Locus 1802

Sequence ID 3L_DroMel_CAF1
Location 5,077,904 – 5,078,063
Length 159
Max. P 0.963369
window2799 window2800 window2801

overview

Window 9

Location 5,077,904 – 5,078,023
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -26.08
Consensus MFE -20.76
Energy contribution -21.44
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -1.95
Structure conservation index 0.80
SVM decision value 0.93
SVM RNA-class probability 0.884373
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5077904 119 + 23771897
ACUUGAUUUUUGAUUAAUCUAAAGCCAGAAAAUA-UUGAUAAAUAUUUGCCAAAUGCAUAUUCGGCUCAGAUGUGGCACAAAAAACCAACUAACAGUAAGAAAAAUUAAUUCGCUGUUUG
......((((((....((((..((((...(((((-((....)))))))((.....))......)))).))))......)))))).......((((((..(((.......))))))))).. ( -18.00)
>DroSec_CAF1 284295 119 + 1
AGUUGAUUUUUGAUUAAUCUAAAGCCAGAAAAUA-UUGGUAAAUAUUUGCCAAAUGCAUAUUCGGCCCAGAUGUGGCACAAAAAACCAACUAACAGUGAGAAAAAUUAAUUCGCUGUUUG
(((((.((((((....((((...(((.(((.((.-(((((((....)))))))....)).))))))..))))......))))))..)))))(((((((((.........))))))))).. ( -25.80)
>DroSim_CAF1 305566 119 + 1
AGUUGAUUUUUGAUUAAUCUAAAGCCAGAAAAUA-UUGGUAAAUAUUUGCCAAAUGCAUAUUCGGCCCAGAUGUGGCACAAAAAACCAACUAACAGUGAGAAAAAUUAAUUCGCUGUUUG
(((((.((((((....((((...(((.(((.((.-(((((((....)))))))....)).))))))..))))......))))))..)))))(((((((((.........))))))))).. ( -25.80)
>DroEre_CAF1 291364 119 + 1
AGUUGAUUUUUGAUUAAUCUAAAGCCAGAAAGCA-UUGGUAAAUAUUUGCCAAAUGCAUUUUCGACCCAGAUGCGGCACAAAAAACCAACCAACAGUGAGAAAAAUUAAUUCGCUGUUGG
.((((.(((((((....))....(((........-(((((((....)))))))..((((((.......)))))))))...))))).))))((((((((((.........)))))))))). ( -30.60)
>DroYak_CAF1 295585 120 + 1
AGUUGAUUUUUGGUUAAUCUAAAGCCAGAAAAUAGUUGGUAAAUAUUUGCCAAAUGCAUAUUUGGCCCAGAUGCGGUGCAAAAAACCAACUAAUAGUGAGAAAAAUUAAUUCGCUGUUCG
......(((((((((.......))))))))).((((((((........(((((((....))))))).....(((...)))....))))))))((((((((.........))))))))... ( -30.20)
>consensus
AGUUGAUUUUUGAUUAAUCUAAAGCCAGAAAAUA_UUGGUAAAUAUUUGCCAAAUGCAUAUUCGGCCCAGAUGUGGCACAAAAAACCAACUAACAGUGAGAAAAAUUAAUUCGCUGUUUG
(((((.((((((....((((...(((.(((.....(((((((....))))))).......))))))..))))......))))))..)))))(((((((((.........))))))))).. (-20.76 = -21.44 +   0.68)

alignment

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secondary structure

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Window 0

Location 5,077,904 – 5,078,023
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -25.30
Consensus MFE -21.54
Energy contribution -21.22
Covariance contribution -0.32
Combinations/Pair 1.19
Mean z-score -1.82
Structure conservation index 0.85
SVM decision value 1.55
SVM RNA-class probability 0.963369
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5077904 119 - 23771897
CAAACAGCGAAUUAAUUUUUCUUACUGUUAGUUGGUUUUUUGUGCCACAUCUGAGCCGAAUAUGCAUUUGGCAAAUAUUUAUCAA-UAUUUUCUGGCUUUAGAUUAAUCAAAAAUCAAGU
((((.(((.(((((((..........))))))).))).)))).((((.......(((((((....)))))))(((((((....))-)))))..))))....((((.......)))).... ( -22.70)
>DroSec_CAF1 284295 119 - 1
CAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUUACCAA-UAUUUUCUGGCUUUAGAUUAAUCAAAAAUCAACU
..(((((.((...........)).)))))(((((((((((...((((.......(((((((....)))))))(((((((....))-)))))..))))....((....))))))))))))) ( -26.20)
>DroSim_CAF1 305566 119 - 1
CAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUUACCAA-UAUUUUCUGGCUUUAGAUUAAUCAAAAAUCAACU
..(((((.((...........)).)))))(((((((((((...((((.......(((((((....)))))))(((((((....))-)))))..))))....((....))))))))))))) ( -26.20)
>DroEre_CAF1 291364 119 - 1
CCAACAGCGAAUUAAUUUUUCUCACUGUUGGUUGGUUUUUUGUGCCGCAUCUGGGUCGAAAAUGCAUUUGGCAAAUAUUUACCAA-UGCUUUCUGGCUUUAGAUUAAUCAAAAAUCAACU
.((((((.((...........)).))))))((((((((((.((.....((((((((((.(((.(((((.((..........))))-)))))).)))).))))))..)).)))))))))). ( -29.20)
>DroYak_CAF1 295585 120 - 1
CGAACAGCGAAUUAAUUUUUCUCACUAUUAGUUGGUUUUUUGCACCGCAUCUGGGCCAAAUAUGCAUUUGGCAAAUAUUUACCAACUAUUUUCUGGCUUUAGAUUAACCAAAAAUCAACU
.....((((((.......))).......((((((((........(((....)))(((((((....)))))))........)))))))).......)))...((((.......)))).... ( -22.20)
>consensus
CAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUUACCAA_UAUUUUCUGGCUUUAGAUUAAUCAAAAAUCAACU
..(((((.((...........)).)))))(((((((((((.((.....(((((((((((((....))))))).........(((.........)))..))))))..)).))))))))))) (-21.54 = -21.22 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,077,943 – 5,078,063
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.00
Mean single sequence MFE -27.24
Consensus MFE -21.82
Energy contribution -21.94
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -1.87
Structure conservation index 0.80
SVM decision value 0.95
SVM RNA-class probability 0.888728
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5077943 120 - 23771897
CAAACCAAAAUUUGGCAAAUACAAUAAAGCCAAUCGUCGACAAACAGCGAAUUAAUUUUUCUUACUGUUAGUUGGUUUUUUGUGCCACAUCUGAGCCGAAUAUGCAUUUGGCAAAUAUUU
............((((....((((.(((((((((.(....).(((((.(((.......)))...))))).))))))))))))))))).......(((((((....)))))))........ ( -25.00)
>DroSec_CAF1 284334 120 - 1
CAAACCAAAAUUUGGCAAAUACAAUAAAGCCAAUCGUCGACAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUU
....(((.....((((....((((.(((((((((.(....).(((((.((...........)).))))).)))))))))))))))))....)))(((((((....)))))))........ ( -28.40)
>DroSim_CAF1 305605 120 - 1
CAAACCAAAAUUUGGCAAAUACAAUAAAGCCAAUCGUCGACAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUU
....(((.....((((....((((.(((((((((.(....).(((((.((...........)).))))).)))))))))))))))))....)))(((((((....)))))))........ ( -28.40)
>DroEre_CAF1 291403 120 - 1
UAAACCAACAUUGGGCAAAUACUAUAAAGCCAAUCGUCGGCCAACAGCGAAUUAAUUUUUCUCACUGUUGGUUGGUUUUUUGUGCCGCAUCUGGGUCGAAAAUGCAUUUGGCAAAUAUUU
....(((....((((((........(((((((.......((((((((.((...........)).)))))))))))))))...)))).))..)))((((((......))))))........ ( -30.01)
>DroYak_CAF1 295625 120 - 1
CAAACCAAAAUUUGGUAAAUACAAUAAAGUCAAUCGACGCCGAACAGCGAAUUAAUUUUUCUCACUAUUAGUUGGUUUUUUGCACCGCAUCUGGGCCAAAUAUGCAUUUGGCAAAUAUUU
....(((.....((((............(((....)))((.(((.(((.(((((((..........))))))).)))))).))))))....)))(((((((....)))))))........ ( -24.40)
>consensus
CAAACCAAAAUUUGGCAAAUACAAUAAAGCCAAUCGUCGACAAACAGCGAAUUAAUUUUUCUCACUGUUAGUUGGUUUUUUGUGCCACAUCUGGGCCGAAUAUGCAUUUGGCAAAUAUUU
....(((.....(((((....(((.(((((((((.(....).(((((.((...........)).))))).)))))))))))))))))....)))(((((((....)))))))........ (-21.82 = -21.94 +   0.12)

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 10:16:56 2006