Locus 2965

Sequence ID 2L_DroMel_CAF1
Location 8,503,457 – 8,503,616
Length 159
Max. P 0.962373
window4709 window4710 window4711

overview

Window 9

Location 8,503,457 – 8,503,577
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.50
Mean single sequence MFE -34.14
Consensus MFE -18.22
Energy contribution -22.38
Covariance contribution 4.16
Combinations/Pair 1.11
Mean z-score -2.32
Structure conservation index 0.53
SVM decision value 0.65
SVM RNA-class probability 0.812367
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8503457 120 + 22407834
CAUUCCAUGACGGCGUAAGCAGCUCAAAAUGAAUCAAAUGGGGUAAGAAAUUACCUGCAGUUAAGCGCCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAAAGGCGAGCAC
((((...(((..((....))...))).)))).(((.....((((((....))))))((((((..((((((....))).)))..)))))).)))......((((...(....)..)))).. ( -34.70)
>DroSec_CAF1 12841 120 + 1
UAUUUCAUGAAGGCGUAAGCAGCUCAAAAUGAAUCAAAUGGGGUAAGGAAUUACCUGCAGUUAAGCGCCCAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAUGGGCGAGCAU
............((....)).((((.......(((.....((((((....))))))((((((..(((.((.....)).)))..)))))).)))......(((((.....))))))))).. ( -36.10)
>DroSim_CAF1 12373 120 + 1
UAUUCCAUGGCGGCGUAAGCAGCUCAAAAUGAAUCAAAUGGGGUAAGGAAUUACCUGCAGUUAAGCGGCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAUGGGCGAGCAC
............((....)).((((.......(((.....((((((....))))))((((((..(((((.......)))))..)))))).)))......(((((.....))))))))).. ( -36.20)
>DroEre_CAF1 12449 115 + 1
UCUUCCAUCAAGGCGUAAGCAGCGCAGAAUUAAUCAAAUGG-GUAAGAAAUUGCCUGCAGUUGAGCGCCAAUAUUGGCUGCAGAAUUGCAGAUAGAGUAGCGCAACCGCAGGGCAG----
...(((......((....)).((((....((.(((....((-((((....))))))((((((..((((((....)))).))..)))))).))).))...)))).......)))...---- ( -37.10)
>DroYak_CAF1 13143 99 + 1
UCUUCCAUU---------CCAGCUCAGAAUGAAUCAAAUGGGGUGAGAAAUUACCUGCAGUUAAGCGCCAAUAU------------UGCAGAUAGAGUAGCUCAACCGAAAGGCGAGCAC
.........---------...((((...............((((((....))))))(((((...........))------------))).....)))).((((..((....)).)))).. ( -26.60)
>consensus
UAUUCCAUGAAGGCGUAAGCAGCUCAAAAUGAAUCAAAUGGGGUAAGAAAUUACCUGCAGUUAAGCGCCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAAGGGCGAGCAC
.....................((((.......(((.....((((((....))))))((((((..(((((......))).))..)))))).)))......((((.......)))))))).. (-18.22 = -22.38 +   4.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,503,497 – 8,503,616
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.70
Mean single sequence MFE -32.16
Consensus MFE -16.80
Energy contribution -19.72
Covariance contribution 2.92
Combinations/Pair 1.21
Mean z-score -2.14
Structure conservation index 0.52
SVM decision value 0.22
SVM RNA-class probability 0.640458
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8503497 119 + 22407834
GGGUAAGAAAUUACCUGCAGUUAAGCGCCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAAAGGCGAGCACCGAAAUAUAUCUGCUAGAUAAACAGGGCUCA-AGGUACUG
((((((....))))))((((((..((((((....))).)))..))))))......((((.((...((.....))((((.((......((((.....))))....)))))).-)).)))). ( -36.50)
>DroSec_CAF1 12881 119 + 1
GGGUAAGGAAUUACCUGCAGUUAAGCGCCCAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAUGGGCGAGCAUCGAAAUAUAUCUGCUAGAUAAACAUGGCUUA-AGUUAAAG
((((((....))))))((((((..(((.((.....)).)))..))))))........(((((.((((.(((..(.((((..((......)))))).).....))).)))).-)))))... ( -32.70)
>DroSim_CAF1 12413 119 + 1
GGGUAAGGAAUUACCUGCAGUUAAGCGGCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAUGGGCGAGCACCGAAAUAUAUCUGCUAGAUAAACAGGGCUUA-AGUUAAAG
((((((....))))))((((((..(((((.......)))))..))))))..........(((((.....)))))((((.((......((((.....))))....)))))).-........ ( -31.50)
>DroEre_CAF1 12489 114 + 1
G-GUAAGAAAUUGCCUGCAGUUGAGCGCCAAUAUUGGCUGCAGAAUUGCAGAUAGAGUAGCGCAACCGCAGGGCAG-----GAAAUGUAUCCGUUAGAUAAAUAGGGCUUAAAAGUAUUG
(-((((....)))))(((..(((((((((........((((......))))........(((....)))..))).(-----((......)))..............))))))..)))... ( -31.50)
>DroYak_CAF1 13174 108 + 1
GGGUGAGAAAUUACCUGCAGUUAAGCGCCAAUAU------------UGCAGAUAGAGUAGCUCAACCGAAAGGCGAGCACCGAAAUGUAUCUCUUAGAUAAAUAGUACUCACAGGUAUUG
((((((....))))))(((((...........))------------))).....(((((((((..((....)).)))).........((((.....)))).....))))).......... ( -28.60)
>consensus
GGGUAAGAAAUUACCUGCAGUUAAGCGCCAAUAUUGGUUGCAGAAUUGCAGAUAAAGUAGCUCAAGCGAAGGGCGAGCACCGAAAUAUAUCUGCUAGAUAAACAGGGCUUA_AGGUAAUG
..((((....))))((((((((..(((((......))).))..))))))))...((((.((((.......)))).............((((.....))))......)))).......... (-16.80 = -19.72 +   2.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,503,497 – 8,503,616
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.70
Mean single sequence MFE -30.04
Consensus MFE -12.82
Energy contribution -13.50
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -3.16
Structure conservation index 0.43
SVM decision value 1.54
SVM RNA-class probability 0.962373
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8503497 119 - 22407834
CAGUACCU-UGAGCCCUGUUUAUCUAGCAGAUAUAUUUCGGUGCUCGCCUUUCGCUUGAGCUACUUUAUCUGCAAUUCUGCAACCAAUAUUGGCGCUUAACUGCAGGUAAUUUCUUACCC
.((((.((-..(((.(((((.....))))).........(((....)))....)))..)).))))(((((((((.((..((..(((....))).))..)).))))))))).......... ( -32.80)
>DroSec_CAF1 12881 119 - 1
CUUUAACU-UAAGCCAUGUUUAUCUAGCAGAUAUAUUUCGAUGCUCGCCCAUCGCUUGAGCUACUUUAUCUGCAAUUCUGCAACCAAUAUGGGCGCUUAACUGCAGGUAAUUCCUUACCC
......((-(((((......((((.....))))......((((......))))))))))).....(((((((((.((..((..((.....))..))..)).))))))))).......... ( -28.50)
>DroSim_CAF1 12413 119 - 1
CUUUAACU-UAAGCCCUGUUUAUCUAGCAGAUAUAUUUCGGUGCUCGCCCAUCGCUUGAGCUACUUUAUCUGCAAUUCUGCAACCAAUAUUGCCGCUUAACUGCAGGUAAUUCCUUACCC
......((-(((((.(((((.....))))).........(((....)))....))))))).....(((((((((.((..((.............))..)).))))))))).......... ( -26.12)
>DroEre_CAF1 12489 114 - 1
CAAUACUUUUAAGCCCUAUUUAUCUAACGGAUACAUUUC-----CUGCCCUGCGGUUGCGCUACUCUAUCUGCAAUUCUGCAGCCAAUAUUGGCGCUCAACUGCAGGCAAUUUCUUAC-C
.........((((...............(((......))-----)((((.((((((((.((.........((((....))))((((....)))))).))))))))))))....)))).-. ( -33.60)
>DroYak_CAF1 13174 108 - 1
CAAUACCUGUGAGUACUAUUUAUCUAAGAGAUACAUUUCGGUGCUCGCCUUUCGGUUGAGCUACUCUAUCUGCA------------AUAUUGGCGCUUAACUGCAGGUAAUUUCUCACCC
...((((((((((((((((.((((.....)))).))...))))))).......((((((((..(..(((.....------------)))..)..)))))))))))))))........... ( -29.20)
>consensus
CAAUACCU_UAAGCCCUGUUUAUCUAGCAGAUAUAUUUCGGUGCUCGCCCUUCGCUUGAGCUACUUUAUCUGCAAUUCUGCAACCAAUAUUGGCGCUUAACUGCAGGUAAUUUCUUACCC
.........((((......((((((.(((((((.........(((((.........))))).....))))))).....................((......))))))))...))))... (-12.82 = -13.50 +   0.68)

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 10:40:48 2006