Locus 6058

Sequence ID 2L_DroMel_CAF1
Location 17,046,920 – 17,047,173
Length 253
Max. P 0.887678
window9619 window9620 window9621 window9622

overview

Window 9

Location 17,046,920 – 17,047,015
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.38
Mean single sequence MFE -25.89
Consensus MFE -6.52
Energy contribution -6.52
Covariance contribution 0.00
Combinations/Pair 1.33
Mean z-score -2.01
Structure conservation index 0.25
SVM decision value 0.95
SVM RNA-class probability 0.887678
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17046920 95 + 22407834
--AUCACUUUAAAGG----------CUAUUAAAAUGAAG-------------AUGGCUUUAAAAGAUUAAAACUCCUGCUGUUAGGGUAUAGGAAGAGAAAACAGCGACUCAAACAGUUG
--....((((.((((----------(((((........)-------------)))))))).))))............((((((.((((....(.........)....)))).)))))).. ( -19.40)
>DroSec_CAF1 11019 95 + 1
--AUCACUUUAAAGU----------CUAAAAUAAUUUAG-------------AUGGCUUUAAAAGAUUGAAGCACCAGCUGUUAGGGUGUAGGAAGAGAAAACAGCGACUCAAACAGUUG
--...........((----------(((((....)))))-------------)).(((((((....)))))))..((((((((.((((((.(..........).)).)))).)))))))) ( -23.30)
>DroSim_CAF1 4675 95 + 1
--AUCACUUUAAAGC----------CUAAAUUUAUUUAG-------------AUGGCUUUAAAAGAUUGAAGCACCCGCUCUUAGGGUGUAGGAAGAGAAAACAGCGACUCAAACAGUUG
--.....((((((((----------(.............-------------..))))))))).(((((..((((((.......)))))).....(((..........)))...))))). ( -23.26)
>DroEre_CAF1 10729 115 + 1
GUAUAACUUUUAUGCAGUAU-----CUGUUCAAGUGCAGAUACUUACAACUUCCGGCUUCAAAAGGUGGAGACGCCUGCUGUUAGGGUAUAGGAAGAGAAAACAGCGCCUCAAACAGUUG
(((((.....)))))(((((-----((((......))))))))).....(((((.(((..((.(((((....)))))....))..)))...)))))......((((..........)))) ( -36.00)
>DroYak_CAF1 8634 115 + 1
-----ACUUUUAUACAGUAUUUUAUUUUUUUAAGUAUAGAGACUUCAGUCUUCUGACUUCAAAAGGUGGAGACGCCCGCUGUUAGGGUAUGGGGAGAGAAAACAGCGACUCAAACAGUUG
-----.(((((...((((.(((((((((((.((((.(((((((....))).)))))))).)))))))))))))((((.......)))).))..))))).......(((((.....))))) ( -27.50)
>consensus
__AUCACUUUAAAGC__________CUAUUAAAAUGUAG_____________AUGGCUUUAAAAGAUUGAAACACCCGCUGUUAGGGUAUAGGAAGAGAAAACAGCGACUCAAACAGUUG
......((((...............((((......))))................(((((((.((.(((......))))).)))))))....))))......((((..........)))) ( -6.52 =  -6.52 +   0.00)

alignment

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secondary structure

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Window 0

Location 17,046,975 – 17,047,094
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.46
Mean single sequence MFE -33.32
Consensus MFE -26.80
Energy contribution -26.88
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.80
SVM decision value 0.43
SVM RNA-class probability 0.735314
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17046975 119 + 22407834
GUUAGGGUAUAGGAAGAGAAAACAGCGACUCAAACAGUUGCAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUUGCAC-UCCUCUUCACACCCCAAACC
(((.(((.....((((((......((((((.....))))))..(((((((....))).)))).((.((..(((((..........)))))..)).))..-..))))))....))).))). ( -33.60)
>DroSec_CAF1 11074 120 + 1
GUUAGGGUGUAGGAAGAGAAAACAGCGACUCAAACAGUUGAAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUUGCACAUCCUCGUUCCACUCCAACCC
((.((((..((((..((((.....(((((((((....))))....))))).(((((.(((.(((....))))))))))))))).))))..)))).))....................... ( -30.90)
>DroSim_CAF1 4730 120 + 1
CUUAGGGUGUAGGAAGAGAAAACAGCGACUCAAACAGUUGCAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUUGCACAUCCUCUUUCCACUCCAACCC
.....((.((.(((((((......((((((.....))))))..(((((((....))).)))).((.((..(((((..........)))))..)).)).....))))))).)).))..... ( -32.80)
>DroEre_CAF1 10804 115 + 1
GUUAGGGUAUAGGAAGAGAAAACAGCGCCUCAAACAGUUGCAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUUGCACCUCCUCUACC-----CCUCCC
....(((((.((((.(((..........)))..((((.((((((((...))))))))(((...(((....))).)))........))))...........)))).))))-----)..... ( -31.30)
>DroYak_CAF1 8709 115 + 1
GUUAGGGUAUGGGGAGAGAAAACAGCGACUCAAACAGUUGCAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUCGUACCUCCUCCACC-----CAUGCC
.....((((((((..(((......((((.....((((.((((((((...))))))))(((...(((....))).)))........))))....)))).....)))..))-----)))))) ( -38.00)
>consensus
GUUAGGGUAUAGGAAGAGAAAACAGCGACUCAAACAGUUGCAAAUGUUGCAUUUGCAUGCAUGGCCAGUCGGCAGCAAAUUUCACCUGUCCCCUUGCACAUCCUCUUCCCAC_CCAACCC
((.((((.(((((..((((.((((((((((.....))))))...))))...(((((.(((.(((....))))))))))))))).))))).)))).))....................... (-26.80 = -26.88 +   0.08)

alignment

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secondary structure

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Window 1

Location 17,047,055 – 17,047,173
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.59
Mean single sequence MFE -32.04
Consensus MFE -26.46
Energy contribution -26.54
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.83
SVM decision value 0.47
SVM RNA-class probability 0.747914
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17047055 118 + 22407834
UUCACCUGUCCCCUUGCAC-UCCUCUUCACACCCCAAACCAUCGUCC-UGGCCACAUCCAUCGGCUGGCCAGUUCGGGUGAGCGUUGUCGUUGCCAUUUAGACAAGUGACAUAUGUGCCA
.((((.((((.....((..-.........(((((.........(..(-(((((((........).)))))))..))))))((((....))))))......)))).))))........... ( -30.80)
>DroSec_CAF1 11154 120 + 1
UUCACCUGUCCCCUUGCACAUCCUCGUUCCACUCCAACCCAUCCCCCAUGGCCCCAUCCAUCGGCUGGCCAGUUCGGGUGAGCGUUGUCGCUGCCAUUUAGACAAGUGACAUAUGCGCCA
.(((((((..(..............(((.......)))..........(((((((.......))..))))))..)))))))(((((((((((............))))))).)))).... ( -30.90)
>DroSim_CAF1 4810 120 + 1
UUCACCUGUCCCCUUGCACAUCCUCUUUCCACUCCAACCCAUCCCCAAUGGCCCCAUCCAUCGGCUGGCCAGUUCGGGUGAGCGUUGUCGCUGCCAUUUAGACAAGUGACAUAUGCGCCA
.((((.((((.....((......................(((((....(((((((.......))..)))))....)))))((((....))))))......)))).))))........... ( -30.30)
>DroEre_CAF1 10884 114 + 1
UUCACCUGUCCCCUUGCACCUCCUCUACC-----CCUCCCAUCCCCC-UGGCCCCAUCCAUCGGUUGGCCAGUUCGGGUGAGCGUUGUCGCUGCCAUUUAGACAAGUGACACAUGCGCCA
.((((.((((.....((............-----.....(((((..(-(((((((.......))..))))))...)))))((((....))))))......)))).))))........... ( -32.00)
>DroYak_CAF1 8789 113 + 1
UUCACCUGUCCCCUCGUACCUCCUCCACC-----CAUGCCAUCCCUC-UGGCCCCAUCCAUCGGUUGGCCAGUUCGGGUG-GCGUUGUCGCUGCCAUUUAGACAAGUGACAUAUGCGCCA
..............((((...........-----.(((((((((..(-(((((((.......))..))))))...)))))-))))(((((((............)))))))..))))... ( -36.20)
>consensus
UUCACCUGUCCCCUUGCACAUCCUCUUCCCAC_CCAACCCAUCCCCC_UGGCCCCAUCCAUCGGCUGGCCAGUUCGGGUGAGCGUUGUCGCUGCCAUUUAGACAAGUGACAUAUGCGCCA
.((((.((((.....(((.....................(((((....(((((((.......))..)))))....))))).(((....))))))......)))).))))........... (-26.46 = -26.54 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,047,055 – 17,047,173
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.59
Mean single sequence MFE -42.40
Consensus MFE -30.44
Energy contribution -31.24
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.72
SVM decision value 0.07
SVM RNA-class probability 0.570351
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17047055 118 - 22407834
UGGCACAUAUGUCACUUGUCUAAAUGGCAACGACAACGCUCACCCGAACUGGCCAGCCGAUGGAUGUGGCCA-GGACGAUGGUUUGGGGUGUGAAGAGGA-GUGCAAGGGGACAGGUGAA
...........((((((((((.....(((.(..(....(.(((((...(((((((.((...))...))))))-)..(((....)))))))).)....)..-))))....)))))))))). ( -43.40)
>DroSec_CAF1 11154 120 - 1
UGGCGCAUAUGUCACUUGUCUAAAUGGCAGCGACAACGCUCACCCGAACUGGCCAGCCGAUGGAUGGGGCCAUGGGGGAUGGGUUGGAGUGGAACGAGGAUGUGCAAGGGGACAGGUGAA
...........((((((((((.....(((((..((((.(((.((((...(((((..((...))....))))))))).)).).))))..))............)))....)))))))))). ( -40.80)
>DroSim_CAF1 4810 120 - 1
UGGCGCAUAUGUCACUUGUCUAAAUGGCAGCGACAACGCUCACCCGAACUGGCCAGCCGAUGGAUGGGGCCAUUGGGGAUGGGUUGGAGUGGAAAGAGGAUGUGCAAGGGGACAGGUGAA
...........((((((((((.....(((((..((((.(((.(((((..(((((..((...))....)))))))))))).).))))..))............)))....)))))))))). ( -42.40)
>DroEre_CAF1 10884 114 - 1
UGGCGCAUGUGUCACUUGUCUAAAUGGCAGCGACAACGCUCACCCGAACUGGCCAACCGAUGGAUGGGGCCA-GGGGGAUGGGAGG-----GGUAGAGGAGGUGCAAGGGGACAGGUGAA
...........((((((((((.....(((.(.((..(.(((((((...((((((..(((.....))))))))-).))).)))).).-----.))......).)))....)))))))))). ( -43.90)
>DroYak_CAF1 8789 113 - 1
UGGCGCAUAUGUCACUUGUCUAAAUGGCAGCGACAACGC-CACCCGAACUGGCCAACCGAUGGAUGGGGCCA-GAGGGAUGGCAUG-----GGUGGAGGAGGUACGAGGGGACAGGUGAA
...........((((((((((.....((..(.((...((-(((((...((((((..(((.....))))))))-).))).))))...-----.)).).....))......)))))))))). ( -41.50)
>consensus
UGGCGCAUAUGUCACUUGUCUAAAUGGCAGCGACAACGCUCACCCGAACUGGCCAGCCGAUGGAUGGGGCCA_GGGGGAUGGGUUGG_GUGGGAAGAGGAGGUGCAAGGGGACAGGUGAA
...........((((((((((.....((((((....))).(((((....(((((..((...))....)))))...))).)).....................)))....)))))))))). (-30.44 = -31.24 +   0.80)

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 12:00:00 2006