Locus 3962

Sequence ID 3R_DroMel_CAF1
Location 10,720,988 – 10,721,342
Length 354
Max. P 0.997734
window6349 window6350 window6351 window6352 window6353 window6354 window6355 window6356

overview

Window 9

Location 10,720,988 – 10,721,105
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.25
Mean single sequence MFE -34.42
Consensus MFE -27.96
Energy contribution -28.08
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.50
Structure conservation index 0.81
SVM decision value 0.33
SVM RNA-class probability 0.689656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10720988 117 + 27905053
AAGGCAUGGAUGGAAAUAUGUCGGCUUACGGUGGACAACAAGUGGCUGUUUAUUUGCGGCAGACACUUUCGCCGGACUUAUCUGCCAAA---CAAGGGAAACCUUAGAAAGGACGCCAUU
..((((((........))))))(((...(((((((.....(((((((((......)))))...)))))))))))..(((.((((.....---..(((....))))))).)))..)))... ( -35.91)
>DroSec_CAF1 8736 120 + 1
AAGGAAUGGAUGGAAAUAUGUCGGCUUACGUUGGACAACAAGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUU
....(((((.(((..(((.((((((....(((....)))((((((((((......)))))...)))))..))).))).)))...)))......((((....))))..........))))) ( -32.30)
>DroSim_CAF1 8723 120 + 1
AAGGAAUGGAUGGAAAUAUGUCGGCUUACGUUGGACAACAAGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUU
....(((((.(((..(((.((((((....(((....)))((((((((((......)))))...)))))..))).))).)))...)))......((((....))))..........))))) ( -32.30)
>DroEre_CAF1 10117 120 + 1
AAGGUAUGGAUGGAAACAUGUCGUCUCACGUUGGACAACAAGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCGGACUUAUCUGCCAAAUAGGAAGGGAAACCUUAAAAAGGACGCCAUU
.........(((....)))((.((((......)))).)).((((((.((((......((((((.....((....))....)))))).......((((....)))).....)))))))))) ( -35.30)
>DroYak_CAF1 8651 120 + 1
AAGGAAUGGAUGGAAAUAUGUCGUCUUACGUUGGACAACAAGUGGCUGUUCAUUUGCGGUCGACACUUUCGUCAGACUUAUCUGCCAAAUAGCAAGGGAAACCUUAGAAAGGACGCCAUU
...((((((((((..((.(((.((((......)))).))).))..))))))))))..((.((...((((((.((((....)))).).......((((....)))).)))))..))))... ( -36.30)
>consensus
AAGGAAUGGAUGGAAAUAUGUCGGCUUACGUUGGACAACAAGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAGGACGCCAUU
...((((((((((..((.(((.(.((......)).).))).))..))))))))))((((((((.....((....))....)))))).......((((....)))).........)).... (-27.96 = -28.08 +   0.12)

alignment

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secondary structure

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Window 0

Location 10,721,028 – 10,721,145
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -39.04
Consensus MFE -37.52
Energy contribution -37.88
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.96
SVM decision value 2.92
SVM RNA-class probability 0.997734
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721028 117 + 27905053
AGUGGCUGUUUAUUUGCGGCAGACACUUUCGCCGGACUUAUCUGCCAAA---CAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCG
((((((.(((..(((..((((((.....((....))....))))))...---.((((....)))).)))..))))))))).....(((((.....))))).((((.((.....)))))). ( -41.00)
>DroSec_CAF1 8776 120 + 1
AGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCG
((((((.(((..(((..((((((.....((....))....)))))).......((((....)))).)))..))))))))).....(((((.....))))).((((.((.....)))))). ( -40.30)
>DroSim_CAF1 8763 120 + 1
AGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCG
((((((.(((..(((..((((((.....((....))....)))))).......((((....)))).)))..))))))))).....(((((.....))))).((((.((.....)))))). ( -40.30)
>DroEre_CAF1 10157 120 + 1
AGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCGGACUUAUCUGCCAAAUAGGAAGGGAAACCUUAAAAAGGACGCCAUUCCAGAAUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUUG
((((((.((((......((((((.....((....))....)))))).......((((....)))).....))))))))))......((((.....))))..((((.((.....)))))). ( -36.80)
>DroYak_CAF1 8691 120 + 1
AGUGGCUGUUCAUUUGCGGUCGACACUUUCGUCAGACUUAUCUGCCAAAUAGCAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAAGAGGAGGAUCCCCUUG
.(((((.((((......(((((((......))).))))..(((((......))((((....)))))))..)))))))))(((...(((((.....)))))))).((((.(....))))). ( -36.80)
>consensus
AGUGGCUGUUCAUUUGCGGCAGACACUUUCGCCAGACUUAUCUGCCAAACAACAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCG
.(((((.((((.(((..((((((.....((....))....)))))).......((((....)))).))).)))))))))(((...(((((.....)))))...))).((((....)))). (-37.52 = -37.88 +   0.36)

alignment

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secondary structure

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Window 1

Location 10,721,028 – 10,721,145
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -37.80
Consensus MFE -34.66
Energy contribution -34.46
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -1.29
Structure conservation index 0.92
SVM decision value 0.71
SVM RNA-class probability 0.829746
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721028 117 - 27905053
CGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUG---UUUGGCAGAUAAGUCCGGCGAAAGUGUCUGCCGCAAAUAAACAGCCACU
.((((((((((...(((...(((((.....)))))...)))..)).))))))))...((((....(((---(((((((((((..((....))...))))))))..))))))..))))... ( -40.10)
>DroSec_CAF1 8776 120 - 1
CGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCUUUUCUAAGGUUUCCCUUGUUGUUUGGCAGAUAAGUCUGGCGAAAGUGUCUGCCGCAAAUGAACAGCCACU
.((((((......)))))).(((((.....))))).......((((.((.....(((((....)))))((((..((((((((..((....))...))))))))))))..))...)))).. ( -40.20)
>DroSim_CAF1 8763 120 - 1
CGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCUUUUCUAAGGUUUCCCUUGUUGUUUGGCAGAUAAGUCUGGCGAAAGUGUCUGCCGCAAAUGAACAGCCACU
.((((((......)))))).(((((.....))))).......((((.((.....(((((....)))))((((..((((((((..((....))...))))))))))))..))...)))).. ( -40.20)
>DroEre_CAF1 10157 120 - 1
CAAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAAUUCUGGAAUGGCGUCCUUUUUAAGGUUUCCCUUCCUAUUUGGCAGAUAAGUCCGGCGAAAGUGUCUGCCGCAAAUGAACAGCCACU
...(((((......))).)).......(((((..(((.((((.((...(((.....)))...)).)))).....((((((((..((....))...))))))))......)))...))))) ( -35.20)
>DroYak_CAF1 8691 120 - 1
CAAGGGGAUCCUCCUCUUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUGCUAUUUGGCAGAUAAGUCUGACGAAAGUGUCGACCGCAAAUGAACAGCCACU
((((((((.(((........(((((.....)))))..(((((.((...)).)))))))).)))))))).....(((((((....))).((....))..................)))).. ( -33.30)
>consensus
CGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUGCUAUUUGGCAGAUAAGUCUGGCGAAAGUGUCUGCCGCAAAUGAACAGCCACU
((((((((.(((........(((((.....)))))..(((((.((...)).)))))))).))))))))......((((((((..((....))...))))))))................. (-34.66 = -34.46 +  -0.20)

alignment

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secondary structure

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Window 2

Location 10,721,068 – 10,721,185
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -33.62
Consensus MFE -24.92
Energy contribution -24.92
Covariance contribution -0.00
Combinations/Pair 1.09
Mean z-score -2.67
Structure conservation index 0.74
SVM decision value 1.02
SVM RNA-class probability 0.901451
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721068 117 + 27905053
UCUGCCAAA---CAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCGGAAAGAGCAUCAAAAGUAUGAAAUCAUGUGCUAAUAGAAG
((((.....---.((((....))))......((.(((.((((...(((((.....))))).((((.((.....)))))))))).).)).))...(((((........)))))..)))).. ( -34.50)
>DroSec_CAF1 8816 120 + 1
UCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCGGAAAGACCGUCAAAAGUAUGAAAUCAUGUGCUAAUAGAAG
((((.........((((....))))......((((.(.((((...(((((.....))))).((((.((.....)))))))))).)..))))...(((((........)))))..)))).. ( -35.30)
>DroSim_CAF1 8803 120 + 1
UCUGCCAAACAACAAGGGAAACCUUAGAAAAGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCGGAAAGACCGUCAAAAGUAUGAAAUCAUGUGCUAAUAGAAG
((((.........((((....))))......((((.(.((((...(((((.....))))).((((.((.....)))))))))).)..))))...(((((........)))))..)))).. ( -35.30)
>DroEre_CAF1 10197 120 + 1
UCUGCCAAAUAGGAAGGGAAACCUUAAAAAGGACGCCAUUCCAGAAUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUUGGAAAGUCCAUUAAAACUAUGAAAUCAUGUUCUAAUAGAAG
....((.....))((((....)))).....((((....((((((..((((.....)))).((.(((......))))))))))).))))((((.(((.(((....)))))).))))..... ( -30.90)
>DroYak_CAF1 8731 120 + 1
UCUGCCAAAUAGCAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAAGAGGAGGAUCCCCUUGGAAAGAGCAUCACAAGCAUGAAAUCAUGUUCUAAUAAAAG
..(((......)))(((....)))((((...((.(((.((((...(((((.....)))))....((((.(....))))))))).).)).))....(((((....)))))))))....... ( -32.10)
>consensus
UCUGCCAAACAACAAGGGAAACCUUAGAAAGGACGCCAUUCCAGAGUUCCACUUAGGAACGGAGGAGGAGGAUCCCCUCGGAAAGACCAUCAAAAGUAUGAAAUCAUGUGCUAAUAGAAG
.............((((....)))).............((((...(((((.....))))).((((.((.....)))))))))).............((((....))))............ (-24.92 = -24.92 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,721,068 – 10,721,185
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -33.28
Consensus MFE -23.74
Energy contribution -22.98
Covariance contribution -0.76
Combinations/Pair 1.16
Mean z-score -2.24
Structure conservation index 0.71
SVM decision value 0.08
SVM RNA-class probability 0.573585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721068 117 - 27905053
CUUCUAUUAGCACAUGAUUUCAUACUUUUGAUGCUCUUUCCGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUG---UUUGGCAGA
.........((.((...............((((((..((((((((((......)))))).(((((.....)))))...)))).)))))).....(((((....)))))---..))))... ( -33.20)
>DroSec_CAF1 8816 120 - 1
CUUCUAUUAGCACAUGAUUUCAUACUUUUGACGGUCUUUCCGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCUUUUCUAAGGUUUCCCUUGUUGUUUGGCAGA
((.(((.(((((...((..((.((.....((((.((.((((((((((......)))))).(((((.....)))))...)))).)))))).....)).))..))...)))))..))).)). ( -32.10)
>DroSim_CAF1 8803 120 - 1
CUUCUAUUAGCACAUGAUUUCAUACUUUUGACGGUCUUUCCGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCUUUUCUAAGGUUUCCCUUGUUGUUUGGCAGA
((.(((.(((((...((..((.((.....((((.((.((((((((((......)))))).(((((.....)))))...)))).)))))).....)).))..))...)))))..))).)). ( -32.10)
>DroEre_CAF1 10197 120 - 1
CUUCUAUUAGAACAUGAUUUCAUAGUUUUAAUGGACUUUCCAAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAAUUCUGGAAUGGCGUCCUUUUUAAGGUUUCCCUUCCUAUUUGGCAGA
..((((((((((((((....))).)))))))))))(((...((((((((((...(((...(((((.....)))))...)))..)).)))))))).)))......((.((.....)).)). ( -33.50)
>DroYak_CAF1 8731 120 - 1
CUUUUAUUAGAACAUGAUUUCAUGCUUGUGAUGCUCUUUCCAAGGGGAUCCUCCUCUUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUGCUAUUUGGCAGA
......((((((((((....)))).....((((((..((((((((((.....))))))..(((((.....)))))...)))).))))))..))))))((....))(((((....))))). ( -35.50)
>consensus
CUUCUAUUAGCACAUGAUUUCAUACUUUUGAUGGUCUUUCCGAGGGGAUCCUCCUCCUCCGUUCCUAAGUGGAACUCUGGAAUGGCGUCCUUUCUAAGGUUUCCCUUGCUAUUUGGCAGA
((.(((.......(((....))).................((((((((.(((........(((((.....)))))..(((((.((...)).)))))))).)))))))).....))).)). (-23.74 = -22.98 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,721,185 – 10,721,305
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.85
Mean single sequence MFE -33.32
Consensus MFE -24.40
Energy contribution -24.56
Covariance contribution 0.16
Combinations/Pair 1.19
Mean z-score -1.86
Structure conservation index 0.73
SVM decision value 0.26
SVM RNA-class probability 0.659469
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721185 120 + 27905053
UAAUAUCAGUUUCAAGAGCGAGGAUUCUGGCAUUGACGAGGAAAGCUUUAAGGAGAGUAAGCCUCAUAAUAAUCCAUGCGCCAAUUGCCUUGAUCUCCAACAGCAAUUGGCAGCAGCUCA
...............((((..(((((..(.......)((((...(((((....)))))...)))).....))))).((((((((((((.(((.....)))..))))))))).))))))). ( -37.60)
>DroSec_CAF1 8936 117 + 1
UAAUAUCAGUUUUAAAAGCGAGGAUUCUGGCAUCGACGAGGAAAGCUUCAAGGAGAGUAAGCCUCAU---AAUCCAUGCGCCAAUUGCCUUGAUCUUCAACAGCAAUUGGCAGCUGCUCA
......(((((......(((.(((((..(((.((..(((((....))))..)..))....)))....---))))).)))(((((((((.(((.....)))..)))))))))))))).... ( -35.00)
>DroSim_CAF1 8923 117 + 1
UAAUAUCAGUUUCAAAAGCGAGGAUUCUGGCAUCGACGAGGAAAGCUUCAGGGAGAGUAAGCCUCAU---AAUCCAUGCGCCAAUUGCCUUGAUCUUCAACAGCAAUUGGCAGCUGCUCA
......(((((......(((.(((((..(((.((..(((((....))))..)..))....)))....---))))).)))(((((((((.(((.....)))..)))))))))))))).... ( -35.00)
>DroEre_CAF1 10317 117 + 1
CAAUAUAAGUUUCAAGAGCGAAGAUUCUGGCAUCGACGAGGAAAGCUUCAAGGAGAGAAAUCCCCAU---GAUCCAUGUGCCAAUUGCCUUGAUCUUAAACAGCAAUUGGCAGCUGCUCU
..............((((((.......(((.((((..((((....))))..((.((....)).)).)---))))))..((((((((((..((........))))))))))))..)))))) ( -33.80)
>DroYak_CAF1 8851 117 + 1
CAUUAUAAGUUUCAAGAGCGACGAUUCUGGCAUCGACGAGGAAAGUUUCAAGGAGAGAAAGCCACAC---GAUCCAUGCGCCAAUUGUCUUGAUCUUAAACAGCAAUUAGCAGCUGCUCU
..............((((((((((((...((((.((((.((....((((.....))))...))...)---).)).))))...)))))))............(((........)))))))) ( -25.20)
>consensus
UAAUAUCAGUUUCAAGAGCGAGGAUUCUGGCAUCGACGAGGAAAGCUUCAAGGAGAGUAAGCCUCAU___AAUCCAUGCGCCAAUUGCCUUGAUCUUCAACAGCAAUUGGCAGCUGCUCA
...............((((..(((((..(((.((..(((((....))))..)..))....))).......)))))..(((((((((((..((........))))))))))).)).)))). (-24.40 = -24.56 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,721,185 – 10,721,305
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.85
Mean single sequence MFE -34.00
Consensus MFE -27.78
Energy contribution -27.50
Covariance contribution -0.28
Combinations/Pair 1.20
Mean z-score -1.70
Structure conservation index 0.82
SVM decision value 0.80
SVM RNA-class probability 0.853345
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721185 120 - 27905053
UGAGCUGCUGCCAAUUGCUGUUGGAGAUCAAGGCAAUUGGCGCAUGGAUUAUUAUGAGGCUUACUCUCCUUAAAGCUUUCCUCGUCAAUGCCAGAAUCCUCGCUCUUGAAACUGAUAUUA
.(((((((.((((((((((.(((.....)))))))))))))))).((((((((((((((....((........))....)))))).)))).....))))..))))............... ( -33.50)
>DroSec_CAF1 8936 117 - 1
UGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU---AUGAGGCUUACUCUCCUUGAAGCUUUCCUCGUCGAUGCCAGAAUCCUCGCUUUUAAAACUGAUAUUA
.((((....((((((((((.(((.....)))))))))))))((((.(((.---..(((((((.(.......))))))))....))).))))..........))))............... ( -34.80)
>DroSim_CAF1 8923 117 - 1
UGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU---AUGAGGCUUACUCUCCCUGAAGCUUUCCUCGUCGAUGCCAGAAUCCUCGCUUUUGAAACUGAUAUUA
.((((....((((((((((.(((.....)))))))))))))((((.(((.---..(((((((.(.......))))))))....))).))))..........))))............... ( -34.80)
>DroEre_CAF1 10317 117 - 1
AGAGCAGCUGCCAAUUGCUGUUUAAGAUCAAGGCAAUUGGCACAUGGAUC---AUGGGGAUUUCUCUCCUUGAAGCUUUCCUCGUCGAUGCCAGAAUCUUCGCUCUUGAAACUUAUAUUG
(((((.(.(((((((((((............)))))))))))).((((((---(((((((((((.......))))...))))))).))).)))........))))).............. ( -37.10)
>DroYak_CAF1 8851 117 - 1
AGAGCAGCUGCUAAUUGCUGUUUAAGAUCAAGACAAUUGGCGCAUGGAUC---GUGUGGCUUUCUCUCCUUGAAACUUUCCUCGUCGAUGCCAGAAUCGUCGCUCUUGAAACUUAUAAUG
.(((((((........)))))))....((((((....(((((..((((((---(((.((.((((.......))))....)).)).)))).)))....))))).))))))........... ( -29.80)
>consensus
UGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU___AUGAGGCUUACUCUCCUUGAAGCUUUCCUCGUCGAUGCCAGAAUCCUCGCUCUUGAAACUGAUAUUA
.((((.((.((((((((((............)))))))))))).((((((...((((((.....((.....))......)))))).))).)))........))))............... (-27.78 = -27.50 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,721,225 – 10,721,342
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -34.24
Consensus MFE -23.26
Energy contribution -23.50
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -1.89
Structure conservation index 0.68
SVM decision value 0.00
SVM RNA-class probability 0.536016
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10721225 117 - 27905053
CUCUUGC---CUUCUUUCCUCAAGUUGCUGAAUGCGAAGAUGAGCUGCUGCCAAUUGCUGUUGGAGAUCAAGGCAAUUGGCGCAUGGAUUAUUAUGAGGCUUACUCUCCUUAAAGCUUUC
.....((---(((.....((((..((((.....))))...)))).(((.((((((((((.(((.....))))))))))))))))...........))))).................... ( -32.70)
>DroSec_CAF1 8976 114 - 1
CUCUCGC---CUUUUUUCCUCCAGCUGCUGAAUGCGAAAAUGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU---AUGAGGCUUACUCUCCUUGAAGCUUUC
.....((---(((...(((...(((((((..((......)).)))))))((((((((((.(((.....)))))))))))))....)))..---..))))).................... ( -39.00)
>DroSim_CAF1 8963 114 - 1
CUCUCGC---CUUCUUUCCUCCAGCUGCUGAAUGCGAAAAUGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU---AUGAGGCUUACUCUCCCUGAAGCUUUC
.....((---(((...(((...(((((((..((......)).)))))))((((((((((.(((.....)))))))))))))....)))..---..))))).................... ( -38.30)
>DroEre_CAF1 10357 114 - 1
CUCUUGC---UUUUUUUCCUCCACCUGCUGAAUGCGAAGAAGAGCAGCUGCCAAUUGCUGUUUAAGAUCAAGGCAAUUGGCACAUGGAUC---AUGGGGAUUUCUCUCCUUGAAGCUUUC
....(((---((((((((........((.....)))))))))))))(((((((((((((............)))))))))).......((---(.(((((....))))).)))))).... ( -37.10)
>DroYak_CAF1 8891 117 - 1
CUCUUGUUCUUUUUUUUCCUCCAACUGCUGAACGCGAAGAAGAGCAGCUGCUAAUUGCUGUUUAAGAUCAAGACAAUUGGCGCAUGGAUC---GUGUGGCUUUCUCUCCUUGAAACUUUC
....(((((((((((....((........))....)))))))))))(((((((((((((...........)).))))))))(((((...)---)))))))((((.......))))..... ( -24.10)
>consensus
CUCUUGC___CUUUUUUCCUCCAGCUGCUGAAUGCGAAGAUGAGCAGCUGCCAAUUGCUGUUGAAGAUCAAGGCAAUUGGCGCAUGGAUU___AUGAGGCUUACUCUCCUUGAAGCUUUC
.....((.........(((...(((((((.............)))))))((((((((((............))))))))))....))).......(((.....)))........)).... (-23.26 = -23.50 +   0.24)

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 11:14:39 2006