Locus 696

Sequence ID X_DroMel_CAF1
Location 1,923,765 – 1,923,925
Length 160
Max. P 0.881532
window1114 window1115 window1116

overview

Window 4

Location 1,923,765 – 1,923,885
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.00
Mean single sequence MFE -44.73
Consensus MFE -37.44
Energy contribution -38.50
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -1.71
Structure conservation index 0.84
SVM decision value 0.55
SVM RNA-class probability 0.778599
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1923765 120 + 22224390
ACACCGGGAAUAGGCGGCCGGAAGGCGGAGCAGCCUGUGGCCAGGUAGAUUUUAUCGUACUUCACCACGUAGCCAUUGCUGCAGUGCAGCUCUUUCUGAGCGGUAUCCAACUUCUCGGCG
...(((((((......(((....)))((((((((..(((((..(((.((............))))).....))))).)))))..(((.((((.....)))).))))))...))))))).. ( -46.40)
>DroSec_CAF1 7735 120 + 1
NNNNNNNNNNNNNNNNNNNCGGAGGCGGAGCAGCCUGUGGCCAGGUAGAUUUUAUCGUACUUCACCACGUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCGGUAUCCAACUUCUCGGCG
..........................(((((.((((((((..((((((((...))).)))))..))))(((((....))))))).)).)))))..(((((.(((.....))).))))).. ( -34.50)
>DroEre_CAF1 7803 120 + 1
ACACCCGGAAUUGGCGGCCGGAAGGCGGAGCAGCCUGUGGCAAGGUAGAUUUUGUCGUACUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCUGUAUCCAGUUUCUCGGCG
...((.(((((((((.(((....))).).(((((..(((((..(((.((............))))).....))))).))))).(((((((((.....)))))))))))))))))..)).. ( -47.90)
>DroYak_CAF1 7839 120 + 1
ACACCCGGAAUAGGCGGCCGGAAGGCGGAGCAGCCGGUGGCCAGGUAGAUUAUGUAUUAAUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCUGUAUCCAGUUUCUCGGCG
...(((......)).)((((..((((((((((((.((((((..(((..((((.....))))..))).....)))))))))))..((((((((.....))))))))))).))))..)))). ( -50.10)
>consensus
ACACCCGGAAUAGGCGGCCGGAAGGCGGAGCAGCCUGUGGCCAGGUAGAUUUUAUCGUACUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCGGUAUCCAACUUCUCGGCG
................((((((((..((((((((..(((((..(((.((............))))).....))))).)))))..((((((((.....)))))))))))..)))).)))). (-37.44 = -38.50 +   1.06) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,923,765 – 1,923,885
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.00
Mean single sequence MFE -43.02
Consensus MFE -36.31
Energy contribution -39.06
Covariance contribution 2.75
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.84
SVM decision value 0.92
SVM RNA-class probability 0.881532
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1923765 120 - 22224390
CGCCGAGAAGUUGGAUACCGCUCAGAAAGAGCUGCACUGCAGCAAUGGCUACGUGGUGAAGUACGAUAAAAUCUACCUGGCCACAGGCUGCUCCGCCUUCCGGCCGCCUAUUCCCGGUGU
.((((.((((.((((....((((.....))))......(((((..((((((.((((................)))).))))))...))))))))).))))))))((((.......)))). ( -46.49)
>DroSec_CAF1 7735 120 - 1
CGCCGAGAAGUUGGAUACCGCUCAGAAGGAGCUGCACUGCAGCAAUGGCUACGUGGUGAAGUACGAUAAAAUCUACCUGGCCACAGGCUGCUCCGCCUCCGNNNNNNNNNNNNNNNNNNN
....(((..((.....))..)))....((((..((...(((((..((((((.((((................)))).))))))...)))))...)))))).................... ( -31.89)
>DroEre_CAF1 7803 120 - 1
CGCCGAGAAACUGGAUACAGCUCAGAAGGAGCUGCACUGCAGCAAUGGCUAUGUGGUGAAGUACGACAAAAUCUACCUUGCCACAGGCUGCUCCGCCUUCCGGCCGCCAAUUCCGGGUGU
.((((.(((..((((..((((((.....))))))....(((((........(((((..(.(((.((.....))))).)..))))).)))))))))..)))))))((((.......)))). ( -45.30)
>DroYak_CAF1 7839 120 - 1
CGCCGAGAAACUGGAUACAGCUCAGAAGGAGCUGCACUGCAGCAAUGGCUAUGUGGUGAAUUAAUACAUAAUCUACCUGGCCACCGGCUGCUCCGCCUUCCGGCCGCCUAUUCCGGGUGU
.((((.(((..((((..((((((.....))))))....(((((..((((((...((((.((((.....)))).))))))))))...)))))))))..)))))))(((((.....))))). ( -48.40)
>consensus
CGCCGAGAAACUGGAUACAGCUCAGAAGGAGCUGCACUGCAGCAAUGGCUACGUGGUGAAGUACGACAAAAUCUACCUGGCCACAGGCUGCUCCGCCUUCCGGCCGCCUAUUCCGGGUGU
.((((.((((.((((..((((((.....))))))....(((((..((((((.((((................)))).))))))...))))))))).))))))))((((.......)))). (-36.31 = -39.06 +   2.75) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,923,805 – 1,923,925
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.25
Mean single sequence MFE -35.50
Consensus MFE -27.67
Energy contribution -29.55
Covariance contribution 1.88
Combinations/Pair 1.11
Mean z-score -1.86
Structure conservation index 0.78
SVM decision value 0.41
SVM RNA-class probability 0.727266
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1923805 120 + 22224390
CCAGGUAGAUUUUAUCGUACUUCACCACGUAGCCAUUGCUGCAGUGCAGCUCUUUCUGAGCGGUAUCCAACUUCUCGGCGGCGACUCCUUGCCACAGUUCGAUAUCGUACUCUUUGUAGA
...(((.((............)))))..(((((....)))))(((((.((((.....))))((((((.((((.....(.(((((....))))).))))).)))))))))))......... ( -33.70)
>DroSec_CAF1 7775 120 + 1
CCAGGUAGAUUUUAUCGUACUUCACCACGUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCGGUAUCCAACUUCUCGGCGGCGACUCCUUGCCACUGUUCAAUAUCGUACUCUUUGUAGA
...(((.((............)))))..(((((....)))))(((((.((((.....))))(((((..(((.....((.(((((....))))).)))))..))))))))))......... ( -28.90)
>DroEre_CAF1 7843 120 + 1
CAAGGUAGAUUUUGUCGUACUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCUGUAUCCAGUUUCUCGGCGGCGACUCCUAGCCACAGUUCGAUAUCGUACGCCUUGUAAA
((((((..((..(((((.(((..........(((...((((..(((((((((.....))))))))).)))).....)))(((........)))..))).)))))..))..)))))).... ( -41.70)
>DroYak_CAF1 7879 120 + 1
CCAGGUAGAUUAUGUAUUAAUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCUGUAUCCAGUUUCUCGGCGGCGACUCCUUGCCACAGUUCGAUAUCGUAUUCCUGGUAGA
(((((.....((((((((.............(((...((((..(((((((((.....))))))))).)))).....)))(((((....))))).......)))).))))..))))).... ( -37.70)
>consensus
CCAGGUAGAUUUUAUCGUACUUCACCACAUAGCCAUUGCUGCAGUGCAGCUCCUUCUGAGCGGUAUCCAACUUCUCGGCGGCGACUCCUUGCCACAGUUCGAUAUCGUACUCCUUGUAGA
(((((...((..(((((.((...........(((...((((..(((((((((.....))))))))).)))).....)))(((((....)))))...)).)))))..))...))))).... (-27.67 = -29.55 +   1.88) 

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 09:51:22 2006