Locus 2699

Sequence ID 3L_DroMel_CAF1
Location 7,537,648 – 7,537,807
Length 159
Max. P 0.920062
window4225 window4226 window4227

overview

Window 5

Location 7,537,648 – 7,537,767
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.34
Mean single sequence MFE -26.34
Consensus MFE -14.90
Energy contribution -14.58
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -2.36
Structure conservation index 0.57
SVM decision value 1.13
SVM RNA-class probability 0.920062
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7537648 119 + 23771897
AAU-UAAAAAACCGUGAAGACUAUAUGGCAAAGAAAUAUCUUUUGGCAACGAUUCAAAAGAUUGAAUCACCUAGUUUUUAUGGGAUUCCCCUUAAAGGCAAAGAUUCUAGGAUAAUACAA
...-.......((((((((((((..((.((((((....)).)))).))..(((((((....)))))))...))))))))))))......(((..((........))..)))......... ( -26.50)
>DroSec_CAF1 6830 120 + 1
AAUUUAAAAAACCGUGAAGACUAGAUGGCAAUAAUAUAACUUUUGGCAAAGAUUCAAAAGAUUGAUUCACCUAGUUUUUAUGGGUUUCCCCUUAAAAGCAGAGAUUCUAGAAUUGUAUUG
(((((......(((((((((((((.((.(((...........))).))..((.((((....)))).))..)))))))))))))(((((..((....))..)))))....)))))...... ( -24.80)
>DroSim_CAF1 6749 119 + 1
AAU-UAAAAAACCGUGAAGACUAGAUGGCAAUGAAAUAACUUUUGGCAACGAUUCAAAAGAUUGAUUCACCUAGUUUUUAUGGGUUUCCCCUUAAAAGCAGAGAUUCUAGGAUUGUAUUG
...-.......(((((((((((((.((.(((...........))).))..((.((((....)))).))..)))))))))))))(((((..((....))..)))))............... ( -24.60)
>DroEre_CAF1 6929 100 + 1
AAU-U-------------------UUAGGAAUGAAAAAGCUUUUGGCAACGAUUCAAAAGAUUGAUUCACCUAGUUUUUAUGGGUUUCCCCGUAAAAGCUGAGACUCUAGGAUUGUAUUA
(((-(-------------------((((((((.((....(((((((.......))))))).)).)))).(.(((((((((((((....))))))))))))).)...))))))))...... ( -27.50)
>DroYak_CAF1 6889 100 + 1
AAU-U-------------------CUGGCCAUGAAAAAUCUUUUGGCAACGAUUCAAAAGAUUGAUUCACCUAGUUUUUAUGGGUUUCCCCUUAAAAGCUAAGAUUCUAGGAUUGUGUUA
(((-(-------------------((((...((((.((((((((((.......))))))))))..))))(.(((((((((.(((....))).))))))))).)...))))))))...... ( -28.30)
>consensus
AAU_UAAAAAACCGUGAAGACUA_AUGGCAAUGAAAUAACUUUUGGCAACGAUUCAAAAGAUUGAUUCACCUAGUUUUUAUGGGUUUCCCCUUAAAAGCAGAGAUUCUAGGAUUGUAUUA
........................................((((((....((.((((....)))).)).....(((((((.(((....))).))))))).......))))))........ (-14.90 = -14.58 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,537,648 – 7,537,767
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -22.88
Consensus MFE -15.58
Energy contribution -16.02
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -2.07
Structure conservation index 0.68
SVM decision value 1.03
SVM RNA-class probability 0.904196
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7537648 119 - 23771897
UUGUAUUAUCCUAGAAUCUUUGCCUUUAAGGGGAAUCCCAUAAAAACUAGGUGAUUCAAUCUUUUGAAUCGUUGCCAAAAGAUAUUUCUUUGCCAUAUAGUCUUCACGGUUUUUUA-AUU
...........(((((.....(((((((.(((....))).)))).((((((((((((((....)))))))...))).(((((....)))))......))))......))).)))))-... ( -20.90)
>DroSec_CAF1 6830 120 - 1
CAAUACAAUUCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCUUUGCCAAAAGUUAUAUUAUUGCCAUCUAGUCUUCACGGUUUUUUAAAUU
...........(((((...(((.(((((.(((....))).)))))((((((((..((((....))))..((((....))))............)))))))).....)))..))))).... ( -23.70)
>DroSim_CAF1 6749 119 - 1
CAAUACAAUCCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAAGUUAUUUCAUUGCCAUCUAGUCUUCACGGUUUUUUA-AUU
...........(((((...(((.(((((.(((....))).)))))((((((((...((((((((((.........)))))).......)))).)))))))).....)))..)))))-... ( -23.31)
>DroEre_CAF1 6929 100 - 1
UAAUACAAUCCUAGAGUCUCAGCUUUUACGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAAGCUUUUUCAUUCCUAA-------------------A-AUU
.............(((....(((((((..(((....)))..........((..(.((((....))))....)..)))))))))..)))........-------------------.-... ( -22.20)
>DroYak_CAF1 6889 100 - 1
UAACACAAUCCUAGAAUCUUAGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAAGAUUUUUCAUGGCCAG-------------------A-AUU
.........((......(((((.(((((.(((....))).))))).)))))((((..(((((((((.........))))))))).)))).))....-------------------.-... ( -24.30)
>consensus
UAAUACAAUCCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAAGAUAUUUCAUUGCCAU_UAGUCUUCACGGUUUUUUA_AUU
.............(((.....((((((..(((....)))..........((..(.((((....))))....)..))))))))...)))................................ (-15.58 = -16.02 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,537,687 – 7,537,807
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.89
Mean single sequence MFE -19.30
Consensus MFE -14.38
Energy contribution -14.30
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -1.52
Structure conservation index 0.75
SVM decision value -0.04
SVM RNA-class probability 0.510693
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7537687 120 - 23771897
GUUCACAAUCACCCAAAUAUGUUUAAAAAAAAAAGCCCGAUUGUAUUAUCCUAGAAUCUUUGCCUUUAAGGGGAAUCCCAUAAAAACUAGGUGAUUCAAUCUUUUGAAUCGUUGCCAAAA
....((((((............................)))))).....(((((...(((.......)))(((...))).......))))).(((((((....))))))).......... ( -18.49)
>DroSec_CAF1 6870 119 - 1
GUUCACACUCACCCAAAUAUGUU-AAAAAAAAAGACCCGCCAAUACAAUUCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCUUUGCCAAAA
.......................-......(((((..((((..........(((.....))).(((((.(((....))).)))))....))))..((((....)))).)))))....... ( -19.30)
>DroSim_CAF1 6788 110 - 1
GUUCACCCUCACCCAA----------AAAAAAAGACCCGCCAAUACAAUCCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAA
.((((((.........----------.........................(((.....))).(((((.(((....))).)))))....))))))((((....))))............. ( -18.50)
>DroEre_CAF1 6949 118 - 1
GUUCACACUCACCCAAAAAUGUA--AAAAAAAAGAACCACUAAUACAAUCCUAGAGUCUCAGCUUUUACGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAA
........(((((.......(((--(((....(((....(((.........)))..)))....))))))(((....)))..........))))).((((....))))............. ( -20.30)
>DroYak_CAF1 6909 118 - 1
GUUCACUCUCGCCUUAAUAUGUA--CCAAAAAAUAAUGACUAACACAAUCCUAGAAUCUUAGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAA
.......................--...............((((.............(((((.(((((.(((....))).))))).))))).((.((((....)))).))))))...... ( -19.90)
>consensus
GUUCACACUCACCCAAAUAUGUA__AAAAAAAAGACCCGCUAAUACAAUCCUAGAAUCUCUGCUUUUAAGGGGAAACCCAUAAAAACUAGGUGAAUCAAUCUUUUGAAUCGUUGCCAAAA
........(((((......................................(((((.......))))).(((....)))..........))))).((((....))))............. (-14.38 = -14.30 +  -0.08)

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 10:39:39 2006