Locus 6166

Sequence ID 3R_DroMel_CAF1
Location 16,157,703 – 16,157,860
Length 157
Max. P 0.998647
window10048 window10049 window10050 window10051

overview

Window 8

Location 16,157,703 – 16,157,822
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.11
Mean single sequence MFE -43.66
Consensus MFE -26.45
Energy contribution -28.57
Covariance contribution 2.12
Combinations/Pair 1.11
Mean z-score -3.07
Structure conservation index 0.61
SVM decision value 3.17
SVM RNA-class probability 0.998647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16157703 119 + 27905053
AAGCUUCAACCAUCACCACCCCCUCUACUCGCUGCGAGCCUGUUCAUCAAUGGCUUGGUAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGC
.((((....((.......(((((.((..((....((((((...........))))))....))..)).)))-))((((((((.(((((((.....))))))).)))))))))).)))).. ( -50.60)
>DroSec_CAF1 27260 115 + 1
CAGCUCCACCCAUCACCACCC-----ACUCGCUGCGAGCCUGUUCAUCAAUGGCAUUGAAAGAAAGGCGGGGGGGUUGAUCAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGC
(((((((...........(((-----.((((((.((((((...........))).))).......)))))))))((((((...(((((((.....)))))))...)))))))).))))). ( -46.20)
>DroSim_CAF1 28790 114 + 1
CAGCUCCACCCAUCACCACCC-----ACUCGCUGCGAGCCUGUUCAUCAAUGGCAUUGAAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGC
(((((((........((.(((-----..(((...)))((((.((..(((((...)))))..)).)))))))-))((((((((.(((((((.....))))))).)))))))))).))))). ( -49.00)
>DroEre_CAF1 27029 101 + 1
A-------------ACCGCCC-----ACUCGCUCCGCGCCUGUUCAUCAAUGGCAUCGAAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGCCAGCUGG
.-------------.(((((.-----...........(((...........))).((....))..)))))(-(.((((((((.(((((((.....))))))).)))))))).))...... ( -45.50)
>DroAna_CAF1 23240 91 + 1
U-------------GCCACCA-----AU------CCAGCCUGUUCAUCAAUCGCACCGAAAGAAAGGCGGA-CG--UGA-GGAGUGGCGGACACUUC-CGAUGUCAUCAGCGACAGCUGC
.-------------((((((.-----.(------((.((((.(((............)))....)))))))-(.--...-)).))))).((((....-...))))..((((....)))). ( -27.00)
>consensus
AAGCU_CA_CCAUCACCACCC_____ACUCGCUGCGAGCCUGUUCAUCAAUGGCAUCGAAAGAAAGGCGGG_GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGC
..............................(((((..((((.(((................)))))))......((((((((.(((((((.....))))))).)))))))).)))))... (-26.45 = -28.57 +   2.12)

alignment

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secondary structure

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Window 9

Location 16,157,703 – 16,157,822
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.11
Mean single sequence MFE -43.04
Consensus MFE -25.26
Energy contribution -26.50
Covariance contribution 1.24
Combinations/Pair 1.17
Mean z-score -2.09
Structure conservation index 0.59
SVM decision value 1.05
SVM RNA-class probability 0.907060
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16157703 119 - 27905053
GCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUACCAAGCCAUUGAUGAACAGGCUCGCAGCGAGUAGAGGGGGUGGUGAUGGUUGAAGCUU
.(((((..(((((((((.(((((((.....))))))).))))).((((-((((((((((....(((....)))..))).))))(((...)))...).))))))))))..)))))...... ( -47.20)
>DroSec_CAF1 27260 115 - 1
GCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUGAUCAACCCCCCCGCCUUUCUUUCAAUGCCAUUGAUGAACAGGCUCGCAGCGAGU-----GGGUGGUGAUGGGUGGAGCUG
.(((((.((((((((.(.(((((((.....))))))).).))).((((((.((((((((..(((((...))))).))).))))(((...)))).-----))).)))....)))))))))) ( -45.10)
>DroSim_CAF1 28790 114 - 1
GCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUUCAAUGCCAUUGAUGAACAGGCUCGCAGCGAGU-----GGGUGGUGAUGGGUGGAGCUG
.(((((.((((((((((.(((((((.....))))))).))))).(((.-((((((((((..(((((...))))).))).))))(((...)))..-----))).)))....)))))))))) ( -49.50)
>DroEre_CAF1 27029 101 - 1
CCAGCUGGCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUUCGAUGCCAUUGAUGAACAGGCGCGGAGCGAGU-----GGGCGGU-------------U
......((.(.((((((.(((((((.....))))))).)))))).)))-.((((((((((((((.((((...........))))))))).))).-----)))))).-------------. ( -41.80)
>DroAna_CAF1 23240 91 - 1
GCAGCUGUCGCUGAUGACAUCG-GAAGUGUCCGCCACUCC-UCA--CG-UCCGCCUUUCUUUCGGUGCGAUUGAUGAACAGGCUGG------AU-----UGGUGGC-------------A
.((((....))))..((((.(.-...))))).((((((..-...--.(-((((((((((..(((((...))))).))).)))).))------))-----.))))))-------------. ( -31.60)
>consensus
GCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC_CCCGCCUUUCUUUCAAUGCCAUUGAUGAACAGGCUCGCAGCGAGU_____GGGUGGUGAUGG_UG_AGCUG
......(((((((((((.(((((((.....))))))).))))).........(((((((..((((.....)))).))).)))).................)))))).............. (-25.26 = -26.50 +   1.24)

alignment

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secondary structure

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Window 0

Location 16,157,743 – 16,157,860
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.61
Mean single sequence MFE -38.98
Consensus MFE -28.12
Energy contribution -30.08
Covariance contribution 1.96
Combinations/Pair 1.15
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 0.14
SVM RNA-class probability 0.604315
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16157743 117 + 27905053
UGUUCAUCAAUGGCUUGGUAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGCGCUCGCGCUUUGAUAUUGAAUUCUUAACAUGAUUGUGU--
...((((....((.(..(((...((((((.(-((((((((((.(((((((.....))))))).)))))))).((....)).))).))))))..)))..)...))....))))......-- ( -40.70)
>DroSec_CAF1 27295 118 + 1
UGUUCAUCAAUGGCAUUGAAAGAAAGGCGGGGGGGUUGAUCAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGCGCUCGCGCUUUGAUAUUGAAUUCUUGACAUGAUUGUGU--
......((((((.(.((....))((((((.(((.((((((...(((((((.....)))))))...)))))).((....)).))).))))))).)))))).......((((....))))-- ( -35.40)
>DroSim_CAF1 28825 117 + 1
UGUUCAUCAAUGGCAUUGAAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGCGCUCGCGCUUUGAUAUUGAAUUCUUGACAUGAUUGUGU--
......((((((.(.((....))((((((.(-((((((((((.(((((((.....))))))).)))))))).((....)).))).))))))).)))))).......((((....))))-- ( -40.50)
>DroEre_CAF1 27051 117 + 1
UGUUCAUCAAUGGCAUCGAAAGAAAGGCGGG-GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGCCAGCUGGGCUCGCGCUUUGAUAUUGAAUUCUUGACAUGAUUGUGU--
......((((((.(.((....))((((((.(-((((((((((.(((((((.....))))))).)))))))).((....)).))).))))))).)))))).......((((....))))-- ( -43.70)
>DroAna_CAF1 23256 115 + 1
UGUUCAUCAAUCGCACCGAAAGAAAGGCGGA-CG--UGA-GGAGUGGCGGACACUUC-CGAUGUCAUCAGCGACAGCUGCGCUCGUGCUUUGAUAUUGAAUUCUUGACAUGAUUGUUUUG
.(((((((((..(((((....)...((((((-((--(..-((((((.....))))))-..)))))..((((....)))))))).)))).))))...)))))....((((....))))... ( -34.60)
>consensus
UGUUCAUCAAUGGCAUCGAAAGAAAGGCGGG_GGGUUGAUGAAAUCGUGGACAUUCCACGAUGUCAUCAGCGGCAGCUGCGCUCGCGCUUUGAUAUUGAAUUCUUGACAUGAUUGUGU__
.(((((((((.(((.((....))...(((((...((((((((.(((((((.....))))))).)))))))).((....)).))))))))))))...))))).....(((....))).... (-28.12 = -30.08 +   1.96)

alignment

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secondary structure

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Window 1

Location 16,157,743 – 16,157,860
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.61
Mean single sequence MFE -30.82
Consensus MFE -23.61
Energy contribution -24.61
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -2.14
Structure conservation index 0.77
SVM decision value 1.01
SVM RNA-class probability 0.900680
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16157743 117 - 27905053
--ACACAAUCAUGUUAAGAAUUCAAUAUCAAAGCGCGAGCGCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUACCAAGCCAUUGAUGAACA
--.(((((((.((.((((((............((....))(((((....)))(((((.(((((((.....))))))).))))).....-...))..)))))).)).)..)))).)).... ( -32.20)
>DroSec_CAF1 27295 118 - 1
--ACACAAUCAUGUCAAGAAUUCAAUAUCAAAGCGCGAGCGCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUGAUCAACCCCCCCGCCUUUCUUUCAAUGCCAUUGAUGAACA
--.(((((((((...(((((............((....))(((((....)))(((.(.(((((((.....))))))).).))).........))..)))))...)))..)))).)).... ( -27.80)
>DroSim_CAF1 28825 117 - 1
--ACACAAUCAUGUCAAGAAUUCAAUAUCAAAGCGCGAGCGCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUUCAAUGCCAUUGAUGAACA
--.(((((((((...(((((............((....))(((((....)))(((((.(((((((.....))))))).))))).....-...))..)))))...)))..)))).)).... ( -31.90)
>DroEre_CAF1 27051 117 - 1
--ACACAAUCAUGUCAAGAAUUCAAUAUCAAAGCGCGAGCCCAGCUGGCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC-CCCGCCUUUCUUUCGAUGCCAUUGAUGAACA
--.((((((..(((((((((...........(((((.(((...))).)))))(((((.(((((((.....))))))).))))).....-.......)))))..))))..)))).)).... ( -36.50)
>DroAna_CAF1 23256 115 - 1
CAAAACAAUCAUGUCAAGAAUUCAAUAUCAAAGCACGAGCGCAGCUGUCGCUGAUGACAUCG-GAAGUGUCCGCCACUCC-UCA--CG-UCCGCCUUUCUUUCGGUGCGAUUGAUGAACA
.....(((((((((((................((....)).((((....)))).)))))).(-((.(((.....))))))-...--..-..((((........)))).)))))....... ( -25.70)
>consensus
__ACACAAUCAUGUCAAGAAUUCAAUAUCAAAGCGCGAGCGCAGCUGCCGCUGAUGACAUCGUGGAAUGUCCACGAUUUCAUCAACCC_CCCGCCUUUCUUUCAAUGCCAUUGAUGAACA
............(((((............((((.((((((((....)).)))(((((.(((((((.....))))))).)))))........)))))))............)))))..... (-23.61 = -24.61 +   1.00)

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 12:14:22 2006