Locus 142

Sequence ID 2R_DroMel_CAF1
Location 1,402,917 – 1,403,056
Length 139
Max. P 0.997724
window307 window308 window309 window310

overview

Window 7

Location 1,402,917 – 1,403,016
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.73
Mean single sequence MFE -44.22
Consensus MFE -33.82
Energy contribution -34.18
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -3.39
Structure conservation index 0.76
SVM decision value 2.84
SVM RNA-class probability 0.997332
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1402917 99 + 20766785
CAGCAUUUCAUCCGCUCAGCCGCUGGGCGGUACUGGUAGUGGUA---------------------CUAGUAGUGGUACUGGUACCAUUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUU
((((...(((.((((((((...))))))))...)))((((((((---------------------((((((....))))))))))))))))))((((..(((.....)))..)))).... ( -42.60)
>DroSec_CAF1 28760 99 + 1
CAGCAUUUCAUCCGCUCAGCCGCUGGGCGGUACUGGUAGUGGUG---------------------CUAGUAGUGGUACUGGUGCCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUU
((((...(((.((((((((...))))))))...)))((((((..---------------------((((((....))))))..))))))))))((((..(((.....)))..)))).... ( -44.10)
>DroSim_CAF1 33730 99 + 1
CAGCAUUUCAUCCGCUCAGCCGCUGGGCGGUACUGGUAGUGGUG---------------------CCAGUAGUGGUACUGGUGCCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUU
((((...(((.((((((((...))))))))...)))((((((..---------------------((((((....))))))..))))))))))((((..(((.....)))..)))).... ( -46.40)
>DroEre_CAF1 27572 120 + 1
CAGAAUUUUAUCCGCUCAGCCGCUGGGCGGCACUGGUAGUGGUAGUGGUAGUGGUACUAGUGGUGCCAGUAGUGGUACUGGUACCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUU
...........((((((((...)))))))).((((((((..(((.((((..((((.(((((((((((((((....)))))))))))))))...))))..)))).)))..))))..)))). ( -51.30)
>DroYak_CAF1 29426 90 + 1
CAGCAUUUUAUCCGCUCAGCCGCUGGGCGGUACUGGUAGUGGUA---------------------CUAGUAGUGGUUCUGCUACCACUGGCUGGCUGAGAUUAGUGCAGU---------U
..(((((.......(((((((((..(.......((((((..(.(---------------------(((....)))).)..)))))))..)).)))))))...)))))...---------. ( -36.71)
>consensus
CAGCAUUUCAUCCGCUCAGCCGCUGGGCGGUACUGGUAGUGGUA_____________________CUAGUAGUGGUACUGGUACCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUU
..(((((...((.((.((((((.(((.((((((((.((.(((.......................))).)).))))))))...))).)))))))).))....)))))............. (-33.82 = -34.18 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,402,917 – 1,403,016
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.73
Mean single sequence MFE -30.15
Consensus MFE -21.14
Energy contribution -22.14
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.70
SVM decision value 0.76
SVM RNA-class probability 0.844566
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1402917 99 - 20766785
AACUGCUGCAACUGCACUAAUCUCAGCCAGCCAAUGGUACCAGUACCACUACUAG---------------------UACCACUACCAGUACCGCCCAGCGGCUGAGCGGAUGAAAUGCUG
..(((((((....)))......((((((......((((((.((((....)))).)---------------------)))))...........((...))))))))))))........... ( -28.40)
>DroSec_CAF1 28760 99 - 1
AACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGCACCAGUACCACUACUAG---------------------CACCACUACCAGUACCGCCCAGCGGCUGAGCGGAUGAAAUGCUG
..(((((((....)))......((((((....(((((..(.((((....)))).)---------------------..))))).........((...))))))))))))........... ( -26.20)
>DroSim_CAF1 33730 99 - 1
AACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGCACCAGUACCACUACUGG---------------------CACCACUACCAGUACCGCCCAGCGGCUGAGCGGAUGAAAUGCUG
..(((((((....)))......((((((....(((((..((((((....))))))---------------------..))))).........((...))))))))))))........... ( -32.70)
>DroEre_CAF1 27572 120 - 1
AACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGUACCAGUACCACUACUGGCACCACUAGUACCACUACCACUACCACUACCAGUGCCGCCCAGCGGCUGAGCGGAUAAAAUUCUG
..(((((((....)))......((((((.((.(((((((....)))))))...(((((...((((...............))))...))))).....))))))))))))........... ( -37.76)
>DroYak_CAF1 29426 90 - 1
A---------ACUGCACUAAUCUCAGCCAGCCAGUGGUAGCAGAACCACUACUAG---------------------UACCACUACCAGUACCGCCCAGCGGCUGAGCGGAUAAAAUGCUG
.---------...(((...((((..(((((((((((((......))))))....(---------------------(((........))))........))))).))))))....))).. ( -25.70)
>consensus
AACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGUACCAGUACCACUACUAG_____________________UACCACUACCAGUACCGCCCAGCGGCUGAGCGGAUGAAAUGCUG
.............(((...((((..((((((((((((((....)))))))..........................................((...))))))).))))))....))).. (-21.14 = -22.14 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,402,957 – 1,403,056
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.03
Mean single sequence MFE -37.52
Consensus MFE -30.78
Energy contribution -30.84
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -3.02
Structure conservation index 0.82
SVM decision value 2.92
SVM RNA-class probability 0.997724
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1402957 99 + 20766785
GGUA---------------------CUAGUAGUGGUACUGGUACCAUUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUUGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
((((---------------------((((((....))))))))))....((..((((..(((.....)))..))))....))....((((..(((((.((....)).)))))..)))).. ( -34.30)
>DroSec_CAF1 28800 99 + 1
GGUG---------------------CUAGUAGUGGUACUGGUGCCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUUGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
...(---------------------((((((((((((....))))))).))))))..........((((.(((((...))))).))))((..(((((.((....)).)))))..)).... ( -36.80)
>DroSim_CAF1 33770 99 + 1
GGUG---------------------CCAGUAGUGGUACUGGUGCCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUUGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
...(---------------------((((((((((((....))))))).))))))..........((((.(((((...))))).))))((..(((((.((....)).)))))..)).... ( -39.10)
>DroEre_CAF1 27612 120 + 1
GGUAGUGGUAGUGGUACUAGUGGUGCCAGUAGUGGUACUGGUACCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUUGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
.(((.((((..((((.(((((((((((((((....)))))))))))))))...))))..)))).)))((.(((((...))))).))((((..(((((.((....)).)))))..)))).. ( -49.50)
>DroYak_CAF1 29466 90 + 1
GGUA---------------------CUAGUAGUGGUUCUGCUACCACUGGCUGGCUGAGAUUAGUGCAGU---------UGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
.(((---------------------(((((..(((((..((((....)))).)))))..))))))))...---------.......((((..(((((.((....)).)))))..)))).. ( -27.90)
>consensus
GGUA_____________________CUAGUAGUGGUACUGGUACCACUGGCUGGCUGAGAUUAGUGCAGUUGCAGCAGUUGCAUCUGCAGUUGCCGUUGUUCUUAUUGCGGUUUCUGUUA
.........................((((((((((((....))))))).))))).........(((((((((...)))))))))..((((..(((((.((....)).)))))..)))).. (-30.78 = -30.84 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,402,957 – 1,403,056
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.03
Mean single sequence MFE -25.20
Consensus MFE -18.66
Energy contribution -20.26
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.74
SVM decision value 2.01
SVM RNA-class probability 0.985617
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1402957 99 - 20766785
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCAACUGCUGCAACUGCACUAAUCUCAGCCAGCCAAUGGUACCAGUACCACUACUAG---------------------UACC
.........................(((...(((((.((((.....)))).)))))((......))...)))...(((((.((((....)))).)---------------------)))) ( -23.20)
>DroSec_CAF1 28800 99 - 1
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCAACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGCACCAGUACCACUACUAG---------------------CACC
...........((............(((...(((((.((((.....)))).)))))((......))...)))(((((........)))))....)---------------------)... ( -23.50)
>DroSim_CAF1 33770 99 - 1
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCAACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGCACCAGUACCACUACUGG---------------------CACC
....(((..(((............)))....(((((.((((.....)))).)))))....)))..(((((..(((((........))))).))))---------------------)... ( -28.10)
>DroEre_CAF1 27612 120 - 1
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCAACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGUACCAGUACCACUACUGGCACCACUAGUACCACUACCACUACC
.........................((..(((((((.((((.....)))).))))..........(((((..(((((((....))))))).)))))......))).))............ ( -32.60)
>DroYak_CAF1 29466 90 - 1
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCA---------ACUGCACUAAUCUCAGCCAGCCAGUGGUAGCAGAACCACUACUAG---------------------UACC
...........((............(((..(((.((((((.---------...)))....))))))...)))((((((......))))))....)---------------------)... ( -18.60)
>consensus
UAACAGAAACCGCAAUAAGAACAACGGCAACUGCAGAUGCAACUGCUGCAACUGCACUAAUCUCAGCCAGCCAGUGGUACCAGUACCACUACUAG_____________________UACC
.........................(((...(((((.((((.....)))).)))))((......))...)))(((((((....))))))).............................. (-18.66 = -20.26 +   1.60)

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 09:29:23 2006