Locus 4570

Sequence ID 3L_DroMel_CAF1
Location 13,120,245 – 13,120,421
Length 176
Max. P 0.974533
window7144 window7145 window7146

overview

Window 4

Location 13,120,245 – 13,120,345
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.87
Mean single sequence MFE -27.90
Consensus MFE -20.98
Energy contribution -21.14
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -1.73
Structure conservation index 0.75
SVM decision value 0.31
SVM RNA-class probability 0.683973
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13120245 100 - 23771897
AAUGGGGCCAAAAGGGUUCA-ACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUACGAA-UCCCAAUUAUGACGUUCAAAGUGCU------------------GUGCAUACUAAGCCAUAAA
.((((.((((....((((((-....))))))((....))))))...((((.......-))))................((((.------------------..))))......))))... ( -25.20)
>DroSec_CAF1 108171 100 - 1
AAUGGGGCCAAAAGGGUUCA-ACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUACGAA-UCCCAAUUAUGAUGUUCAAAGUGUU------------------GAGCAUACUAAGCCAUAAA
.((((.((((....((((((-....))))))((....))))))...((((.......-)))).......((((((((....))------------------))))))......))))... ( -30.50)
>DroSim_CAF1 106322 100 - 1
AAUGGAGCCAAAAGGGUUCA-ACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUACGAA-UCCCAAUUAUGAUGCUCAAAGUGCU------------------GUGCAUACUAAGCCAUAAA
.((((.((((....((((((-....))))))((....))))))...((((.......-)))).......((((.((......)------------------).))))......))))... ( -28.20)
>DroEre_CAF1 104918 96 - 1
AAUGGGGCCAAAAGGGUUCU-ACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUACGAA-CCCCAAUUAUGAUGUUCAAAGUACUU-------------------GCAUACUAAGCUAU---
..(((((((....))(((((-..(((.(((.......))).)))...))))).....-)))))..((((..((.......))..-------------------.)))).........--- ( -21.10)
>DroYak_CAF1 108288 120 - 1
AAUGGGGCCAAAAGGGUUCAAACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUUCGUAUUCCCAAUUAUGAUGUUCAAAGUGCUCCGCAUACUGAACAUACUGAGCAUACUAAGCUAAAAA
......((((....((((((.....))))))((....))))))...((((((....)))))).......(((((((..((((...))))..)))))))....(((.......)))..... ( -34.50)
>consensus
AAUGGGGCCAAAAGGGUUCA_ACUGUGAGCCGCAUUUGCUGGCAAAGGGAAUACGAA_UCCCAAUUAUGAUGUUCAAAGUGCU__________________GAGCAUACUAAGCCAUAAA
.((((.((((....(((((.......)))))((....))))))...((((........))))...................................................))))... (-20.98 = -21.14 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,120,267 – 13,120,385
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.97
Mean single sequence MFE -28.53
Consensus MFE -25.04
Energy contribution -25.08
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 0.88
SVM decision value 1.73
SVM RNA-class probability 0.974533
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13120267 118 + 23771897
ACUUUGAACGUCAUAAUUGGGA-UUCGUAUUCCCUUUGCCAGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
...((((..((((.....(((.-((((..........(((.((....))))).......-)))))))...))))...((((((((((........)))))))))).)))).......... ( -27.43)
>DroSec_CAF1 108193 118 + 1
ACUUUGAACAUCAUAAUUGGGA-UUCGUAUUCCCUUUGCCAGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
....(((...........((((-.......))))...(((.((....)))))))).(((-(((..((....))....((((((((((........)))))))))).))))))........ ( -26.70)
>DroSim_CAF1 106344 118 + 1
ACUUUGAGCAUCAUAAUUGGGA-UUCGUAUUCCCUUUGCCAGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCUCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
....(((((.........((((-.......)))).......((....)).))))).(((-(((..((....))....((((((((((........)))))))))).))))))........ ( -28.90)
>DroEre_CAF1 104936 118 + 1
ACUUUGAACAUCAUAAUUGGGG-UUCGUAUUCCCUUUGCCAGCAAAUGCGGCUCACAGU-AGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
.............(((((((((-(((.((((......(((.((....)))))....)))-)))))))..........((((((((((........))))))))))..))))))....... ( -30.10)
>DroYak_CAF1 108328 120 + 1
ACUUUGAACAUCAUAAUUGGGAAUACGAAUUCCCUUUGCCAGCAAAUGCGGCUCACAGUUUGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
....(((...........((((((....))))))...(((.((....))))))))..(((((...((....))....((((((((((........))))))))))........))))).. ( -29.50)
>consensus
ACUUUGAACAUCAUAAUUGGGA_UUCGUAUUCCCUUUGCCAGCAAAUGCGGCUCACAGU_UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAA
...((((...........((((........))))...((((((....))((.(((.....))).))....))))...((((((((((........)))))))))).)))).......... (-25.04 = -25.08 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,120,306 – 13,120,421
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.02
Mean single sequence MFE -24.20
Consensus MFE -17.60
Energy contribution -17.12
Covariance contribution -0.48
Combinations/Pair 1.09
Mean z-score -2.60
Structure conservation index 0.73
SVM decision value 1.15
SVM RNA-class probability 0.922601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13120306 115 + 23771897
AGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAGGCCCACGCCCACACACACCU---ACAAC-CAAACAU
.((....))((((...(((-((.......((((....((((((((((........)))))))))).)))).......))))).)))).................---.....-....... ( -22.54)
>DroSec_CAF1 108232 116 + 1
AGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAGGCCCACGCCCACACACACCU---ACACCCCACGCAU
.....((((((((...(((-(((..((....))....((((((((((........)))))))))).))))))...))).....(((....)))...........---........))))) ( -27.00)
>DroSim_CAF1 106383 116 + 1
AGCAAAUGCGGCUCACAGU-UGAACCCUUUUGGCUCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAGGCCCACGCCCACACACACCU---ACACCCCACGCAU
.....((((((((...(((-(((..((....))....((((((((((........)))))))))).))))))...))).....(((....)))...........---........))))) ( -27.00)
>DroEre_CAF1 104975 103 + 1
AGCAAAUGCGGCUCACAGU-AGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAGG------CCCACACA---------CAC-CUACACAU
.((....))........((-((.........((((..((((((((((........))))))))))..........((...)).))------))......---------...-)))).... ( -19.57)
>DroYak_CAF1 108368 119 + 1
AGCAAAUGCGGCUCACAGUUUGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAUGGCCAAGCCAACACAUACCCCAUCCAC-CUGCACAU
......(((((......(((((...((....))....((((((((((........))))))))))........))))).....((((...)))).................-)))))... ( -24.90)
>consensus
AGCAAAUGCGGCUCACAGU_UGAACCCUUUUGGCCCCAUUAGGCUGCCACUCACAGCAGUUUAAUAUCAAUUACAAGCAACUAGGCCCACGCCCACACACACCU___ACACCCCACACAU
......(((((((.(.((........)).).))))..((((((((((........))))))))))...........)))....((.......)).......................... (-17.60 = -17.12 +  -0.48)

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 11:26:57 2006