Locus 8290

Sequence ID 3L_DroMel_CAF1
Location 21,740,056 – 21,740,251
Length 195
Max. P 0.999931
window13558 window13559 window13560 window13561 window13562 window13563

overview

Window 8

Location 21,740,056 – 21,740,176
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -37.72
Consensus MFE -34.36
Energy contribution -36.20
Covariance contribution 1.84
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.91
SVM decision value 3.21
SVM RNA-class probability 0.998747
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740056 120 + 23771897
GGCAUUCCGGCCUCAAGUCAGCUUUGGAAGAUUUGUCGCCUAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
........((((..((..(((((.(((((((...(((((......((((.......))))))))).))))))).))......)))..))...))))((((((((.......)))))))). ( -38.00)
>DroSec_CAF1 21951 120 + 1
GGCAUUCCGGCUUCAAGUCAGCUUCGGAAGAUUUGUCGCCUAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
(((...(((((..((((((..(....)..))))))..))).......((((.....))))((((......))))..........)).......)))((((((((.......)))))))). ( -39.80)
>DroSim_CAF1 26838 120 + 1
GGCAUUCCGGCUUCAAGUCAGCUUCGGAAGAUUUGUCGCCUAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
(((...(((((..((((((..(....)..))))))..))).......((((.....))))((((......))))..........)).......)))((((((((.......)))))))). ( -39.80)
>DroEre_CAF1 7922 120 + 1
GGCAUUCCGGCUUCAAGUCAGCUUCGGAAGAUUUGUCGCCUAUUUUGUUUGUGCCUCGCAGUGAUUUCUCUCGUAGAUUCGUCUUGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
((((....(((..((((((..(....)..))))))..))).....))))...(((..((((.(((.(((.....)))...))))))).....)))(((((((((.......))))))))) ( -34.70)
>DroYak_CAF1 79587 120 + 1
GGUAUUCCGGCUUCAAGUCAGCUUCGGAAGAUUUGUCGCCUAUUUUGUUUGUGCCUCGCAGUGAUUUCUUUCGCAGAUUCGUCUUCUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
((....))(((..((((((..(....)..))))))..)))............(((.....((((......))))(((.......))).....)))(((((((((.......))))))))) ( -36.30)
>consensus
GGCAUUCCGGCUUCAAGUCAGCUUCGGAAGAUUUGUCGCCUAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUG
(((((...(((..((((((..(....)..))))))..)))..........)))))..((.((((......))))(((....))).........))(((((((((.......))))))))) (-34.36 = -36.20 +   1.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,740,056 – 21,740,176
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -31.31
Consensus MFE -28.55
Energy contribution -29.19
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.36
Structure conservation index 0.91
SVM decision value 3.38
SVM RNA-class probability 0.999108
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740056 120 - 23771897
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUAGGCGACAAAUCUUCCAAAGCUGACUUGAGGCCGGAAUGCC
(((((((((.......)))))))))(((........(((....)))((((......)))).....)))............((((.......((((...(((.......))).)))))))) ( -30.51)
>DroSec_CAF1 21951 120 - 1
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUAGGCGACAAAUCUUCCGAAGCUGACUUGAAGCCGGAAUGCC
(((((((((.......)))))))))(((........(((....)))((((......)))).....)))............((((.......(((((..(((.......)))))))))))) ( -33.41)
>DroSim_CAF1 26838 120 - 1
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUAGGCGACAAAUCUUCCGAAGCUGACUUGAAGCCGGAAUGCC
(((((((((.......)))))))))(((........(((....)))((((......)))).....)))............((((.......(((((..(((.......)))))))))))) ( -33.41)
>DroEre_CAF1 7922 120 - 1
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACAAGACGAAUCUACGAGAGAAAUCACUGCGAGGCACAAACAAAAUAGGCGACAAAUCUUCCGAAGCUGACUUGAAGCCGGAAUGCC
(((((((((.......)))))))))(((...........((......)).((....)).......)))............((((.......(((((..(((.......)))))))))))) ( -31.11)
>DroYak_CAF1 79587 120 - 1
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAAGAAGACGAAUCUGCGAAAGAAAUCACUGCGAGGCACAAACAAAAUAGGCGACAAAUCUUCCGAAGCUGACUUGAAGCCGGAAUACC
(((((((((.......)))))))))(((........(((....))).(....)............)))............(((..(((.((..........)).)))..)))........ ( -28.10)
>consensus
CAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUAGGCGACAAAUCUUCCGAAGCUGACUUGAAGCCGGAAUGCC
(((((((((.......)))))))))(((.......((((....))))(....)............)))............((((.......(((((..(((.......)))))))))))) (-28.55 = -29.19 +   0.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,740,096 – 21,740,216
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -40.42
Consensus MFE -36.00
Energy contribution -36.20
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -3.78
Structure conservation index 0.89
SVM decision value 4.28
SVM RNA-class probability 0.999860
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740096 120 + 23771897
UAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCAAGUGUUUGCCAAUCU
..(((((((((((((.....((((......))))(((....))))))....((((.((((((((.......))))))))))))))))))))))(((((((.....)).)))))....... ( -43.20)
>DroSec_CAF1 21991 120 + 1
UAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCGAGUGUUUGCCAAUCU
..(((((((((((((.....((((......))))(((....))))))....((((.((((((((.......))))))))))))))))))))))(((((((.....)).)))))....... ( -42.50)
>DroSim_CAF1 26878 120 + 1
UAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCGAGUGUUUGCCAAUCU
..(((((((((((((.....((((......))))(((....))))))....((((.((((((((.......))))))))))))))))))))))(((((((.....)).)))))....... ( -42.50)
>DroEre_CAF1 7962 120 + 1
UAUUUUGUUUGUGCCUCGCAGUGAUUUCUCUCGUAGAUUCGUCUUGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUUAAAUGUUUGGCAAUCU
...........((((..((((.((....)).).(((((..((((.((((((((((.((((((((.......))))))))))))).....)))))))))..)))))..)))..)))).... ( -35.70)
>DroYak_CAF1 79627 120 + 1
UAUUUUGUUUGUGCCUCGCAGUGAUUUCUUUCGCAGAUUCGUCUUCUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUUAAGUGUUUGGCAAUCU
....((((((((((...((.((((......)))).................((((.((((((((.......))))))))))))))))))))..(((((((.....)).)))))))))... ( -38.20)
>consensus
UAUUUUGUGUGUGCCUCGCAGCGAUUUCUUUCGCAGAUUCGUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCAAGUGUUUGCCAAUCU
..((((((((((........((((......)))).................((((.((((((((.......))))))))))))))))))))))(((((((.....)).)))))....... (-36.00 = -36.20 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,740,096 – 21,740,216
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -36.42
Consensus MFE -30.22
Energy contribution -30.62
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -3.58
Structure conservation index 0.83
SVM decision value 3.03
SVM RNA-class probability 0.998189
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740096 120 - 23771897
AGAUUGGCAAACACUUGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUA
(((((..(((....)))....)))))((((((((.((((((((((((((.......)))))))).)))......((((.(((.....(....)...)))))).).)))...)))))))). ( -36.30)
>DroSec_CAF1 21991 120 - 1
AGAUUGGCAAACACUCGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUA
...(((.......((((...((((.(((((.((....((((((((((((.......)))))))).))))....)).))))).))))((((......))))..)))).......))).... ( -36.34)
>DroSim_CAF1 26878 120 - 1
AGAUUGGCAAACACUCGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUA
...(((.......((((...((((.(((((.((....((((((((((((.......)))))))).))))....)).))))).))))((((......))))..)))).......))).... ( -36.34)
>DroEre_CAF1 7962 120 - 1
AGAUUGCCAAACAUUUAAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACAAGACGAAUCUACGAGAGAAAUCACUGCGAGGCACAAACAAAAUA
....((((............((((.((((((((....((((((((((((.......)))))))).))))....)))))))).))))....((....)).......))))........... ( -37.70)
>DroYak_CAF1 79627 120 - 1
AGAUUGCCAAACACUUAAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAAGAAGACGAAUCUGCGAAAGAAAUCACUGCGAGGCACAAACAAAAUA
....((((...........(((((.((((((.(....((((((((((((.......)))))))).))))....).)))))).)))))(....)............))))........... ( -35.40)
>consensus
AGAUUGGCAAACACUUGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGACGAAUCUGCGAAAGAAAUCGCUGCGAGGCACACACAAAAUA
...(((.......((((..(((((.(((((.((....((((((((((((.......)))))))).))))....)).))))).)))))(....).........)))).......))).... (-30.22 = -30.62 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,740,136 – 21,740,251
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.63
Mean single sequence MFE -36.54
Consensus MFE -30.22
Energy contribution -31.42
Covariance contribution 1.20
Combinations/Pair 1.05
Mean z-score -2.71
Structure conservation index 0.83
SVM decision value 2.85
SVM RNA-class probability 0.997385
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740136 115 + 23771897
GUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCAAGUGUUUGCCAAUCUCCGAUUGGCUUGACUGAAGUUUUCACUGAAAAUUU-----
(((((.(((((((((.((((((((.......))))))))))))).....)))))))))...((((.(((...(((((((...)))))))..(((....)))..))))))).....----- ( -37.50)
>DroSec_CAF1 22031 115 + 1
GUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCGAGUGUUUGCCAAUCUCCGAUUGGCUUGACUGGAGUUUUCUCUGAAAAUUU-----
(((((.(((((((((.((((((((.......))))))))))))).....)))))))))...(((....(((.(((((((...)))))))..))).((((....))))))).....----- ( -38.80)
>DroSim_CAF1 26918 115 + 1
GUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCGAGUGUUUGCCAAUCUCCGAUUGGCUUGACUGGAGUUUUCUCUGAAAAUUU-----
(((((.(((((((((.((((((((.......))))))))))))).....)))))))))...(((....(((.(((((((...)))))))..))).((((....))))))).....----- ( -38.80)
>DroEre_CAF1 8002 120 + 1
GUCUUGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUUAAAUGUUUGGCAAUCUCCGAUUGGCUUGGCUGAAGUUUUCUCUGAAAAGUUUUAGG
(((..(((..((((..((((((((.......))))))))(((((.(((..(((((....)))))...)))))))).....))))..)))..))).(((.(((((...))))).))).... ( -33.80)
>DroYak_CAF1 79667 115 + 1
GUCUUCUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUUAAGUGUUUGGCAAUCUCCGAUUG-----ACUGAAGUUUUCUUUAAAAAGUUUGAGG
(((.......(((((.((((((((.......))))))))))))).((((.(((((....)))))..))))..)))...(((.((((.-----..(((((....)))))...)))).))). ( -33.80)
>consensus
GUCUGGUUUUUUGGCCAUGGCCAAUUUGUAUUUGGCCAUGCCAGCGCACAAAACAGACCUGUUCAAGUGUUUGCCAAUCUCCGAUUGGCUUGACUGAAGUUUUCUCUGAAAAUUU_____
((((.((((((((((.((((((((.......))))))))))))).....)))))))))..........(((.(((((((...)))))))..)))..((((((((...))))))))..... (-30.22 = -31.42 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,740,136 – 21,740,251
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.63
Mean single sequence MFE -32.80
Consensus MFE -30.22
Energy contribution -30.02
Covariance contribution -0.20
Combinations/Pair 1.14
Mean z-score -2.87
Structure conservation index 0.92
SVM decision value 4.63
SVM RNA-class probability 0.999931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21740136 115 - 23771897
-----AAAUUUUCAGUGAAAACUUCAGUCAAGCCAAUCGGAGAUUGGCAAACACUUGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGAC
-----........(((....)))...(((..(((((((...)))))))...(((..(((((....))))).)))...((((((((((((.......)))))))).))))........))) ( -36.00)
>DroSec_CAF1 22031 115 - 1
-----AAAUUUUCAGAGAAAACUCCAGUCAAGCCAAUCGGAGAUUGGCAAACACUCGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGAC
-----.........(((....)))..(((..(((((((...)))))))...(((..(((((....))))).)))...((((((((((((.......)))))))).))))........))) ( -35.00)
>DroSim_CAF1 26918 115 - 1
-----AAAUUUUCAGAGAAAACUCCAGUCAAGCCAAUCGGAGAUUGGCAAACACUCGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGAC
-----.........(((....)))..(((..(((((((...)))))))...(((..(((((....))))).)))...((((((((((((.......)))))))).))))........))) ( -35.00)
>DroEre_CAF1 8002 120 - 1
CCUAAAACUUUUCAGAGAAAACUUCAGCCAAGCCAAUCGGAGAUUGCCAAACAUUUAAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACAAGAC
(((....(((....))).........(.(((.((....))...))).)............)))...(((((((....((((((((((((.......)))))))).))))....))))))) ( -28.80)
>DroYak_CAF1 79667 115 - 1
CCUCAAACUUUUUAAAGAAAACUUCAGU-----CAAUCGGAGAUUGCCAAACACUUAAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAAGAAGAC
.....................((((.(.-----(((((...))))).)...(((..(((((....))))).)))...((((((((((((.......)))))))).)))).....)))).. ( -29.20)
>consensus
_____AAAUUUUCAGAGAAAACUUCAGUCAAGCCAAUCGGAGAUUGGCAAACACUUGAACAGGUCUGUUUUGUGCGCUGGCAUGGCCAAAUACAAAUUGGCCAUGGCCAAAAAACCAGAC
.......................(((((...(((((((...)))))))...(((..(((((....))))).))).)))))(((((((((.......)))))))))............... (-30.22 = -30.02 +  -0.20)

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 13:11:38 2006