Locus 5390

Sequence ID 2L_DroMel_CAF1
Location 15,373,368 – 15,373,501
Length 133
Max. P 0.992240
window8555 window8556 window8557 window8558

overview

Window 5

Location 15,373,368 – 15,373,464
Length 96
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 84.88
Mean single sequence MFE -27.70
Consensus MFE -20.20
Energy contribution -20.93
Covariance contribution 0.74
Combinations/Pair 1.05
Mean z-score -2.94
Structure conservation index 0.73
SVM decision value 0.52
SVM RNA-class probability 0.768005
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15373368 96 + 22407834
UGUAGAUUCUCCCACC-UU------CCAC---AGUUCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA
................-..------.(((---(....))))..........(((.((((((((.((.((((....(((....))).)))).)))))))))).))). ( -28.70)
>DroSec_CAF1 119194 96 + 1
UGUUGAUUCUCCCACC-UU------CCAC---AGUUCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA
................-..------.(((---(....))))..........(((.((((((((.((.((((....(((....))).)))).)))))))))).))). ( -28.70)
>DroSim_CAF1 123294 96 + 1
UGUAGAUUCUCCCACC-UU------CCAC---AGUUCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA
................-..------.(((---(....))))..........(((.((((((((.((.((((....(((....))).)))).)))))))))).))). ( -28.70)
>DroEre_CAF1 125423 96 + 1
UGUAGAUUCUCCCACC-UU------CCAC---AGUUCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGCUGCAUUUGCUGCGUUGCAGCCGCAA
................-..------.(((---(....))))..........(((.((((((((.((.((((....(((....))).)))).)))))))))).))). ( -28.70)
>DroYak_CAF1 125416 90 + 1
UCUAGAUUCUCCCACC-UUUCACAUCCAC---AGUUCUGUGACAAUAUUCCUGCCGCUGCAACUGUUGCAACUU------------UUGCUGCGUUGCAGCCGCAA
................-.........(((---(....))))..........(((.((((((((.((.(((....------------.))).)))))))))).))). ( -25.30)
>DroAna_CAF1 127139 89 + 1
UGCA-AUUCCACUACCACU------CGACGCGGGUUUUGUGACAAUAUUUCUGCCACUGCAG-UGGUGCAACUUC---------AGUUGCUGCGUUGCAGCCGCAA
....-..............------....((((...(((..((.........(((((....)-))))(((((...---------.)))))...))..))))))).. ( -26.10)
>consensus
UGUAGAUUCUCCCACC_UU______CCAC___AGUUCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA
...................................................(((.((((((((.((.((((....(((....))).)))).)))))))))).))). (-20.20 = -20.93 +   0.74)

alignment

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secondary structure

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Window 6

Location 15,373,368 – 15,373,464
Length 96
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 84.88
Mean single sequence MFE -34.28
Consensus MFE -25.44
Energy contribution -26.27
Covariance contribution 0.82
Combinations/Pair 1.12
Mean z-score -3.93
Structure conservation index 0.74
SVM decision value 1.24
SVM RNA-class probability 0.934304
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15373368 96 - 22407834
UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGAACU---GUGG------AA-GGUGGGAGAAUCUACA
((((.(((((((((((((...(((....)))...)))))....)))))))).))))........(((((....)---))))------..-.((((......)))). ( -35.60)
>DroSec_CAF1 119194 96 - 1
UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGAACU---GUGG------AA-GGUGGGAGAAUCAACA
((((.(((((((((((((...(((....)))...)))))....)))))))).))))........(((((....)---))))------..-(((......))).... ( -33.60)
>DroSim_CAF1 123294 96 - 1
UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGAACU---GUGG------AA-GGUGGGAGAAUCUACA
((((.(((((((((((((...(((....)))...)))))....)))))))).))))........(((((....)---))))------..-.((((......)))). ( -35.60)
>DroEre_CAF1 125423 96 - 1
UUGCGGCUGCAACGCAGCAAAUGCAGCAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGAACU---GUGG------AA-GGUGGGAGAAUCUACA
((((.(((((((((((.....))).(((((....)))))....)))))))).))))........(((((....)---))))------..-.((((......)))). ( -37.50)
>DroYak_CAF1 125416 90 - 1
UUGCGGCUGCAACGCAGCAA------------AAGUUGCAACAGUUGCAGCGGCAGGAAUAUUGUCACAGAACU---GUGGAUGUGAAA-GGUGGGAGAAUCUAGA
((((.(((((((((((((..------------..)))))....)))))))).))))........(((((....)---)))).......(-(((......))))... ( -30.40)
>DroAna_CAF1 127139 89 - 1
UUGCGGCUGCAACGCAGCAACU---------GAAGUUGCACCA-CUGCAGUGGCAGAAAUAUUGUCACAAAACCCGCGUCG------AGUGGUAGUGGAAU-UGCA
((((....)))).((((((((.---------...))))).(((-((((.(((((((.....)))))))......(((....------.))))))))))...-))). ( -33.00)
>consensus
UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGAACU___GUGG______AA_GGUGGGAGAAUCUACA
((((.(((((((((((((...(((....)))...)))))....)))))))).))))...................................((((......)))). (-25.44 = -26.27 +   0.82)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,373,393 – 15,373,501
Length 108
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 91.40
Mean single sequence MFE -27.98
Consensus MFE -24.30
Energy contribution -25.03
Covariance contribution 0.74
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.87
SVM decision value 2.06
SVM RNA-class probability 0.986977
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15373393 108 + 22407834
UCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA-AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.((((....(((....))).)))).)))))))))).))).-.........((((((........)))))).))).... ( -29.40)
>DroSec_CAF1 119219 108 + 1
UCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA-AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.((((....(((....))).)))).)))))))))).))).-.........((((((........)))))).))).... ( -29.40)
>DroSim_CAF1 123319 108 + 1
UCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA-AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.((((....(((....))).)))).)))))))))).))).-.........((((((........)))))).))).... ( -29.40)
>DroEre_CAF1 125448 108 + 1
UCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGCUGCAUUUGCUGCGUUGCAGCCGCAA-AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.((((....(((....))).)))).)))))))))).))).-.........((((((........)))))).))).... ( -29.40)
>DroYak_CAF1 125447 96 + 1
UCUGUGACAAUAUUCCUGCCGCUGCAACUGUUGCAACUU------------UUGCUGCGUUGCAGCCGCAA-AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.(((....------------.))).)))))))))).))).-.........((((((........)))))).))).... ( -26.00)
>DroAna_CAF1 127167 99 + 1
UUUGUGACAAUAUUUCUGCCACUGCAG-UGGUGCAACUUC---------AGUUGCUGCGUUGCAGCCGCAAAAAGCUCUUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.(((..((.........(((((....)-))))(((((...---------.)))))...))..)))......((((((....((((((........)))))))))))).. ( -24.30)
>consensus
UCUGUGACAAUAUUUCUGCCGCUGCAACUGUUGCAACUUCUGCUGUUGCAUUUGCUGCGUUGCAGCCGCAA_AAGCCCCUCUAUAUCAUUUAUCAGAUGUAAGUUUUCC
.....(((........(((.((((((((.((.((((....(((....))).)))).)))))))))).)))...........((((((........)))))).))).... (-24.30 = -25.03 +   0.74)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,373,393 – 15,373,501
Length 108
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 91.40
Mean single sequence MFE -32.60
Consensus MFE -27.65
Energy contribution -28.08
Covariance contribution 0.43
Combinations/Pair 1.07
Mean z-score -3.23
Structure conservation index 0.85
SVM decision value 2.32
SVM RNA-class probability 0.992240
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15373393 108 - 22407834
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU-UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGA
............(((((((.....))).((.((..((-((((.(((((((((((((...(((....)))...)))))....)))))))).))))))...)).)).)))) ( -34.40)
>DroSec_CAF1 119219 108 - 1
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU-UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGA
............(((((((.....))).((.((..((-((((.(((((((((((((...(((....)))...)))))....)))))))).))))))...)).)).)))) ( -34.40)
>DroSim_CAF1 123319 108 - 1
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU-UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGA
............(((((((.....))).((.((..((-((((.(((((((((((((...(((....)))...)))))....)))))))).))))))...)).)).)))) ( -34.40)
>DroEre_CAF1 125448 108 - 1
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU-UUGCGGCUGCAACGCAGCAAAUGCAGCAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGA
............(((((((.....))).((.((..((-((((.(((((((((((.....))).(((((....)))))....)))))))).))))))...)).)).)))) ( -36.30)
>DroYak_CAF1 125447 96 - 1
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU-UUGCGGCUGCAACGCAGCAA------------AAGUUGCAACAGUUGCAGCGGCAGGAAUAUUGUCACAGA
............(((((((.....))).((.((..((-((((.(((((((((((((..------------..)))))....)))))))).))))))...)).)).)))) ( -30.10)
>DroAna_CAF1 127167 99 - 1
GGAAAACUUACAUCUGAUAAAUGAUAUAGAAGAGCUUUUUGCGGCUGCAACGCAGCAACU---------GAAGUUGCACCA-CUGCAGUGGCAGAAAUAUUGUCACAAA
...........(((........)))...((.((..(((((((.((((((.....(((((.---------...)))))....-.)))))).)))))))..)).))..... ( -26.00)
>consensus
GGAAAACUUACAUCUGAUAAAUGAUAUAGAGGGGCUU_UUGCGGCUGCAACGCAGCAAAUGCAACAGCAGAAGUUGCAACAGUUGCAGCGGCAGAAAUAUUGUCACAGA
...........(((........)))...((.((.....((((.(((((((((((((...(((....)))...)))))....)))))))).)))).....)).))..... (-27.65 = -28.08 +   0.43)

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 11:43:00 2006