Locus 2555

Sequence ID 2R_DroMel_CAF1
Location 9,072,741 – 9,073,021
Length 280
Max. P 0.998794
window4202 window4203 window4204 window4205 window4206

overview

Window 2

Location 9,072,741 – 9,072,861
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -45.18
Consensus MFE -42.90
Energy contribution -42.82
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -1.05
Structure conservation index 0.95
SVM decision value 0.05
SVM RNA-class probability 0.557495
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9072741 120 - 20766785
CCAUUUUGGCCAACUGCUGGAUGUACGGAGGCAAUGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGCGUGUUGAGAUGUGGCUUGGUCACGGGGGCAGGUGUGGUUG
.......(((((.((((((((((..(((((((((..........))).))))))))))).((((..(((((((((...((((......))))))).)))))))))))))))...))))). ( -43.10)
>DroSec_CAF1 37806 120 - 1
CCAUUUUGGCCAACUGCUGGAUGUGUGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGCGUGUUGAGAUGUGGCUUGGUCACCGGAGCAGGUGUUGUUG
.......(((((((..(.(((((((..(.((((((........)))))))..)))))))(((((((((..(.....)..)))).))))).)..).))))))(((......)))....... ( -40.90)
>DroSim_CAF1 39457 120 - 1
CCAUUUUGGCCAACUGCUGAAUGUGUGGAGGCAGAGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGCGUGUUGAGAUGUGGCUUGGUCACGGGAGCAGGUGUUGUUG
(((..(((..((..(((.((..(((((((((((((........)))).)))))))))..))..)))))..)))..)))((.((((....((((((...))))))..)))).))....... ( -39.90)
>DroEre_CAF1 43394 120 - 1
CCAUUUUGGCCAACUGCUGGAUGUGCGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGCGUGUUGAGAUGUGGCUUGGUCACAGGAGCAGGGGUGGUCG
.......(((((.((((.(((((((.(..((((((........))))))..))))))))(((((..(((((((((...((((......))))))).)))))))))))))))...))))). ( -48.50)
>DroYak_CAF1 39854 120 - 1
CCAUUUUGGCCAGCUGCUGGAUGUGCGGAGGCAGGGUUGAGUACUUGCCCUCCGCAUCCUCCUGCAUGAUCAGCUUGGGCGUGUUGAGAUGCGGCUUGGUCACAGGAGCAGGUGUGGUCG
.......(((((.((((.(((((((.(..((((((........))))))..))))))))(((((..(((((((((...((((......))))))).)))))))))))))))...))))). ( -53.50)
>consensus
CCAUUUUGGCCAACUGCUGGAUGUGCGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGCGUGUUGAGAUGUGGCUUGGUCACAGGAGCAGGUGUGGUUG
.......(((((.((((.(((((((.((.((((((........)))))))).)))))))(((((..(((((((((...((((......))))))).)))))))))))))))...))))). (-42.90 = -42.82 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,072,781 – 9,072,901
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.75
Mean single sequence MFE -40.00
Consensus MFE -34.34
Energy contribution -35.06
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -1.78
Structure conservation index 0.86
SVM decision value 1.51
SVM RNA-class probability 0.959970
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9072781 120 + 20766785
GCCCAAGCUGAUCAUGCAAGAGGAUGCGGAGGGCAAAUACUCAACAUUGCCUCCGUACAUCCAGCAGUUGGCCAAAAUGGCCAAUAUUUCGCCGCAAGUCGUGGAAAUCUUUCUGGAGCG
(((((.((.......))(((((((((((((((.(((..........)))))))))..)))))....(((((((.....))))))).(((((((....)..)))))).))))..))).)). ( -42.10)
>DroSec_CAF1 37846 120 + 1
GCCCAAGCUGAUCAUGCAAGAGGAUGCGGAGGGCAAAUACUCAACCCUGCCUCCACACAUCCAGCAGUUGGCCAAAAUGGCCAAUAUCUCGCCCCAAGUCGUGGAAAUCUUUCUGGAGCG
(((((....(((...((.((((((((.((..((((............))))..).).)))))....(((((((.....))))))).))).)).(((.....)))..)))....))).)). ( -37.60)
>DroSim_CAF1 39497 120 + 1
GCCCAAGCUGAUCAUGCAAGAGGAUGCGGAGGGCAAAUACUCAACUCUGCCUCCACACAUUCAGCAGUUGGCCAAAAUGGCCAAUAUCUCGCCGCAAGUCGUGGAAAUCUUUCUGGAGCG
(((((.(((((((......))(((.((((((.............)))))).)))......))))).(((((((.....)))))))......((((.....)))).........))).)). ( -41.12)
>DroEre_CAF1 43434 120 + 1
GCCCAAGCUGAUCAUGCAAGAGGAUGCGGAGGGCAAAUACUCAACCCUGCCUCCGCACAUCCAGCAGUUGGCCAAAAUGGCUAAUAUCUCGCCCCAAGUUGUGGAAAUCUUUCUGGAACG
..(((((((......((.((((((((((((((.((............))))))))))..)))....(((((((.....))))))).))).))....)))).)))...(((....)))... ( -36.20)
>DroYak_CAF1 39894 120 + 1
GCCCAAGCUGAUCAUGCAGGAGGAUGCGGAGGGCAAGUACUCAACCCUGCCUCCGCACAUCCAGCAGCUGGCCAAAAUGGCCAAUAUCUCACCGCAAGUCGUGGAAAUCUUUCUGGAGCG
((((((((((.((......))(((((((((((.((.((.....))..))))))))))..)))..)))))((((.....)))).........((((.....)))).........))).)). ( -43.00)
>consensus
GCCCAAGCUGAUCAUGCAAGAGGAUGCGGAGGGCAAAUACUCAACCCUGCCUCCGCACAUCCAGCAGUUGGCCAAAAUGGCCAAUAUCUCGCCGCAAGUCGUGGAAAUCUUUCUGGAGCG
(((((.((.......))(((((((((((((((.((............))))))))..)))))....(((((((.....)))))))......((((.....))))...))))..))).)). (-34.34 = -35.06 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,072,781 – 9,072,901
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.75
Mean single sequence MFE -42.79
Consensus MFE -37.46
Energy contribution -37.78
Covariance contribution 0.32
Combinations/Pair 1.16
Mean z-score -1.33
Structure conservation index 0.88
SVM decision value 0.43
SVM RNA-class probability 0.733070
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9072781 120 - 20766785
CGCUCCAGAAAGAUUUCCACGACUUGCGGCGAAAUAUUGGCCAUUUUGGCCAACUGCUGGAUGUACGGAGGCAAUGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGC
.((((.((...((((..((.((...((((.......((((((.....)))))))))).(((((..(((((((((..........))).))))))))))))).))...))))..)).)))) ( -38.71)
>DroSec_CAF1 37846 120 - 1
CGCUCCAGAAAGAUUUCCACGACUUGGGGCGAGAUAUUGGCCAUUUUGGCCAACUGCUGGAUGUGUGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGC
.((((.((...((((((((.....))))((((((..((((((.....)))))).....(((((((..(.((((((........)))))))..)))))))))))))..))))..)).)))) ( -46.80)
>DroSim_CAF1 39497 120 - 1
CGCUCCAGAAAGAUUUCCACGACUUGCGGCGAGAUAUUGGCCAUUUUGGCCAACUGCUGAAUGUGUGGAGGCAGAGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGC
.((((.((...((((....((.....))((((((..((((((.....)))))).........(((((((((((((........)))).)))))))))..))))))..))))..)).)))) ( -41.80)
>DroEre_CAF1 43434 120 - 1
CGUUCCAGAAAGAUUUCCACAACUUGGGGCGAGAUAUUAGCCAUUUUGGCCAACUGCUGGAUGUGCGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGC
((((((((...............)))))))).........(((..(((..((..(((.(((.(((((((((((((........)))).)))))))))..))).)))))..)))..))).. ( -39.36)
>DroYak_CAF1 39894 120 - 1
CGCUCCAGAAAGAUUUCCACGACUUGCGGUGAGAUAUUGGCCAUUUUGGCCAGCUGCUGGAUGUGCGGAGGCAGGGUUGAGUACUUGCCCUCCGCAUCCUCCUGCAUGAUCAGCUUGGGC
.((((.((...(((((((((........))).))..((((((.....)))))).(((.(((.(((((((((((((........)))).)))))))))..))).))).))))..)).)))) ( -47.30)
>consensus
CGCUCCAGAAAGAUUUCCACGACUUGCGGCGAGAUAUUGGCCAUUUUGGCCAACUGCUGGAUGUGCGGAGGCAGGGUUGAGUAUUUGCCCUCCGCAUCCUCUUGCAUGAUCAGCUUGGGC
.((((.((...((((.............((((((..((((((.....)))))).....(((((((.((.((((((........)))))))).)))))))))))))..))))..)).)))) (-37.46 = -37.78 +   0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,072,901 – 9,073,021
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -48.52
Consensus MFE -42.38
Energy contribution -42.50
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.60
Structure conservation index 0.87
SVM decision value 1.29
SVM RNA-class probability 0.938517
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9072901 120 + 20766785
GCAGCCCAAGUUGGCGGAACUGGCCAAGCGCCUGAGCACCCUGGCACUCAGUCCCGAACAGACCCAGGCCAUGGACACCCAGGUGCUCAAGGCCGUGCAGCACGCACUGAGCAACAACGA
...((.((..(((((.......)))))(.(((((((((((.((((.((..(((.......)))..))))))(((....)))))))))).)))))((((.....)))))).))........ ( -44.20)
>DroSec_CAF1 37966 120 + 1
GCAACCCAAGCUUGCGGAACUUGCCAAGCGCCUGAGCACCCUGGCACUCAGUCCGGAGCAGACCCAGGCCAUGGACGCCCAGGUGCUCAAGGCCGUGCAGCACGCCCUGAGCAACAACGA
.........(((((.((....(((...(((((((((((((..(((.....(((((..((........))..))))))))..))))))).))).)))...)))..)).)))))........ ( -44.90)
>DroSim_CAF1 39617 120 + 1
GCAACCCAAGCUGGCGGAACUGGCCAAGCGCCUGAGCACCCUGGCACUCAGUCCGGAGCAGACCCAGGCCAUGGACGCCCAGGUGCUCAAGGCCGUGCAGCACGCCCUGAGCAACAACGA
.........((((((((.((.((((.((((((((.((..((((((.((..(((.......)))..)))))).))..)).))))))))...))))))....).))))...)))........ ( -46.60)
>DroEre_CAF1 43554 120 + 1
GCAGCCCAAGCUGGCCGAACUGGCCAAGCGCCUGAGCACCCUGGCCCUCAGUCCGGAGCAGACCCAGGCCAUGGGCAACCAGGUGCUCAGGGCCGUGCAGAACGCACUGCGCAACAACGA
...((((..(((((((.....)))).)))...((((((((.(((((....(((.......)))...)))))(((....))))))))))))))).((((((......))))))........ ( -57.70)
>DroYak_CAF1 40014 120 + 1
GCAGCCCAAGCUGGCGGAACUGGCCAAGCGCUUGAGCACCCUGGCACUCAGUCCGGAGCAGACCCAGGCCAUGGACGCCCAGGUGCUCAAGGCCGUGCAGCACGCACUGAGCAGCAACGA
((.((.((.((((((.......))).))).((((((((((..(((.....(((((..((........))..))))))))..))))))))))...((((.....)))))).)).))..... ( -49.20)
>consensus
GCAGCCCAAGCUGGCGGAACUGGCCAAGCGCCUGAGCACCCUGGCACUCAGUCCGGAGCAGACCCAGGCCAUGGACGCCCAGGUGCUCAAGGCCGUGCAGCACGCACUGAGCAACAACGA
((.......((((((.......))).)))(((((((((((.((((.((..(((.......)))..))))))(((....)))))))))).)))).((((.....))))...))........ (-42.38 = -42.50 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,072,901 – 9,073,021
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -59.98
Consensus MFE -54.56
Energy contribution -54.44
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.13
Structure conservation index 0.91
SVM decision value 3.23
SVM RNA-class probability 0.998794
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9072901 120 - 20766785
UCGUUGUUGCUCAGUGCGUGCUGCACGGCCUUGAGCACCUGGGUGUCCAUGGCCUGGGUCUGUUCGGGACUGAGUGCCAGGGUGCUCAGGCGCUUGGCCAGUUCCGCCAACUUGGGCUGC
.....((.(((((((((.....))))((((..((((.((((((..(((.((((((.(((((.....))))).)).)))))))..)))))).)))))))).............))))).)) ( -59.40)
>DroSec_CAF1 37966 120 - 1
UCGUUGUUGCUCAGGGCGUGCUGCACGGCCUUGAGCACCUGGGCGUCCAUGGCCUGGGUCUGCUCCGGACUGAGUGCCAGGGUGCUCAGGCGCUUGGCAAGUUCCGCAAGCUUGGGUUGC
.....((.(((((((.(.(((.(.((.(((..((((.(((((((..((.((((((.((((((...)))))).)).))))))..))))))).)))))))..)).).))).)))))))).)) ( -59.10)
>DroSim_CAF1 39617 120 - 1
UCGUUGUUGCUCAGGGCGUGCUGCACGGCCUUGAGCACCUGGGCGUCCAUGGCCUGGGUCUGCUCCGGACUGAGUGCCAGGGUGCUCAGGCGCUUGGCCAGUUCCGCCAGCUUGGGUUGC
.....((.(((((.((((.(((....((((..((((.(((((((..((.((((((.((((((...)))))).)).))))))..))))))).)))))))))))..))))....))))).)) ( -60.90)
>DroEre_CAF1 43554 120 - 1
UCGUUGUUGCGCAGUGCGUUCUGCACGGCCCUGAGCACCUGGUUGCCCAUGGCCUGGGUCUGCUCCGGACUGAGGGCCAGGGUGCUCAGGCGCUUGGCCAGUUCGGCCAGCUUGGGCUGC
..........((((......)))).((((((.((((.(((((..((((.((((((.((((((...))))))..))))))))))..))))).))))((((.....)))).....)))))). ( -62.80)
>DroYak_CAF1 40014 120 - 1
UCGUUGCUGCUCAGUGCGUGCUGCACGGCCUUGAGCACCUGGGCGUCCAUGGCCUGGGUCUGCUCCGGACUGAGUGCCAGGGUGCUCAAGCGCUUGGCCAGUUCCGCCAGCUUGGGCUGC
.((..((((..((((((.....))))((((((((((((((((....)).((((((.((((((...)))))).)).))))))))))))))).)))))..))))..)).((((....)))). ( -57.70)
>consensus
UCGUUGUUGCUCAGUGCGUGCUGCACGGCCUUGAGCACCUGGGCGUCCAUGGCCUGGGUCUGCUCCGGACUGAGUGCCAGGGUGCUCAGGCGCUUGGCCAGUUCCGCCAGCUUGGGCUGC
.....((.((((((.(((((..((..((((..((((.(((((((((((.((((((.(((((.....))))).)).))))))))))))))).)))))))).))..)))..)))))))).)) (-54.56 = -54.44 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:55 2006