Locus 7888

Sequence ID X_DroMel_CAF1
Location 19,664,686 – 19,664,926
Length 240
Max. P 0.885259
window12938 window12939 window12940 window12941

overview

Window 8

Location 19,664,686 – 19,664,778
Length 92
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 84.28
Mean single sequence MFE -14.73
Consensus MFE -9.85
Energy contribution -10.60
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.67
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19664686 92 + 22224390
CUUUAUUUCACUGCCUUACUUAAUUGUUUAUACAUUGAGUUCGAAAUGUGUAAGCAAACAAUACGAAAAC-AAAGAAUACAAAUCAUAUGUAA--
.......................(((((((((((((........))))))))))))).............-......((((.......)))).-- ( -14.00)
>DroSec_CAF1 38190 94 + 1
CUUUAAUUCACUGCAUUACUAAAUUGUUUAUACAUUCAGUUCGAAACGUGUAAGCAAACAAAACGGAAAC-AACGGAAACAAAUCAUGUGUAAAA
...............((((....((((((((((.(((.....)))..))))))))))(((....(....)-...(....)......))))))).. ( -15.70)
>DroSim_CAF1 29939 85 + 1
CUUUAAUUCACUGCAUUACUUAAUUGUUUAAACAUUCAGUUCGAAACGUGUAAGCAAACAAAACGG----------AAACAAAUCAUGUGUAAAA
........((((((.((((.....(((((.(((.....)))..))))).)))))))........(.----------...).......)))..... ( -10.00)
>DroYak_CAF1 52191 93 + 1
AUUUAUUUCACUGCAUUACUUAAUUGUUUAUACAUUGAGUUCGAAAUGUGUAAGCAAACGA-ACGGAAACAAAAGAAUACAAAUAAUGUGUUAA-
............((((((.....(((((((((((((........)))))))))))))....-..(....).............)))))).....- ( -19.20)
>consensus
CUUUAAUUCACUGCAUUACUUAAUUGUUUAUACAUUCAGUUCGAAACGUGUAAGCAAACAAAACGGAAAC_AAAGAAAACAAAUCAUGUGUAAA_
.......................(((((((((((((........)))))))))))))...................................... ( -9.85 = -10.60 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,664,778 – 19,664,895
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 92.44
Mean single sequence MFE -23.90
Consensus MFE -20.32
Energy contribution -20.77
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.85
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19664778 117 + 22224390
GAUGGCAAACAAAAAUGAUUUAAAAUGCUUUCUGUAGCUAAAGCAUGGAGUAAGUUUCUAGAUUCAAGUUUCUAGAUUUAUCUUCUGCCUUUACUUUAAUAACAUACAUUUCUAUGU
...((((.................(((((((........)))))))((((......((((((........)))))).....))))))))............(((((......))))) ( -22.00)
>DroSec_CAF1 38284 109 + 1
UAUGGCAAACAAAAAUGAUUUAAAAUGCUUUCUGUAGCUAAAGCA-GGAGUAAGUUUCUAGAUUCAGGUUUCUAGAUUUAUCUUUUGCCA-----UUAAUAACAUACAUUU--GUGU
.((((((((.......((((((...((((((........))))))-....))))))((((((........)))))).......)))))))-----).....(((((....)--)))) ( -23.60)
>DroSim_CAF1 30024 110 + 1
GAUGGCAAACAAAAAUGAUUUAAAAUGCUUUCUGUAGCUAAAGCAUGGAGUAAGUUUCUAGAUUCAGGUUUCUAGAUUUAUCUUUUGCCA-----UUAAUAACAUACAUUU--GUGU
(((((((((.......((((((..(((((((........)))))))....))))))((((((........)))))).......)))))))-----))....(((((....)--)))) ( -26.10)
>consensus
GAUGGCAAACAAAAAUGAUUUAAAAUGCUUUCUGUAGCUAAAGCAUGGAGUAAGUUUCUAGAUUCAGGUUUCUAGAUUUAUCUUUUGCCA_____UUAAUAACAUACAUUU__GUGU
...((((((.......((((((..(((((((........)))))))....))))))((((((........)))))).......))))))................((((....)))) (-20.32 = -20.77 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,664,778 – 19,664,895
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 92.44
Mean single sequence MFE -20.53
Consensus MFE -18.82
Energy contribution -18.60
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.92
SVM decision value 0.34
SVM RNA-class probability 0.696698
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19664778 117 - 22224390
ACAUAGAAAUGUAUGUUAUUAAAGUAAAGGCAGAAGAUAAAUCUAGAAACUUGAAUCUAGAAACUUACUCCAUGCUUUAGCUACAGAAAGCAUUUUAAAUCAUUUUUGUUUGCCAUC
.....(((((((.(((..((((((((..((.(((((.....((((((........))))))..))).)))).))))))))..)))....)))))))..................... ( -20.60)
>DroSec_CAF1 38284 109 - 1
ACAC--AAAUGUAUGUUAUUAA-----UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCC-UGCUUUAGCUACAGAAAGCAUUUUAAAUCAUUUUUGUUUGCCAUA
....--...............(-----(((((((.......((((((........))))))..........-((((((........))))))................)))))))). ( -20.40)
>DroSim_CAF1 30024 110 - 1
ACAC--AAAUGUAUGUUAUUAA-----UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCCAUGCUUUAGCUACAGAAAGCAUUUUAAAUCAUUUUUGUUUGCCAUC
....--...............(-----(((((((.......((((((........))))))..........(((((((........)))))))...............)))))))). ( -20.60)
>consensus
ACAC__AAAUGUAUGUUAUUAA_____UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCCAUGCUUUAGCUACAGAAAGCAUUUUAAAUCAUUUUUGUUUGCCAUC
............................((((((.......((((((........))))))...........((((((........))))))................))))))... (-18.82 = -18.60 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,664,816 – 19,664,926
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 91.95
Mean single sequence MFE -17.37
Consensus MFE -15.53
Energy contribution -15.53
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.89
SVM decision value 0.94
SVM RNA-class probability 0.885259
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19664816 110 - 22224390
UAAAUAAAUUUAUAUGAAAUGACACGCAUAUACAUAGAAAUGUAUGUUAUUAAAGUAAAGGCAGAAGAUAAAUCUAGAAACUUGAAUCUAGAAACUUACUCCAUGCUUUA
............(((..(((((((..(((..........)))..)))))))...)))((((((..((.(((.((((((........))))))...)))))...)))))). ( -18.40)
>DroSec_CAF1 38322 102 - 1
UAAAUAAAUUUAUAUAAAAUGACACGCAUAUACAC--AAAUGUAUGUUAUUAA-----UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCC-UGCUUUA
.................(((((((..(((......--..)))..)))))))..-----.((((..((.(((.((((((........))))))...)))))..-))))... ( -17.30)
>DroSim_CAF1 30062 103 - 1
UAAAUAAAUUUAUAUAAAAUGACACGCAUAUACAC--AAAUGUAUGUUAUUAA-----UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCCAUGCUUUA
.................(((((((..(((......--..)))..))))))).(-----(((...(((.....((((((........))))))..)))...))))...... ( -16.40)
>consensus
UAAAUAAAUUUAUAUAAAAUGACACGCAUAUACAC__AAAUGUAUGUUAUUAA_____UGGCAAAAGAUAAAUCUAGAAACCUGAAUCUAGAAACUUACUCCAUGCUUUA
.................(((((((..(((..........)))..)))))))........((((..((.(((.((((((........))))))...)))))...))))... (-15.53 = -15.53 +  -0.00)

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 12:50:02 2006