Locus 1405

Sequence ID 3R_DroMel_CAF1
Location 4,094,382 – 4,094,542
Length 160
Max. P 0.976063
window2319 window2320 window2321

overview

Window 9

Location 4,094,382 – 4,094,502
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.17
Mean single sequence MFE -41.57
Consensus MFE -38.00
Energy contribution -38.52
Covariance contribution 0.52
Combinations/Pair 1.12
Mean z-score -1.66
Structure conservation index 0.91
SVM decision value 1.76
SVM RNA-class probability 0.976063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094382 120 + 27905053
UAGCAGUUUAGUUAGCUCCACUUUCUGGUUGAUCUUCAGGAAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGAGCGUUGCCCUCGUUUCCCUGCCGAGCCGUGCGACCUAC
............(((.((.(((((((((.......)))))))))((((..(((...))).(((.((((((.(((((...((.((...)).)).))))))))))).))).)))))).))). ( -40.90)
>DroSec_CAF1 6300 120 + 1
UAGCAGUUCAGUUAGCUCCACUUUCUGGUUGAUCUUCAGGAAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACAAGGGCGUUGCCUUCGUUCCCCUGCCGAGCAGUGCGUCCGAC
((((......)))).....(((((((((.......)))))))))((((..(((...))).(((.((((((.(((.....(((((...)))))..))).)))))).))).))))....... ( -41.80)
>DroSim_CAF1 6337 120 + 1
UAACAGUUCAGUUAGCUCCACUUUCUGGUUAAUCUUCAGGAAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCGUUGCCUUCGUUCCCCUGCCGAGCAGUGCGGCCUAC
((((......))))....((((((((((.......))))))))))....(((((...((.(((.((((((.(((.....(((((...)))))..))).)))))).)))))....))))). ( -45.10)
>DroEre_CAF1 6344 120 + 1
GAGCAGUUUAGUUAGCUCCACCUUCUGAUUGAUCUUCAGGAAGUGCACAUAAGCAUCUUCGCUGGGCAGGAGAAACACCAGAGCGUUGCCCUCGUUUCCCUGUCGAGCAGUGCGUCCCAC
((((..........))))(((...((((.......))))(((((((......))).))))(((.((((((.(((((...((.((...)).)).))))))))))).))).)))........ ( -37.00)
>DroYak_CAF1 6301 120 + 1
AAGCAGUUCAGUUAACUCCACCUUUUGGUUGAUCUUCAAGAAAUGCACAUAAGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCAUUGCCCUCGUUUCCCUGCCGAGCAGUGCGUCCCAC
..(((.(((.......((.(((....))).)).......))).)))......((((....(((.((((((.(((((...(((((...))))).))))))))))).))).))))....... ( -43.04)
>consensus
UAGCAGUUCAGUUAGCUCCACUUUCUGGUUGAUCUUCAGGAAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCGUUGCCCUCGUUUCCCUGCCGAGCAGUGCGUCCCAC
..................((((((((((.......)))))))))).......((((....(((.((((((.(((((...(((((...))))).))))))))))).))).))))....... (-38.00 = -38.52 +   0.52)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,094,382 – 4,094,502
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.17
Mean single sequence MFE -41.69
Consensus MFE -37.87
Energy contribution -37.23
Covariance contribution -0.64
Combinations/Pair 1.23
Mean z-score -1.16
Structure conservation index 0.91
SVM decision value 0.05
SVM RNA-class probability 0.558760
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094382 120 - 27905053
GUAGGUCGCACGGCUCGGCAGGGAAACGAGGGCAACGCUCUGGUGUUUCUCCUGCCCAGCGAGGAUGCCUAUGUGCACUUCCUGAAGAUCAACCAGAAAGUGGAGCUAACUAAACUGCUA
((((.......((((((((((((((((((((((...)))))..)))))).))))))(((.((((.(((......))))))))))..................))))).......)))).. ( -43.14)
>DroSec_CAF1 6300 120 - 1
GUCGGACGCACUGCUCGGCAGGGGAACGAAGGCAACGCCCUUGUGUUUCUCCUGCCCAGCGAGGAUGCCUAUGUGCACUUCCUGAAGAUCAACCAGAAAGUGGAGCUAACUGAACUGCUA
.((((..((((((((.(((((((((((((.(((...))).))))...))))))))).))))(((...)))..))))((((.(((.........))).))))........))))....... ( -40.90)
>DroSim_CAF1 6337 120 - 1
GUAGGCCGCACUGCUCGGCAGGGGAACGAAGGCAACGCCCUGGUGUUUCUCCUGCCCAGCGAGGAUGCCUAUGUGCACUUCCUGAAGAUUAACCAGAAAGUGGAGCUAACUGAACUGUUA
((((((..(..((((.((((((((((((.(((......)))..)))))).)))))).))))..)..))))))((.(((((.(((.........))).)))))..))((((......)))) ( -43.60)
>DroEre_CAF1 6344 120 - 1
GUGGGACGCACUGCUCGACAGGGAAACGAGGGCAACGCUCUGGUGUUUCUCCUGCCCAGCGAAGAUGCUUAUGUGCACUUCCUGAAGAUCAAUCAGAAGGUGGAGCUAACUAAACUGCUC
(..(........((((.((((((((((((((((...)))))..)))))).)))...(((.((((.(((......))))))))))...............)).))))........)..).. ( -36.39)
>DroYak_CAF1 6301 120 - 1
GUGGGACGCACUGCUCGGCAGGGAAACGAGGGCAAUGCCCUGGUGUUUCUCCUGCCCAGCGAGGAUGCUUAUGUGCAUUUCUUGAAGAUCAACCAAAAGGUGGAGUUAACUGAACUGCUU
(((((.((..(((((.(((((((((((((((((...)))))..)))))).)))))).))).))..)))))))..(((.(((.......((.(((....))).)).......))).))).. ( -44.44)
>consensus
GUAGGACGCACUGCUCGGCAGGGAAACGAGGGCAACGCCCUGGUGUUUCUCCUGCCCAGCGAGGAUGCCUAUGUGCACUUCCUGAAGAUCAACCAGAAAGUGGAGCUAACUGAACUGCUA
((((........(((((((((((((((((((((...)))))..)))))).))))))(((.((((.(((......))))))))))..................))))........)))).. (-37.87 = -37.23 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,094,422 – 4,094,542
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -45.30
Consensus MFE -42.88
Energy contribution -42.76
Covariance contribution -0.12
Combinations/Pair 1.16
Mean z-score -1.29
Structure conservation index 0.95
SVM decision value 0.96
SVM RNA-class probability 0.890447
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094422 120 + 27905053
AAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGAGCGUUGCCCUCGUUUCCCUGCCGAGCCGUGCGACCUACACGGUGUACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAC
.......(((..((..(((((((.((((((.(((((...((.((...)).)).))))))))))).))).((((.(((.....))))))).......))))..))..)))((((...)))) ( -42.90)
>DroSec_CAF1 6340 120 + 1
AAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACAAGGGCGUUGCCUUCGUUCCCCUGCCGAGCAGUGCGUCCGACACGGUGUACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAC
.......(((..((..(((((((.((((((.(((.....(((((...)))))..))).)))))).))).(((((.(((...)))))))).......))))..))..)))((((...)))) ( -44.90)
>DroSim_CAF1 6377 120 + 1
AAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCGUUGCCUUCGUUCCCCUGCCGAGCAGUGCGGCCUACACGGUGUACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAC
..((((((.(((((...((.(((.((((((.(((.....(((((...)))))..))).)))))).)))))....)))))....))))))..(((((....)))))....((((...)))) ( -46.80)
>DroEre_CAF1 6384 120 + 1
AAGUGCACAUAAGCAUCUUCGCUGGGCAGGAGAAACACCAGAGCGUUGCCCUCGUUUCCCUGUCGAGCAGUGCGUCCCACACGGUGCACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAU
((.(((.....(((......(((.((((((.(((((...((.((...)).)).))))))))))).))).(((((.((.....)))))))...)))....))).)).((((......)))) ( -40.70)
>DroYak_CAF1 6341 120 + 1
AAAUGCACAUAAGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCAUUGCCCUCGUUUCCCUGCCGAGCAGUGCGUCCCACACGAUGUACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAU
..((.(((...(((..(((((((.((((((.(((((...(((((...))))).))))))))))).))).(((((((......))))))).......))))..)))....))).))..... ( -51.20)
>consensus
AAGUGCACAUAGGCAUCCUCGCUGGGCAGGAGAAACACCAGGGCGUUGCCCUCGUUUCCCUGCCGAGCAGUGCGUCCCACACGGUGUACAAAGCUGGAGGCAGUUGAUGGUGGAUCCCAC
..((.(((...(((..(((((((.((((((.(((((...(((((...))))).))))))))))).))).(((((.((.....))))))).......))))..)))....))).))..... (-42.88 = -42.76 +  -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 10:09:22 2006