Locus 1160

Sequence ID 2L_DroMel_CAF1
Location 3,172,948 – 3,173,086
Length 138
Max. P 0.977396
window1878 window1879 window1880

overview

Window 8

Location 3,172,948 – 3,173,046
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 87.97
Mean single sequence MFE -20.73
Consensus MFE -17.37
Energy contribution -17.27
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.80
Structure conservation index 0.84
SVM decision value 0.13
SVM RNA-class probability 0.596014
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3172948 98 - 22407834
UCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAGGUUUACGGAUUUUCUUUAUUUUUCAACAUUCUCUAUUCUAUUCUCUAUU
.((((.....))))((((.(((((.(((........)))....(((((.(((.(..(((.......)))..).))).)))))...))))).))))... ( -17.90)
>DroSec_CAF1 8512 95 - 1
UCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU-UACAAAUUU--UUUAUUUUUUAACAUUCUCGACUAUACUAAGCAUU
......((((...))))(((((((.......)))))......((((((.((-((.(((...--.....))).)))).))))))..........))... ( -22.40)
>DroSim_CAF1 8959 91 - 1
UCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU-UACAAAUUU--UUUAUUUUUUAACAUUCUCGACUAUAC----CAUU
.(((.(((((...))))).(((((.......)))))...)))((((((.((-((.(((...--.....))).)))).)))))).......----.... ( -21.90)
>consensus
UCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU_UACAAAUUU__UUUAUUUUUUAACAUUCUCGACUAUACU___CAUU
.(((.(((((...))))).(((((.......)))))...)))((((((.((....((((.......))))....)).))))))............... (-17.37 = -17.27 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,172,966 – 3,173,086
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.30
Mean single sequence MFE -34.50
Consensus MFE -32.02
Energy contribution -32.02
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.93
SVM decision value 1.79
SVM RNA-class probability 0.977396
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3172966 120 + 22407834
GAAUGUUGAAAAAUAAAGAAAAUCCGUAAACCUUCUCGCAGUCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCUAGUCAGACGCCUUAACCGCUCGGCCACGACUGCUG
...((((....))))......................((((((((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..))))))).. ( -33.22)
>DroSec_CAF1 8530 117 + 1
GAAUGUUAAAAAAUAAA--AAAUUUGUA-ACUUUCUCGCAGUCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCUAGUCAGACGCCUUAACCGCUCGGCCACGACUGCUG
(((.((((.(((.....--...))).))-)).)))..((((((((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..))))))).. ( -34.62)
>DroSim_CAF1 8973 117 + 1
GAAUGUUAAAAAAUAAA--AAAUUUGUA-ACUUUCUCGCAGUCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCUAGUCAGACGCCUUAACCGCUCGGCCACGACUGCUG
(((.((((.(((.....--...))).))-)).)))..((((((((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..))))))).. ( -34.62)
>DroYak_CAF1 8710 109 + 1
AAGU---AAA-----AA--AGAAUUUUA-CUUCUCUCGCAGUCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCUAGUCAGACGCCUUAACCGCUCGGCCACGACUGCUG
((((---(((-----(.--....)))))-))).....((((((((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..))))))).. ( -35.52)
>consensus
GAAUGUUAAAAAAUAAA__AAAUUUGUA_ACUUUCUCGCAGUCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCUAGUCAGACGCCUUAACCGCUCGGCCACGACUGCUG
.....................................((((((((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..))))))).. (-32.02 = -32.02 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,172,966 – 3,173,086
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.30
Mean single sequence MFE -36.60
Consensus MFE -32.90
Energy contribution -32.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.90
SVM decision value 0.97
SVM RNA-class probability 0.891913
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3172966 120 - 22407834
CAGCAGUCGUGGCCGAGCGGUUAAGGCGUCUGACUAGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAGGUUUACGGAUUUUCUUUAUUUUUCAACAUUC
..((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))(((((((((....)))))))))............... ( -38.30)
>DroSec_CAF1 8530 117 - 1
CAGCAGUCGUGGCCGAGCGGUUAAGGCGUCUGACUAGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU-UACAAAUUU--UUUAUUUUUUAACAUUC
..((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))..(((.((-((.(((...--.....))).)))).))) ( -35.30)
>DroSim_CAF1 8973 117 - 1
CAGCAGUCGUGGCCGAGCGGUUAAGGCGUCUGACUAGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU-UACAAAUUU--UUUAUUUUUUAACAUUC
..((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))..(((.((-((.(((...--.....))).)))).))) ( -35.30)
>DroYak_CAF1 8710 109 - 1
CAGCAGUCGUGGCCGAGCGGUUAAGGCGUCUGACUAGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAGAAG-UAAAAUUCU--UU-----UUU---ACUU
..((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......)))))))))))).....(((-(((((....--.)-----)))---)))) ( -37.50)
>consensus
CAGCAGUCGUGGCCGAGCGGUUAAGGCGUCUGACUAGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGACUGCGAGAAAGU_UACAAAUUU__UUUAUUUUUUAACAUUC
..((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))..................................... (-32.90 = -32.90 +  -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 09:55:06 2006