Locus 4683

Sequence ID 2R_DroMel_CAF1
Location 15,323,395 – 15,323,524
Length 129
Max. P 0.973059
window7535 window7536 window7537

overview

Window 5

Location 15,323,395 – 15,323,487
Length 92
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 79.07
Mean single sequence MFE -26.01
Consensus MFE -13.99
Energy contribution -13.88
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.54
SVM decision value 0.28
SVM RNA-class probability 0.664712
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15323395 92 - 20766785
UGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCUCGGCCAACCCCCGAAACAUUUUGCCGGGG-----CAAAGGAGAUGCAGACGGA----
(((((((((((((....))))))))))))).......(((.((((..((...(((((...........)))))-----....)).)).))..)))..---- ( -28.50)
>DroPse_CAF1 154931 97 - 1
AGUAAAUUAUGCAUAGAUGGAUAAUUUAUAACUUAUGCGUGGCAGUGCCAACCCCCGAAACAUUUUGCAUGGUACGCUGACGGGGGAAUCAGGCGGA----
.(((((((((.((....)).)))))))))......(((.((((...)))).((((((...((....((.......)))).))))))......)))..---- ( -24.80)
>DroEre_CAF1 116050 91 - 1
UGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCUC-GCCAACCCCCGAAACAUUUUGCCCUGG-----CAAAGGAGAUGCAGACGGA----
(((((((((((((....))))))))))))).((..(((((((...-.)).............((((((....)-----)))))...)))))...)).---- ( -25.50)
>DroWil_CAF1 257462 98 - 1
UGUAAAUUAUGCAUAGAGGCAUAAUUUAUAACUUAUGCGUGGCAUAGCCAACCCUCGAAACAUUUCGCAAUGCACACGCA---GAGAGACGGACGGACAUU
((((((((((((......)))))))))))).(((.((((((((((.((..................)).)))).))))))---..)))............. ( -28.57)
>DroAna_CAF1 103151 80 - 1
UGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCUCGGCCAACCCCCGAAACAUUUCGCCAGAG-----------------ACACGGA----
(((((((((((((....))))))))))))).......((((.((((((..................))).)))-----------------.))))..---- ( -23.87)
>DroPer_CAF1 113893 97 - 1
AGUAAAUUAUGCAUAGAUGGAUAAUUUAUAACUUAUGCGUGGCAGUGCCAACCCCCGAAACAUUUUGCAUGGUACGCUGACGGGGGAAUCAGGCGGA----
.(((((((((.((....)).)))))))))......(((.((((...)))).((((((...((....((.......)))).))))))......)))..---- ( -24.80)
>consensus
UGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCACGGCCAACCCCCGAAACAUUUUGCAAGGG_____CA__GGAGAAGCAGACGGA____
.(((((((((((......)))))))))))........((((((...)))......((((....)))).........................)))...... (-13.99 = -13.88 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,323,426 – 15,323,524
Length 98
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.43
Mean single sequence MFE -29.07
Consensus MFE -15.34
Energy contribution -15.73
Covariance contribution 0.39
Combinations/Pair 1.09
Mean z-score -1.97
Structure conservation index 0.53
SVM decision value 0.55
SVM RNA-class probability 0.777255
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15323426 98 + 20766785
GU--UUCGGGGG--UUG-----------G--CCGAGCCACGCAUAAGUUAUAAAUUAUGCAUCUAUGCAUAAUUUACAGCCAGUAAGGUCA---GACAGUUGCAUUUGCCAGUUCAGU
..--.....(..--(((-----------(--(.((((.((..........(((((((((((....)))))))))))..(((.....)))..---....)).)).)).)))))..)... ( -26.20)
>DroVir_CAF1 161056 98 + 1
GU--AUCGGAGG--UUC-----------GGCCCCAGCCACGCAUAAGUUAUAAAUUAUGCAUAGAUGCAUAAUUUACAGCUCGUAAGGUCA---GACAGUUGCAUUUGCCAA--CAGC
..--.......(--(..-----------((((...((...))(..((((.(((((((((((....))))))))))).))))..)..)))).---.)).(((((....).)))--)... ( -24.40)
>DroPse_CAF1 154967 98 + 1
GU--UUCGGGGG--UUG-----------G--CACUGCCACGCAUAAGUUAUAAAUUAUCCAUCUAUGCAUAAUUUACUGCCCGAAAGGUCA---GACAGUUGUAUUUGCCAUUUCCCU
..--...(((((--.((-----------(--((.(((.((..........((((((((.((....)).))))))))(((.((....)).))---)...)).)))..))))).))))). ( -29.30)
>DroGri_CAF1 134175 116 + 1
GUUUUUGGGGGAGGUUGGCUGGUUGGUUGGUCCCUGCCACGCAUAAGUUAUAAAUUAUGCAUAGAUGCAUAAUUUACAGCUUGUAAGGUCAGCAGACAGUUGCAUUUGCCAA--CCCU
.........((.(((((((((((.((......)).)))).(((((((((.(((((((((((....))))))))))).)))))))...(((....)))....))....)))))--)))) ( -40.90)
>DroWil_CAF1 257499 95 + 1
GU--UUCGAGGG--UUG-----------G--CUAUGCCACGCAUAAGUUAUAAAUUAUGCCUCUAUGCAUAAUUUACAGCUCGUAAGGUCA---GACAGUUGCAUUUGCUAGCCC---
..--.....(((--(((-----------(--(.((((.((.....((((.((((((((((......)))))))))).))))(....)....---....)).))))..))))))))--- ( -31.20)
>DroMoj_CAF1 164833 89 + 1
GU--UUCGGGGGGUUUG-----------GGUCCCA-----------GUUAUAAAUUAUGCAUAGAUGCAUAAUUUACAGCUCGUAAGGUCA---GACAGUUGCAUUUGCCAA--CAGU
((--((.((((((....-----------..))))(-----------(((.(((((((((((....))))))))))).)))).......)))---))).(((((....).)))--)... ( -22.40)
>consensus
GU__UUCGGGGG__UUG___________G__CCCAGCCACGCAUAAGUUAUAAAUUAUGCAUAGAUGCAUAAUUUACAGCUCGUAAGGUCA___GACAGUUGCAUUUGCCAA__CAGU
.......((.....................................(((.((((((((((......)))))))))).)))..((((.(((....)))..)))).....))........ (-15.34 = -15.73 +   0.39)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,323,426 – 15,323,524
Length 98
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.43
Mean single sequence MFE -28.45
Consensus MFE -13.32
Energy contribution -15.23
Covariance contribution 1.92
Combinations/Pair 1.08
Mean z-score -2.80
Structure conservation index 0.47
SVM decision value 1.70
SVM RNA-class probability 0.973059
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15323426 98 - 20766785
ACUGAACUGGCAAAUGCAACUGUC---UGACCUUACUGGCUGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCUCGG--C-----------CAA--CCCCCGAA--AC
.......((((..(((((...(((---..........)))(((((((((((((....))))))))))))).....)))))......)--)-----------)).--........--.. ( -24.00)
>DroVir_CAF1 161056 98 - 1
GCUG--UUGGCAAAUGCAACUGUC---UGACCUUACGAGCUGUAAAUUAUGCAUCUAUGCAUAAUUUAUAACUUAUGCGUGGCUGGGGCC-----------GAA--CCUCCGAU--AC
..((--((((...(((((...((.---.......))(((.(((((((((((((....))))))))))))).))).)))))(((....)))-----------...--...)))))--). ( -27.10)
>DroPse_CAF1 154967 98 - 1
AGGGAAAUGGCAAAUACAACUGUC---UGACCUUUCGGGCAGUAAAUUAUGCAUAGAUGGAUAAUUUAUAACUUAUGCGUGGCAGUG--C-----------CAA--CCCCCGAA--AC
.(((...(((((..(((.((((((---(((....)))))))))(((((((.((....)).)))))))...........)))....))--)-----------)).--..)))...--.. ( -30.90)
>DroGri_CAF1 134175 116 - 1
AGGG--UUGGCAAAUGCAACUGUCUGCUGACCUUACAAGCUGUAAAUUAUGCAUCUAUGCAUAAUUUAUAACUUAUGCGUGGCAGGGACCAACCAACCAGCCAACCUCCCCCAAAAAC
.(((--(((((..(((((...(((....))).....(((.(((((((((((((....))))))))))))).))).)))))((..((......))..)).))))))))........... ( -39.90)
>DroWil_CAF1 257499 95 - 1
---GGGCUAGCAAAUGCAACUGUC---UGACCUUACGAGCUGUAAAUUAUGCAUAGAGGCAUAAUUUAUAACUUAUGCGUGGCAUAG--C-----------CAA--CCCUCGAA--AC
---.(((((((..(((((...((.---.......))(((.((((((((((((......)))))))))))).))).))))).)).)))--)-----------)..--........--.. ( -27.80)
>DroMoj_CAF1 164833 89 - 1
ACUG--UUGGCAAAUGCAACUGUC---UGACCUUACGAGCUGUAAAUUAUGCAUCUAUGCAUAAUUUAUAAC-----------UGGGACC-----------CAAACCCCCCGAA--AC
...(--(..(((........)).)---..))....((((.(((((((((((((....))))))))))))).)-----------)(((...-----------.....))).))..--.. ( -21.00)
>consensus
ACUG__UUGGCAAAUGCAACUGUC___UGACCUUACGAGCUGUAAAUUAUGCAUAGAUGCAUAAUUUAUAACUUAUGCGUGGCAGGG__C___________CAA__CCCCCGAA__AC
.........((..(((((...(((....))).....(((.((((((((((((......)))))))))))).))).))))).))................................... (-13.32 = -15.23 +   1.92)

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 11:26:42 2006