Locus 296

Sequence ID X_DroMel_CAF1
Location 970,942 – 971,047
Length 105
Max. P 0.976183
window446 window447 window448 window449

overview

Window 6

Location 970,942 – 971,033
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.22
Mean single sequence MFE -20.43
Consensus MFE -12.29
Energy contribution -14.53
Covariance contribution 2.24
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.60
SVM decision value 1.61
SVM RNA-class probability 0.967502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 970942 91 + 22224390
--------------------CACACAU--------GGAGAGCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAA
--------------------.......--------...((((((.................(((((.................)))))..(((((((.....)))))))))))))-.... ( -22.43)
>DroSec_CAF1 53884 91 + 1
--------------------CACACAU--------GGAGAGCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAA
--------------------.......--------...((((((.................(((((.................)))))..(((((((.....)))))))))))))-.... ( -22.43)
>DroEre_CAF1 66976 91 + 1
--------------------CACACAU--------GGAGAGCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAA
--------------------.......--------...((((((.................(((((.................)))))..(((((((.....)))))))))))))-.... ( -22.43)
>DroYak_CAF1 58687 92 + 1
A-------------------CACACAU--------GGAGAGCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAA
.-------------------.......--------...((((((.................(((((.................)))))..(((((((.....)))))))))))))-.... ( -22.43)
>DroMoj_CAF1 113309 120 + 1
ACACAGAUAGAGCACAUACACCCAUAUAAAGUAGCCGAAAGCAAAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAAAAGUGGUCGCCACUCUCGAA
.....((.((.((((.(((...........)))(.(....))...))))............(((((.................)))))..(((((((.....)))))))...)).))... ( -22.53)
>DroAna_CAF1 43037 75 + 1
--------------------GAGUCCU---------GGCAGCCGAGUGCAUGAAUAUUUCACAAGGAUAAAUAAGGAUAAAAACUUGAAGCCACUA------------GCCACUU-G---
--------------------......(---------(((..((..(((.(........))))..)).....((((........))))..))))...------------.......-.--- ( -10.30)
>consensus
____________________CACACAU________GGAGAGCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU_GAAA
......................................((((((.................(((((.................)))))..(((((((.....)))))))))))))..... (-12.29 = -14.53 +   2.24) 

alignment

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secondary structure

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dotplot

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Window 7

Location 970,942 – 971,033
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.22
Mean single sequence MFE -20.06
Consensus MFE -14.73
Energy contribution -15.06
Covariance contribution 0.32
Combinations/Pair 1.26
Mean z-score -2.01
Structure conservation index 0.73
SVM decision value 1.76
SVM RNA-class probability 0.976183
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 970942 91 - 22224390
UUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGCUCUCC--------AUGUGUG--------------------
....-.(((((.((((((.....))))))((.((((..((((((..............))))))..)))).))...)))))....--------.......-------------------- ( -19.84)
>DroSec_CAF1 53884 91 - 1
UUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGCUCUCC--------AUGUGUG--------------------
....-.(((((.((((((.....))))))((.((((..((((((..............))))))..)))).))...)))))....--------.......-------------------- ( -19.84)
>DroEre_CAF1 66976 91 - 1
UUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGCUCUCC--------AUGUGUG--------------------
....-.(((((.((((((.....))))))((.((((..((((((..............))))))..)))).))...)))))....--------.......-------------------- ( -19.84)
>DroYak_CAF1 58687 92 - 1
UUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGCUCUCC--------AUGUGUG-------------------U
....-.(((((.((((((.....))))))((.((((..((((((..............))))))..)))).))...)))))....--------.......-------------------. ( -19.84)
>DroMoj_CAF1 113309 120 - 1
UUCGAGAGUGGCGACCACUUUUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUUUGCUUUCGGCUACUUUAUAUGGGUGUAUGUGCUCUAUCUGUGU
....((((((((((((((.....)))))))))(((((....((....)).....))))).........(((((((((.((.....))..........))))))))).)))))........ ( -29.70)
>DroAna_CAF1 43037 75 - 1
---C-AAGUGGC------------UAGUGGCUUCAAGUUUUUAUCCUUAUUUAUCCUUGUGAAAUAUUCAUGCACUCGGCUGCC---------AGGACUC--------------------
---.-..(..((------------(((((.....(((........)))..........((((.....)))).)))).)))..).---------.......-------------------- ( -11.30)
>consensus
UUUC_AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGCUCUCC________AUGUGUG____________________
......(((((.((((((.....))))))((.((((..((((((..............))))))..)))).))...)))))....................................... (-14.73 = -15.06 +   0.32) 

alignment

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secondary structure

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Window 8

Location 970,954 – 971,047
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -24.78
Consensus MFE -18.47
Energy contribution -18.45
Covariance contribution -0.03
Combinations/Pair 1.10
Mean z-score -2.26
Structure conservation index 0.75
SVM decision value 0.57
SVM RNA-class probability 0.784816
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 970954 93 + 22224390
GCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAAGUGGACC------AA------CAGCA--------------
((......(((((.....)))))...........((..............(((((((.....)))))))(..((.-...))..).))------..------..)).-------------- ( -20.70)
>DroVir_CAF1 115647 119 + 1
GCAAAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAAAAGUGGUCGCCGCUC-CGAAAUGGACCUGGGCCAAAGGAUGCAGCAUCAGCACCAGCAGC
((...((((.(((........(((((.................)))))...((((((.....))))))((.((((-(....(((.(....))))..))).)).)).)))))))..))... ( -33.93)
>DroSec_CAF1 53896 93 + 1
GCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAAGUGGACC------AA------CAGCA--------------
((......(((((.....)))))...........((..............(((((((.....)))))))(..((.-...))..).))------..------..)).-------------- ( -20.70)
>DroEre_CAF1 66988 93 + 1
GCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAAGUGGACC------AA------CAGCA--------------
((......(((((.....)))))...........((..............(((((((.....)))))))(..((.-...))..).))------..------..)).-------------- ( -20.70)
>DroYak_CAF1 58700 93 + 1
GCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU-GAAAGUGGACC------AG------CAGCA--------------
((.....))............(((((.................)))))...((((((.....))))))((((((.-(........).------))------)))).-------------- ( -23.73)
>DroMoj_CAF1 113349 114 + 1
GCAAAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAAAAGUGGUCGCCACUCUCGAAAUGGAGCUGGACCAAAGUGUGCAGCAUCAA------CGGC
((...((((.((.(((((((.(((((.................)))))..(((((((.....)))))))(((((((......)))).)))...))))))).))))))...------..)) ( -28.93)
>consensus
GCAGAGUGCAUGAAUAUUUUAUGAAGAUAAAUAAGGAUAAAAACUUCAAACGACCACGAUAAGUGGUCGCUGCUU_GAAAGUGGACC______AA______CAGCA______________
......(((............(((((.................)))))..(((((((.....)))))))(((((.....)))))...................))).............. (-18.47 = -18.45 +  -0.03) 

alignment

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secondary structure

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dotplot

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Window 9

Location 970,954 – 971,047
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -25.96
Consensus MFE -18.33
Energy contribution -17.97
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 0.75
SVM RNA-class probability 0.842139
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 970954 93 - 22224390
--------------UGCUG------UU------GGUCCACUUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGC
--------------.((((------((------((.......))-.))))))((((((.....))))))((.((((..((((((..............))))))..)))).))....... ( -21.74)
>DroVir_CAF1 115647 119 - 1
GCUGCUGGUGCUGAUGCUGCAUCCUUUGGCCCAGGUCCAUUUCG-GAGCGGCGACCACUUUUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUUUGC
...((.((((((((.(((((.(((..((((....).)))....)-)))))))((((((.....))))))...(((((....((....)).....)))))........))).)))))..)) ( -37.00)
>DroSec_CAF1 53896 93 - 1
--------------UGCUG------UU------GGUCCACUUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGC
--------------.((((------((------((.......))-.))))))((((((.....))))))((.((((..((((((..............))))))..)))).))....... ( -21.74)
>DroEre_CAF1 66988 93 - 1
--------------UGCUG------UU------GGUCCACUUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGC
--------------.((((------((------((.......))-.))))))((((((.....))))))((.((((..((((((..............))))))..)))).))....... ( -21.74)
>DroYak_CAF1 58700 93 - 1
--------------UGCUG------CU------GGUCCACUUUC-AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGC
--------------.((((------((------((.......))-.))))))((((((.....))))))((.((((..((((((..............))))))..)))).))....... ( -24.14)
>DroMoj_CAF1 113349 114 - 1
GCCG------UUGAUGCUGCACACUUUGGUCCAGCUCCAUUUCGAGAGUGGCGACCACUUUUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUUUGC
..((------.((..((((.((......)).))))..))...))((((((((((((((.....)))))))).(((((....((....)).....))))).............)))))).. ( -29.40)
>consensus
______________UGCUG______UU______GGUCCACUUUC_AAGCAGCGACCACUUAUCGUGGUCGUUUGAAGUUUUUAUCCUUAUUUAUCUUCAUAAAAUAUUCAUGCACUCUGC
...............................................(((((((((((.....)))))))).(((((....((....)).....)))))...........)))....... (-18.33 = -17.97 +  -0.36) 

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 09:41:04 2006