Locus 4081

Sequence ID 3R_DroMel_CAF1
Location 11,122,271 – 11,122,448
Length 177
Max. P 0.996389
window6538 window6539 window6540 window6541

overview

Window 8

Location 11,122,271 – 11,122,368
Length 97
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.47
Mean single sequence MFE -25.97
Consensus MFE -18.24
Energy contribution -18.35
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.28
Structure conservation index 0.70
SVM decision value 0.38
SVM RNA-class probability 0.713668
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11122271 97 - 27905053
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAUAU------A--AUAUAGUGUGGAUGGUA----GAGUAUAUAGACCC--CAU
..((((((.(((...........))).))))))((.(((.....(((((((.(((((((((.------.--.))))))))...).)))----))))....))).))--... ( -28.50)
>DroSec_CAF1 32757 94 - 1
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAUAU------G--AUAUAGUGUGGAUU-------CAAUAUAUAGACCC--CAU
..((((((.(((...........))).))))))((((.....((((((.....((((((((.------.--.)))))))))))))-------)........)))).--... ( -24.92)
>DroSim_CAF1 31903 93 - 1
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAU-U------G--AUAUAGUGUGGAUU-------CAAUAUAUAGACCC--CAU
..((((((.(((...........))).))))))((((.....((((((.....(((((((-.------.--..))))))))))))-------)........)))).--... ( -25.02)
>DroWil_CAF1 36745 87 - 1
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUACGAGCACUAUAUGUA---------U-----ACAU--------AUAUAUGCAGAUCA--CAA
..((((((.(((...........))).))))))(((((....)))))......(((.(((((((.---------.-----..))--------))))))))......--... ( -25.40)
>DroYak_CAF1 33766 109 - 1
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAUAUAUAUCGUAUAUAUAGUAGAGAUGGUAGAGUACAUAUAUAGACCC--CAU
..((((((.(((...........))).))))))((((.......(((((((.(.(((((((((((...)))))))))).)...).))))))).........)))).--... ( -28.99)
>DroAna_CAF1 33014 85 - 1
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUCUUGCGAGCACUAUAU-------------A---------GUU----GAAUAUAUAUAUCGGAUAU
..((((((.(((...........))).)))))).((((.((((...)))).))))..(((((-------------(---------...----...)))))).......... ( -23.00)
>consensus
GAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAUAU_________AUAUAGUGUGGAU________AAAUAUAUAGACCC__CAU
..((((((.(((...........))).)))))).((((.((((...)))).))))........................................................ (-18.24 = -18.35 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,122,297 – 11,122,408
Length 111
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 88.66
Mean single sequence MFE -33.60
Consensus MFE -31.01
Energy contribution -31.32
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.45
Structure conservation index 0.92
SVM decision value 0.71
SVM RNA-class probability 0.829917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11122297 111 + 27905053
CACUAUAU--U------AUAUAGUGCUCGCAAAAUUCUUGAGAACCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCUCUCGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
(((((((.--.------.))))))).........(((((((((...(((.((.(((...........))).)).))))))))))))(((((..(((((((....))))))))))))... ( -36.80)
>DroVir_CAF1 37648 107 + 1
------------UGUAUAUAUAGUGCUCGCAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCACUUGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
------------.............(((....((((((..((....(((.((.(((...........))).)).))).))..))))))(((..(((((((....))))))))))))).. ( -31.80)
>DroGri_CAF1 36955 107 + 1
------------AAUAUAUAUAGUGCUCGCAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCACUUGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
------------.............(((....((((((..((....(((.((.(((...........))).)).))).))..))))))(((..(((((((....))))))))))))).. ( -31.80)
>DroWil_CAF1 36766 106 + 1
----A---------UACAUAUAGUGCUCGUAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCUCUUGAGAAUCAAUUGAAGGAAGCACGUUUCCUUGCUGAGGA
----.---------...........(((....((((((..(((...(((.((.(((...........))).)).))))))..)))))).....(((((((....)))))))...))).. ( -31.70)
>DroMoj_CAF1 38099 107 + 1
------------ACUAUAUACAGUGCACGCAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCUCUUGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
------------........((((.((.((..((((((..(((...(((.((.(((...........))).)).))))))..)))))).))))(((((((....))))))))))).... ( -33.50)
>DroPer_CAF1 39060 119 + 1
UAUUCAAUAAAAAAUAUAUAUAGUGCUCGCAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCUCUCGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
.........................(((....(((((((((((...(((.((.(((...........))).)).))))))))))))))(((..(((((((....))))))))))))).. ( -36.00)
>consensus
____________A_UAUAUAUAGUGCUCGCAAGAUUCUUGAGAAUCGCGCCCUUGCCGAUGAAGAACGCAUGGACGCUCUUGAGAAUCAGCUGAAGGAAGCGCGUUUCCUUGCUGAGGA
.........................(((((..(((((((((((...(((.((.(((...........))).)).)))))))))))))).....(((((((....))))))))).))).. (-31.01 = -31.32 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,122,297 – 11,122,408
Length 111
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 88.66
Mean single sequence MFE -34.87
Consensus MFE -32.36
Energy contribution -32.42
Covariance contribution 0.06
Combinations/Pair 1.14
Mean z-score -2.47
Structure conservation index 0.93
SVM decision value 2.69
SVM RNA-class probability 0.996389
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11122297 111 - 27905053
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCGAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUCAAGAAUUUUGCGAGCACUAUAU------A--AUAUAGUG
..(((.(((((....(((((..((((..((((((....((((((((....)))))))).)))))))))))))))((((....))))))))))))(((((((.------.--.))))))) ( -39.10)
>DroVir_CAF1 37648 107 - 1
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGUGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUGCGAGCACUAUAUAUACA------------
...(((((((((((......))))))..)))))......(((((.((((.(((((((((....).))))))))(((((....))))).)).))))))).........------------ ( -33.70)
>DroGri_CAF1 36955 107 - 1
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGUGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUGCGAGCACUAUAUAUAUU------------
...(((((((((((......))))))..)))))......(((((.((((.(((((((((....).))))))))(((((....))))).)).))))))).........------------ ( -33.70)
>DroWil_CAF1 36766 106 - 1
UCCUCAGCAAGGAAACGUGCUUCCUUCAAUUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUACGAGCACUAUAUGUA---------U----
......(((.(....)((((((.........((((((..(((((((((.(((...........))).))))))...)))..))))))....))))))....))).---------.---- ( -30.42)
>DroMoj_CAF1 38099 107 - 1
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUGCGUGCACUGUAUAUAGU------------
....(((...(....)((((..((((..((((((....((((((((....)))))))).))))))))))(((.(((((....))))).))))))).)))........------------ ( -35.30)
>DroPer_CAF1 39060 119 - 1
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCGAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUGCGAGCACUAUAUAUAUUUUUUAUUGAAUA
..(((.(((((....)((((..((((..((((((....((((((((....)))))))).))))))))))))))(((((....))))))))))))......................... ( -37.00)
>consensus
UCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUCAAGAAUCUUGCGAGCACUAUAUAUA_U____________
..(((.(((((....(((((..((((..((((((....((((((((....)))))))).)))))))))))))))((((....))))))))))))......................... (-32.36 = -32.42 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,122,328 – 11,122,448
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -32.32
Consensus MFE -31.08
Energy contribution -31.16
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -0.75
Structure conservation index 0.96
SVM decision value 0.06
SVM RNA-class probability 0.564847
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11122328 120 - 27905053
AUUGGUUUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCGAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUC
..........((((((.((...........((((((.......(((((((((((......))))))..))))).....((((((((....))))))))....)))))))).))))))... ( -34.70)
>DroVir_CAF1 37675 120 - 1
AUUGGUAUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGUGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUC
.((((...(((((((........(((.((((((((...........))))))))))).........)))))))...)))).(((((((.(((...........))).)))))))...... ( -31.83)
>DroGri_CAF1 36982 120 - 1
AUUGGUAUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGUGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUC
.((((...(((((((........(((.((((((((...........))))))))))).........)))))))...)))).(((((((.(((...........))).)))))))...... ( -31.83)
>DroWil_CAF1 36792 120 - 1
AUUGGUUUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGUGCUUCCUUCAAUUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUC
...(((.(......).)))..(((((..((((((((.........((((.(....).))))..........(((....((((((((....)))))))).))))))))))).))))).... ( -28.00)
>DroMoj_CAF1 38126 120 - 1
AUUGGUAUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUC
...........((((((...............)).)))).((((.....))))..(((((..((((..((((((....((((((((....)))))))).)))))))))))))))...... ( -33.26)
>DroAna_CAF1 33059 120 - 1
AUUGGUUUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGGUUCUC
..........((((((.((...........((((((.......(((((((((((......))))))..))))).....((((((((....))))))))....)))))))).))))))... ( -34.30)
>consensus
AUUGGUAUUUAGCUGCACCUCAUCGUAUUUCUUGUCAGCCUCCUCAGCAAGGAAACGCGCUUCCUUCAGCUGAUUCUCAAGAGCGUCCAUGCGUUCUUCAUCGGCAAGGGCGCGAUUCUC
...........((((((...............)).)))).((((.....))))..(((((..((((..((((((....((((((((....)))))))).)))))))))))))))...... (-31.08 = -31.16 +   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 11:17:43 2006