Locus 3150

Sequence ID X_DroMel_CAF1
Location 8,368,337 – 8,368,495
Length 158
Max. P 0.999282
window5161 window5162 window5163

overview

Window 1

Location 8,368,337 – 8,368,457
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.54
Mean single sequence MFE -26.33
Consensus MFE -18.48
Energy contribution -18.80
Covariance contribution 0.32
Combinations/Pair 1.17
Mean z-score -1.66
Structure conservation index 0.70
SVM decision value 0.53
SVM RNA-class probability 0.772146
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8368337 120 + 22224390
UUAGUUUGAUGAAUAUCUUAUACUUCUUUUUUUUUUUUUUUAGUUUUUUGUUCGUGUUGUGGGGCUACUAAACUUCCGUUUAGUGCGUUAGUUGGCCCGCUUUAAAUGUGGUUAAACUGA
(((((((((((((((......(((.................)))....))))).((..(((((.(.(((((((....)))))))((....)).).)))))..))......)))))))))) ( -24.83)
>DroSec_CAF1 33491 109 + 1
UUAGUUUGAUGAAUAUCUUAUUCUUAUU----UUAU-------UUUUUCGGUCGUGUUGUGGGGCCACUAAACUUCCGUUUAGUGCGUUAGUUGGCCCGCUUUAAAUGUGGUUAAGCUGA
(((((((((((((((...))))).....----....-------.........((..((..(((((((....(((..(((.....)))..))))))))).)....))..)))))))))))) ( -26.90)
>DroSim_CAF1 36696 113 + 1
UUAGUUUGAUGAAUAUCUUAUUCUUAUUUGUUUUUU-------UUUUUCGGUCGUGUUGUGGGGCCACUAAACUUCCGUUUAGUGCGUUAGUUGGCCCGCUUUAAAUGUGGUUAAACUGA
(((((((((((((((...))))).............-------.........((..((..(((((((....(((..(((.....)))..))))))))).)....))..)))))))))))) ( -26.90)
>DroEre_CAF1 30162 96 + 1
UUACUGUGAUGAAUAUUCC--------U----CAUU-------UUUAGCC---GUGUUGCG-GGCC-UAAAAGUUUCGUUUAGUGCGCUAGUUGGCCCGCUUUAAAUGUGGUUAAGCUGA
.....((((.((....)).--------)----))).-------(((((((---(..(((((-((((-....((...(((.....)))))....)))))))....))..)))))))).... ( -27.20)
>DroYak_CAF1 32466 100 + 1
UUAGUUUGAUGAGUAUCCU--------U----UUGU-------UUUGGCGUUGGUGUUGUGGGGCC-CAAAACUUCCGCUUAGUGCGUUAGUUGGCCCGCUUUAAAUGUGGUUAAAUGGA
...............(((.--------(----(((.-------..(.(((((......(((((.((-...((((..(((.....)))..)))))))))))....))))).).)))).))) ( -25.80)
>consensus
UUAGUUUGAUGAAUAUCUUAU_CUU_UU____UUUU_______UUUUUCGGUCGUGUUGUGGGGCCACUAAACUUCCGUUUAGUGCGUUAGUUGGCCCGCUUUAAAUGUGGUUAAACUGA
((((((((((...................................................(((((....((((..(((.....)))..)))))))))((.......)).)))))))))) (-18.48 = -18.80 +   0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,368,337 – 8,368,457
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.54
Mean single sequence MFE -20.93
Consensus MFE -11.86
Energy contribution -13.30
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -3.10
Structure conservation index 0.57
SVM decision value 3.04
SVM RNA-class probability 0.998220
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8368337 120 - 22224390
UCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUAGCCCCACAACACGAACAAAAAACUAAAAAAAAAAAAAAAGAAGUAUAAGAUAUUCAUCAAACUAA
..(((((.............(.((((...(....).(((((((....))))))).)))))...........................................(((....)))))))).. ( -18.80)
>DroSec_CAF1 33491 109 - 1
UCAGCUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGACCGAAAAA-------AUAA----AAUAAGAAUAAGAUAUUCAUCAAACUAA
((.((((...........))))(((((..(....).(((((((....))))))))))))............))....-------....----.....(((((...))))).......... ( -23.60)
>DroSim_CAF1 36696 113 - 1
UCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGACCGAAAAA-------AAAAAACAAAUAAGAAUAAGAUAUUCAUCAAACUAA
..(((((.............(.(((((..(....).(((((((....))))))))))))).................-------.............(((((...)))))...))))).. ( -24.10)
>DroEre_CAF1 30162 96 - 1
UCAGCUUAACCACAUUUAAAGCGGGCCAACUAGCGCACUAAACGAAACUUUUA-GGCC-CGCAACAC---GGCUAAA-------AAUG----A--------GGAAUAUUCAUCACAGUAA
....................(((((((......((.......)).........-))))-))).....---.(((...-------.(((----(--------(.....)))))...))).. ( -17.86)
>DroYak_CAF1 32466 100 - 1
UCCAUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAGCGGAAGUUUUG-GGCCCCACAACACCAACGCCAAA-------ACAA----A--------AGGAUACUCAUCAAACUAA
(((.(((((......)))))(.(((((((((..(((.....)))..))))...-)))))).................-------....----.--------.)))............... ( -20.30)
>consensus
UCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGAACGAAAAA_______AAAA____AA_AAG_AUAAGAUAUUCAUCAAACUAA
......................(((((..(....).(((((((....))))))))))))............................................................. (-11.86 = -13.30 +   1.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,368,377 – 8,368,495
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.26
Mean single sequence MFE -23.85
Consensus MFE -11.86
Energy contribution -13.30
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -3.22
Structure conservation index 0.50
SVM decision value 3.48
SVM RNA-class probability 0.999282
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8368377 118 - 22224390
UAAUAUCCACACUAUAUCCACAACAUACGCUAG--UAUCCUCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUAGCCCCACAACACGAACAAAAAACUA
........................((((....)--)))....(((((...............((((...(....).(((((((....))))))).))))...............))))). ( -18.11)
>DroSec_CAF1 33523 106 - 1
---------CACUAUAUCCCCACCAUACGCUAG--UAUCCUCAGCUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGACCGAAAAA---
---------...............((((....)--)))..((.((((...........))))(((((..(....).(((((((....))))))))))))............))....--- ( -23.40)
>DroSim_CAF1 36732 108 - 1
---------CACCAUAUCCCCACCAUACGCUAGUGUAUCCUCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGACCGAAAAA---
---------..................((...((((.......((((...........))))(((((..(....).(((((((....))))))))))))....))))...)).....--- ( -25.20)
>DroEre_CAF1 30186 98 - 1
----------A-CAUGGCCCCACCAUAUA---GCAUAUCCUCAGCUUAACCACAUUUAAAGCGGGCCAACUAGCGCACUAAACGAAACUUUUA-GGCC-CGCAACAC---GGCUAAA---
----------.-..(((((.........(---((.........)))..............(((((((......((.......)).........-))))-))).....---)))))..--- ( -22.56)
>DroYak_CAF1 32490 106 - 1
UGAUAU----G-CAUAGCCAC---AUAUAU--GCAUAUCCUCCAUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAGCGGAAGUUUUG-GGCCCCACAACACCAACGCCAAA---
.(((((----(-((((.....---...)))--))))))).....................(.(((((((((..(((.....)))..))))...-)))))).................--- ( -30.00)
>consensus
_________CACCAUAUCCCCACCAUACGCUAG__UAUCCUCAGUUUAACCACAUUUAAAGCGGGCCAACUAACGCACUAAACGGAAGUUUAGUGGCCCCACAACACGAACGAAAAA___
..............................................................(((((..(....).(((((((....))))))))))))..................... (-11.86 = -13.30 +   1.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:18 2006