGGAAUCCUGGGUUUGGAUAGUUCUGGG
---------(((((.((........---...(((((((((......)))))))))((((.(((..((.....((((........))))....))..)))))))..)).)))))....... ( -27.00)
>consensus
AUCCAUUUCCUGUUGGAUAUCCUUG___UACUACCCAUUGGCUCCACGGUGGGUACCAGAGGUAUUUAUUAAUUUCAUUUUGUGGAUAACAAAGGUAUCCUGGGUUUGGAUACUUUUGGG
.................(((((((.......(((((((((......)))))))))...(((((........))))).....))))))).(((((((((((.......))))))))))).. (-24.50 = -26.88 +   2.38)

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 10:08:41 2006