Locus 4339

Sequence ID X_DroMel_CAF1
Location 11,408,569 – 11,408,718
Length 149
Max. P 0.998467
window7126 window7127 window7128

overview

Window 6

Location 11,408,569 – 11,408,683
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.08
Mean single sequence MFE -33.40
Consensus MFE -21.18
Energy contribution -21.26
Covariance contribution 0.08
Combinations/Pair 1.42
Mean z-score -2.09
Structure conservation index 0.63
SVM decision value 0.49
SVM RNA-class probability 0.756299
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11408569 114 - 22224390
-GGCGGUCAAGCCGUAGUUAAGUACCGACUACGCUCGAUCGCCC----GA-ACGGGAAAGGUGAAUUUAAUAAUAUUAUGUUUGUAUACAGCAAAUAGGUCUCUCAUACAAAAUUCAAUA
-(((((((.(((.((((((.......))))))))).))))))).----..-..........(((((((..........(((((((.....))))))).............)))))))... ( -29.00)
>DroSec_CAF1 1658 115 - 1
-GGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUUGACCGCCC----GAAACGGGAAAGGUGAAUAUAAUAACAUCUAGUUUUUAUACAGCUAAUAGGUCUCUCAUAGAAAAUUCAAUA
-(((((((((((.((((((.......))))))))))))))))).----.....((((..(((...(((((.(((.....))).)))))..)))......))))................. ( -35.10)
>DroSim_CAF1 2585 116 - 1
GGGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUUGACCGCCC----GAAACGGGAAAGGUGAAUUUAAUAACGUCUAGGUUUUAUACAGCUAAUAGGUCUCUCAUAGAAAAUUCAAUA
((((((((((((.((((((.......))))))))))))))))))----.............(((((((.......((((((((......))))..))))(((.....))))))))))... ( -37.70)
>DroEre_CAF1 1563 114 - 1
-GACGGUCGAGCCGUAGUUAAGAACCGACUGCGAUCGACCGCCU-----GAGCGGUAAAGGUGAAUUUAACAAUAUCAAGUCUGCAUACAGCUGAUAGGUCUCUCAUAGAUAAUUCAUUA
-...((((((..(((((((.......))))))).))))))(((.-----....)))...((((((((......(((((.(.(((....))))))))).((((.....)))))))))))). ( -32.30)
>DroYak_CAF1 2628 119 - 1
-GACGGUCGAGCCGUAGUUAAGCACCGACUACGAUCAGGCGGUCGAUCGUAGCGGAGAGGGUGAAUUUAACAAUAUCAAGUCUGCAUACAGCUGAUAGGUCUCUCAUAGAUAAUUCAUUA
-.((((.....)))).........(((.((((((((........)))))))))))....((((((((......(((((.(.(((....))))))))).((((.....)))))))))))). ( -32.90)
>consensus
_GGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUCGACCGCCC____GAAACGGGAAAGGUGAAUUUAAUAAUAUCAAGUUUGUAUACAGCUAAUAGGUCUCUCAUAGAAAAUUCAAUA
.(((((((((((.((((((.......)))))))))))))))))........(((((...((((..........))))...)))))................................... (-21.18 = -21.26 +   0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,408,609 – 11,408,718
Length 109
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 85.54
Mean single sequence MFE -45.08
Consensus MFE -34.37
Energy contribution -36.29
Covariance contribution 1.92
Combinations/Pair 1.13
Mean z-score -2.08
Structure conservation index 0.76
SVM decision value 0.95
SVM RNA-class probability 0.888007
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11408609 109 + 22224390
CAUAAUAUUAUUAAAUUCACCUUUCCCGU-UC----GGGCGAUCGAGCGUAGUCGGUACUUAACUACGGCUUGACCGCC-CCGGAGAUCGGGACGUGCUGGGGGAGCUACCCCCG
.................(((...(((((.-((----(((((.(((((((((((..(...)..))))).)))))).))))-)....)).))))).)))..(((((.....))))). ( -43.60)
>DroSec_CAF1 1698 110 + 1
CUAGAUGUUAUUAUAUUCACCUUUCCCGUUUC----GGGCGGUCAAGCGUAGUCGGUACUUAACUACGGCUCGACCGCC-CCGGGGAUCGGGACGUGCUGGGGGAGCUACCCCCG
.................(((...((((((..(----((((((((.((((((((..(...)..))))).))).)))))))-)..)..).))))).)))..(((((.....))))). ( -47.70)
>DroSim_CAF1 2625 111 + 1
CUAGACGUUAUUAAAUUCACCUUUCCCGUUUC----GGGCGGUCAAGCGUAGUCGGUACUUAACUACGGCUCGACCGCCCCCGGGGAUCGGGACGUGCUGGGGGAGCUACCCCCG
..(((((((..........((.((((((....----((((((((.((((((((..(...)..))))).))).)))))))).))))))..))))))).))(((((.....))))). ( -48.90)
>DroEre_CAF1 1603 109 + 1
CUUGAUAUUGUUAAAUUCACCUUUACCGCUC-----AGGCGGUCGAUCGCAGUCGGUUCUUAACUACGGCUCGACCGUC-CCGGGGAUCGGGACGUGCUGGGGGAGCUACCCCCA
.................(((....(((((..-----..))))).(.(((.(((((...........)))))))).)(((-(((.....)))))))))..(((((.....))))). ( -38.40)
>DroYak_CAF1 2668 114 + 1
CUUGAUAUUGUUAAAUUCACCCUCUCCGCUACGAUCGACCGCCUGAUCGUAGUCGGUGCUUAACUACGGCUCGACCGUC-CCGGGGAUCGGGCCGUGCUGGGGGAGCUACCCCCG
.........(((((...((((......((((((((((......)))))))))).)))).)))))((((((((((((...-....)).))))))))))..(((((.....))))). ( -46.80)
>consensus
CUUGAUAUUAUUAAAUUCACCUUUCCCGUUUC____GGGCGGUCGAGCGUAGUCGGUACUUAACUACGGCUCGACCGCC_CCGGGGAUCGGGACGUGCUGGGGGAGCUACCCCCG
.................(((...(((((.........((((((((((((((((..(...)..))))).))))))))))).........))))).)))..(((((.....))))). (-34.37 = -36.29 +   1.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,408,609 – 11,408,718
Length 109
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 85.54
Mean single sequence MFE -48.96
Consensus MFE -39.41
Energy contribution -40.65
Covariance contribution 1.24
Combinations/Pair 1.17
Mean z-score -3.33
Structure conservation index 0.80
SVM decision value 3.11
SVM RNA-class probability 0.998467
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11408609 109 - 22224390
CGGGGGUAGCUCCCCCAGCACGUCCCGAUCUCCGG-GGCGGUCAAGCCGUAGUUAAGUACCGACUACGCUCGAUCGCCC----GA-ACGGGAAAGGUGAAUUUAAUAAUAUUAUG
.(((((.....)))))..(((.(((((.((....(-(((((((.(((.((((((.......))))))))).))))))))----))-.)))))...)))................. ( -47.70)
>DroSec_CAF1 1698 110 - 1
CGGGGGUAGCUCCCCCAGCACGUCCCGAUCCCCGG-GGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUUGACCGCCC----GAAACGGGAAAGGUGAAUAUAAUAACAUCUAG
.(((((.....)))))..(((.(((((.......(-(((((((((((.((((((.......))))))))))))))))))----....)))))...)))................. ( -52.30)
>DroSim_CAF1 2625 111 - 1
CGGGGGUAGCUCCCCCAGCACGUCCCGAUCCCCGGGGGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUUGACCGCCC----GAAACGGGAAAGGUGAAUUUAAUAACGUCUAG
.(((((.....)))))..(((.(((((..(....)((((((((((((.((((((.......))))))))))))))))))----....)))))...)))................. ( -53.80)
>DroEre_CAF1 1603 109 - 1
UGGGGGUAGCUCCCCCAGCACGUCCCGAUCCCCGG-GACGGUCGAGCCGUAGUUAAGAACCGACUGCGAUCGACCGCCU-----GAGCGGUAAAGGUGAAUUUAACAAUAUCAAG
((((((.....))))))((..((((((.....)))-)))((((((..(((((((.......))))))).))))))....-----..))((((...((.......))..))))... ( -46.80)
>DroYak_CAF1 2668 114 - 1
CGGGGGUAGCUCCCCCAGCACGGCCCGAUCCCCGG-GACGGUCGAGCCGUAGUUAAGCACCGACUACGAUCAGGCGGUCGAUCGUAGCGGAGAGGGUGAAUUUAACAAUAUCAAG
.(((((.....)))))((((((((.(((((.....-...))))).))))).))).....(((.((((((((........))))))))))).((..((.......))....))... ( -44.20)
>consensus
CGGGGGUAGCUCCCCCAGCACGUCCCGAUCCCCGG_GGCGGUCGAGCCGUAGUUAAGUACCGACUACGCUCGACCGCCC____GAAACGGGAAAGGUGAAUUUAAUAAUAUCAAG
.(((((.....)))))..(((.(((((.........(((((((((((.((((((.......))))))))))))))))).........)))))...)))................. (-39.41 = -40.65 +   1.24)

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 11:22:31 2006