Locus 3541

Sequence ID 2L_DroMel_CAF1
Location 10,334,840 – 10,335,023
Length 183
Max. P 0.999901
window5588 window5589 window5590 window5591 window5592 window5593

overview

Window 8

Location 10,334,840 – 10,334,943
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -23.30
Consensus MFE -19.55
Energy contribution -19.15
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -1.64
Structure conservation index 0.84
SVM decision value 0.70
SVM RNA-class probability 0.826771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334840 103 + 22407834
CAAAGAAACGAAUUUACAUUAAUUACGCACAUACACAAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACA
......................(((((((((......((....))......)))))))))((.((...(((((.(((....))).)))))...)).))..... ( -21.30)
>DroSec_CAF1 701 103 + 1
CAAAGAAACGAAUUUACAUUAAUUACGCACAUACACCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCUCGCACACA
..((((....((((......))))..((..........))....))))....((((((((((......(((((.(((....))).)))))..)))))))))). ( -23.30)
>DroSim_CAF1 701 103 + 1
CAAAGAAACGAAUUUACAUUAAUUACGCACAUACACCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACA
......................(((((((((......((....))......)))))))))((.((...(((((.(((....))).)))))...)).))..... ( -21.30)
>DroEre_CAF1 392 103 + 1
CAAAGAAACGAAUUUACAUUAAUUACGCACACACACCAGCGUGCGCAUACCUGUGUGUGUGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACA
...............((((......(((((.(......).))))).......))))((((((.((...(((((.(((....))).)))))...)).)))))). ( -28.92)
>DroYak_CAF1 686 103 + 1
CAAAGAAACGAAUUUACAUUAAUUACGCACACACACAAGCGCGCACAUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACA
..........................((.........(((.(((((((....))))))).)))((...(((((.(((....))).)))))...)).))..... ( -21.70)
>consensus
CAAAGAAACGAAUUUACAUUAAUUACGCACAUACACCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACA
........((((((......)))).))((((((((................)))))))).((.((...(((((.(((....))).)))))...)).))..... (-19.55 = -19.15 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,334,840 – 10,334,943
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -32.00
Consensus MFE -27.52
Energy contribution -26.96
Covariance contribution -0.56
Combinations/Pair 1.10
Mean z-score -2.69
Structure conservation index 0.86
SVM decision value 3.07
SVM RNA-class probability 0.998336
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334840 103 - 22407834
UGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUUGUGUAUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
.(((.(..((...(((((((((....)))))))))...))..).)))(((((((((......)))))))))...(((((.....))))).............. ( -29.30)
>DroSec_CAF1 701 103 - 1
UGUGUGCGAGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGGUGUAUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
((((((.(((...(((((((((....))))))))).......))).))))))...((((((((((....))))))(((.((((......))))))).)))).. ( -29.00)
>DroSim_CAF1 701 103 - 1
UGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGGUGUAUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
((((((.(((...(((((((((....))))))))).......))).))))))...((((((((((....))))))(((.((((......))))))).)))).. ( -28.10)
>DroEre_CAF1 392 103 - 1
UGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACACACACACAGGUAUGCGCACGCUGGUGUGUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
((((((..((...(((((((((....)))))))))...))..)))))).(((..(((((((((((....))))))))))).....)))............... ( -39.70)
>DroYak_CAF1 686 103 - 1
UGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAUGUGCGCGCUUGUGUGUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
.(((((..((...(((((((((....)))))))))...))....)))))(((..((((..(((((....)))))..)))).....)))............... ( -33.90)
>consensus
UGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGGUGUAUGUGCGUAAUUAAUGUAAAUUCGUUUCUUUG
((((((.(((...(((((((((....))))))))).......))).)))))).......((((((....))))))(((.((((......)))))))....... (-27.52 = -26.96 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,334,875 – 10,334,983
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 93.24
Mean single sequence MFE -41.52
Consensus MFE -36.22
Energy contribution -35.90
Covariance contribution -0.32
Combinations/Pair 1.12
Mean z-score -2.68
Structure conservation index 0.87
SVM decision value 3.66
SVM RNA-class probability 0.999502
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334875 108 + 22407834
CAAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACUUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGU
...(((((((.......(((((((....((...(((((.(((....))).)))))...))..)))))))((((((....((((....)))).)))))).))))))).. ( -39.90)
>DroSec_CAF1 736 108 + 1
CCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCUCGCACACACGCGCACAUUUGCGAGUACUUGCCGUGCGCUGGUGUGUGU
...(((((((......(((((((((((......(((((.(((....))).)))))..))))))))))).((((((....((((....)))).)))))).))))))).. ( -42.20)
>DroSim_CAF1 736 108 + 1
CCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACAUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGU
(((((............(((((((.((.((...(((((.(((....))).)))))...)).)).)))))))((((....((((....)))).)))))))))....... ( -40.00)
>DroEre_CAF1 427 108 + 1
CCAGCGUGCGCAUACCUGUGUGUGUGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACAAGCGCACUUUUGCGAGUGCUUGCCGUGCGGUGGUAUGUGU
((((((..(((((....)))))..))))))...(((((.(((....))).)))))((((((((((.(((((((.(......).)))))))..)))))..))))).... ( -45.50)
>DroYak_CAF1 721 108 + 1
CAAGCGCGCACAUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACAAGCACACUUCUGCGAGUGCUUGCCGUGCGCUAGUGUGUGU
...((((((((.....((((((((....((...(((((.(((....))).)))))...))))))))))(((.(((....((((....)))).))).))).)))))))) ( -40.00)
>consensus
CCAGCAUGCUCUUACCUGUGUGUGAGUUGGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACUUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGU
...((((((.......((((((((....((...(((((.(((....))).)))))...)))))))))).((((((....((((....)))).))))))..)))))).. (-36.22 = -35.90 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,334,875 – 10,334,983
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 93.24
Mean single sequence MFE -40.50
Consensus MFE -34.52
Energy contribution -34.64
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -3.58
Structure conservation index 0.85
SVM decision value 3.99
SVM RNA-class probability 0.999746
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334875 108 - 22407834
ACACACACCAGCGCACGGCAAGCACUCGCAAAAGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUUG
......(((.((((((.((........))....))))))(((((((..((...(((((((((....)))))))))...))....))))))).)))..(((....))). ( -41.00)
>DroSec_CAF1 736 108 - 1
ACACACACCAGCGCACGGCAAGUACUCGCAAAUGUGCGCGUGUGUGCGAGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGG
.......(((((((((.((........))....))))((.((((((.(((...(((((((((....))))))))).......))).)))))).))........))))) ( -39.50)
>DroSim_CAF1 736 108 - 1
ACACACACCAGCGCACGGCAAGCACUCGCAAAUGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGG
......(((.(((((((....((....))...)))))))(((((((..((...(((((((((....)))))))))...))....))))))).)))............. ( -40.50)
>DroEre_CAF1 427 108 - 1
ACACAUACCACCGCACGGCAAGCACUCGCAAAAGUGCGCUUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACACACACACAGGUAUGCGCACGCUGG
.(.((((((..(((((.((........))....)))))..((((((..((...(((((((((....)))))))))...))..))))))....)))))).)........ ( -39.60)
>DroYak_CAF1 721 108 - 1
ACACACACUAGCGCACGGCAAGCACUCGCAGAAGUGUGCUUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAUGUGCGCGCUUG
..........(((((((....(((((......)))))(((((((((.(((...(((((((((....))))))))).......))).))))))))).)))))))..... ( -41.90)
>consensus
ACACACACCAGCGCACGGCAAGCACUCGCAAAAGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCCAACUCACACACAGGUAAGAGCAUGCUGG
.......((((((....((..((((........))))((.((((((.(((...(((((((((....))))))))).......))).)))))).))....)).)))))) (-34.52 = -34.64 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,334,903 – 10,335,023
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -36.92
Consensus MFE -32.88
Energy contribution -33.32
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.89
SVM decision value 1.97
SVM RNA-class probability 0.984460
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334903 120 + 22407834
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACUUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((...(((((.(((....))).)))))...)).((((((((((((((....((((....)))).))))))..))))))))..(((((...(((..(((.......)))..))).))))). ( -37.50)
>DroSec_CAF1 764 120 + 1
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCUCGCACACACGCGCACAUUUGCGAGUACUUGCCGUGCGCUGGUGUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((((((((((.(((....))).)))))......((((((((((((((....((((....)))).))))))..)))))))))))))..........(((.......)))............ ( -36.10)
>DroSim_CAF1 764 120 + 1
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACAUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((...(((((.(((....))).)))))...)).((((((((((((((....((((....)))).))))))..))))))))..(((((...(((..(((.......)))..))).))))). ( -37.50)
>DroEre_CAF1 455 120 + 1
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACAAGCGCACUUUUGCGAGUGCUUGCCGUGCGGUGGUAUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((...(((((.(((....))).)))))...))(((((.(((((((.(......).)))))))..)))))(((((...(((.(((.....))).)))..)))))................. ( -37.20)
>DroYak_CAF1 749 120 + 1
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACAAGCACACUUCUGCGAGUGCUUGCCGUGCGCUAGUGUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((...(((((.(((....))).)))))...))(((((.(((((((.(......).)))))))..)))))...((((((((((((.....)))...)))).)))))............... ( -36.30)
>consensus
GGAUAUAUCGCGUAUAUGUACACGAUAAUGCCCGCACACACGCGCACUUUUGCGAGUGCUUGCCGUGCGCUGGUGUGUGUUAUCUAUGUGAUUACGACACCACACGUCAAAAUAAUAGGA
((...(((((.(((....))).)))))...))(((((((..((((((....((((....)))).))))))..)))))))...(((((...(((..(((.......)))..))).))))). (-32.88 = -33.32 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,334,903 – 10,335,023
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -40.96
Consensus MFE -37.76
Energy contribution -38.04
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -3.16
Structure conservation index 0.92
SVM decision value 4.45
SVM RNA-class probability 0.999901
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10334903 120 - 22407834
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACACACCAGCGCACGGCAAGCACUCGCAAAAGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
.(((.((((((....(((((((......)))))))))))))(((((((..((((((.((........))....))))))))))))).)))...(((((((((....)))))))))..... ( -41.50)
>DroSec_CAF1 764 120 - 1
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACACACCAGCGCACGGCAAGUACUCGCAAAUGUGCGCGUGUGUGCGAGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
...............(((((((......))))))).((((.(((((((..((((((.((........))....))))))))))))).......(((((((((....))))))))))))). ( -40.00)
>DroSim_CAF1 764 120 - 1
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACACACCAGCGCACGGCAAGCACUCGCAAAUGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
.(((.((((((....(((((((......)))))))))))))(((((((..(((((((....((....))...)))))))))))))).)))...(((((((((....)))))))))..... ( -41.70)
>DroEre_CAF1 455 120 - 1
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACAUACCACCGCACGGCAAGCACUCGCAAAAGUGCGCUUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
...............(((((((......))))))).((((..........(((((((.(((((.(.(......).).))))))))))))....(((((((((....))))))))))))). ( -39.70)
>DroYak_CAF1 749 120 - 1
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACACACUAGCGCACGGCAAGCACUCGCAGAAGUGUGCUUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
...............(((((.((((...........)))).))))).....((((((.(((((((.(......).)))))))))))))((...(((((((((....)))))))))...)) ( -41.90)
>consensus
UCCUAUUAUUUUGACGUGUGGUGUCGUAAUCACAUAGAUAACACACACCAGCGCACGGCAAGCACUCGCAAAAGUGCGCGUGUGUGCGGGCAUUAUCGUGUACAUAUACGCGAUAUAUCC
...............(((((((......))))))).((((.(((((((..((((((.((........))....))))))))))))).......(((((((((....))))))))))))). (-37.76 = -38.04 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:01 2006