Locus 8431

Sequence ID 3R_DroMel_CAF1
Location 22,484,126 – 22,484,257
Length 131
Max. P 0.920261
window13573 window13574 window13575

overview

Window 3

Location 22,484,126 – 22,484,225
Length 99
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 82.52
Mean single sequence MFE -28.27
Consensus MFE -17.97
Energy contribution -17.63
Covariance contribution -0.33
Combinations/Pair 1.24
Mean z-score -3.56
Structure conservation index 0.64
SVM decision value 1.13
SVM RNA-class probability 0.920261
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22484126 99 + 27905053
CCCAACAUUUAGUUCUCUGCUGGCGUGGGCCU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
..(((.(..(((((..(.((..((((((((((---........))))).)))))(((((((((.......)))))))))...)))..)))))..).)))... ( -31.00)
>DroVir_CAF1 190292 95 + 1
U-AUGCAUUUA--UCUGCGCUGGCUUGUGUCU---GGCACAA-UGGUCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
.-..(((....--..)))((..((....).).---.))....-((((..((((((((((((((.......))))))))).)))))...)))).......... ( -26.70)
>DroGri_CAF1 161896 95 + 1
U-AUGCAUUUA--UCUCGGCUAGCUUGUGUUU---GGCACAA-UGGACUUACGUGUUGCACAAACAUAAAUUGUGCAACAGCGUGUAAACUACUUUUUGACU
(-((((.....--...((...((((((((...---..)))).-.)).))..))((((((((((.......)))))))))))))))................. ( -22.40)
>DroWil_CAF1 126552 88 + 1
UAU-ACAUUU----------UGGCUUUGAAUU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
...-......----------((((........---))))(((((((...((((((((((((((.......))))))))).))))).......)))))))... ( -26.40)
>DroMoj_CAF1 214007 98 + 1
U-CUACAUUUA--UCUCCAGAGGCUUGUGCCUCUGUGCACAA-UGGUCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
.-.........--....(((((((....))))))).......-((((..((((((((((((((.......))))))))).)))))...)))).......... ( -31.70)
>DroAna_CAF1 128331 98 + 1
CACAACAUUUAGUUUUGGCCAGGC-UGAGCCU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
...............((((.((((-...))))---))))(((((((...((((((((((((((.......))))))))).))))).......)))))))... ( -31.40)
>consensus
U_CUACAUUUA__UCUCCGCUGGCUUGUGCCU___GCCACAA_AGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACU
.....................(((....)))..................((((((((((((((.......))))))))).)))))................. (-17.97 = -17.63 +  -0.33)

alignment

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secondary structure

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Window 4

Location 22,484,126 – 22,484,225
Length 99
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 82.52
Mean single sequence MFE -28.47
Consensus MFE -17.73
Energy contribution -17.73
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -3.07
Structure conservation index 0.62
SVM decision value 0.81
SVM RNA-class probability 0.857050
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22484126 99 - 27905053
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGGCCUUUUGUGGC---AGGCCCACGCCAGCAGAGAACUAAAUGUUGGG
..((((....((((((.(((((.(((((((((.......)))))))))))))...(((......)))---.(((....)))....).))))))....)))). ( -32.70)
>DroVir_CAF1 190292 95 - 1
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGACCA-UUGUGCC---AGACACAAGCCAGCGCAGA--UAAAUGCAU-A
.(((.....(((...)))((((.(((((((((.......)))))))))))))..)))..-(((((..---...)))))......(((..--....)))..-. ( -25.40)
>DroGri_CAF1 161896 95 - 1
AGUCAAAAAGUAGUUUACACGCUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGUCCA-UUGUGCC---AAACACAAGCUAGCCGAGA--UAAAUGCAU-A
..........((((((..(((.((((((((((.......))))))))))))).......-..(((..---...))))))))).......--.........-. ( -22.00)
>DroWil_CAF1 126552 88 - 1
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGGCCUUUUGUGGC---AAUUCAAAGCCA----------AAAUGU-AUA
.....(((((..((((..((((.(((((((((.......))))))))))))).))))))))).((((---........))))----------......-... ( -23.80)
>DroMoj_CAF1 214007 98 - 1
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGACCA-UUGUGCACAGAGGCACAAGCCUCUGGAGA--UAAAUGUAG-A
.(((.....(((...)))((((.(((((((((.......)))))))))))))..)))((-((...(.(((((((....)))))))..).--..))))...-. ( -33.80)
>DroAna_CAF1 128331 98 - 1
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGGCCUUUUGUGGC---AGGCUCA-GCCUGGCCAAAACUAAAUGUUGUG
...(((....((((((..((((.(((((((((.......)))))))))))))..((((......(((---.......-))).)))).))))))....))).. ( -33.10)
>consensus
AGUCAAAAAGUAGUUUACACGUUGUUGCACAAUUUAUGUUUGUGCAACACGUAAGGCCA_UUGUGCC___AGGCACAAGCCAGCCGAGA__UAAAUGUAG_A
.(((.....(((...)))(((.((((((((((.......)))))))))))))..)))............................................. (-17.73 = -17.73 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,484,151 – 22,484,257
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.10
Mean single sequence MFE -26.12
Consensus MFE -17.44
Energy contribution -17.75
Covariance contribution 0.31
Combinations/Pair 1.16
Mean z-score -2.54
Structure conservation index 0.67
SVM decision value 0.74
SVM RNA-class probability 0.838785
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22484151 106 + 27905053
---UGGGCCU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGCAUAAAGCCCACGAUUCCCAU-UCCUGUUG-------CC
---(((((.(---((..(((((((...((((((((((((((.......))))))))).))))).......)))))))...)))....)))))..........-........-------.. ( -30.70)
>DroGri_CAF1 161918 104 + 1
---UGUGUUU---GGCACAA-UGGACUUACGUGUUGCACAAACAUAAAUUGUGCAACAGCGUGUAAACUACUUUUUGACUGCAUAAAAUGCCCCAUUCAUAU-GCCC-UUG-------CC
---...((..---((((.((-(((...((((((((((((((.......)))))))))).)))).................((((...)))).)))))....)-))).-..)-------). ( -27.20)
>DroWil_CAF1 126566 107 + 1
---UUGAAUU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGUAUAAAACGCUCCAUUCCCAUAUCCUGCCA-------GC
---..((((.---((..(((((((...((((((((((((((.......))))))))).))))).......)))))))...((.....))))...)))).............-------.. ( -22.20)
>DroMoj_CAF1 214029 107 + 1
---UGUGCCUCUGUGCACAA-UGGUCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGCAUAAAAUGCCCCAUUCAUAU-GCCU-UUG-------CC
---(((((......))))).-((((..((((((((((((((.......))))))))).)))))...))))..........(((((.((((...))))..)))-))..-...-------.. ( -28.00)
>DroAna_CAF1 128355 113 + 1
---UGAGCCU---GCCACAAAAGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGCAUGAAGCGCACCAUUCCCAC-UCCUAUUCCCCAAUCCC
---((.((.(---((..(((((((...((((((((((((((.......))))))))).))))).......)))))))...)))....)).))..........-................. ( -24.20)
>DroPer_CAF1 142102 102 + 1
AGCUGAGCCU---GCCACAA-AGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGCAUGAAACGCGCCAUUCCCAU-CCC-------------C
.((...((((---.......-))))......((((((((((.......)))))))))).((((((..(........)..))))))....))...........-...-------------. ( -24.40)
>consensus
___UGAGCCU___GCCACAA_AGGCCUUACGUGUUGCACAAACAUAAAUUGUGCAACAACGUGUAAACUACUUUUUGACUGCAUAAAACGCACCAUUCCCAU_UCCU_UUG_______CC
......((.....(((......)))..((((((((((((((.......))))))))).))))).................))...................................... (-17.44 = -17.75 +   0.31)

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 13:11:19 2006