Locus 693

Sequence ID 3R_DroMel_CAF1
Location 2,469,927 – 2,470,087
Length 160
Max. P 0.987187
window1101 window1102 window1103 window1104

overview

Window 1

Location 2,469,927 – 2,470,047
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.40
Mean single sequence MFE -34.95
Consensus MFE -16.09
Energy contribution -16.95
Covariance contribution 0.86
Combinations/Pair 1.26
Mean z-score -2.24
Structure conservation index 0.46
SVM decision value 1.07
SVM RNA-class probability 0.910606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469927 120 + 27905053
GUUGGACAACCUUUUUUGCGCCAAUCUUAAGAGCCUUCUUCUCGGCGGCGGUGAAAUCUUCCUUCUGGCCUACAUCGGCCAGGACGCAAAUGACCUCAUACUGCUUGUCCAGCAACCACU
(((((((((....(((..((((..((....))(((........)))))).)..)))......((((((((......)))))))).(((.(((....)))..))))))))))))....... ( -41.20)
>DroVir_CAF1 23181 117 + 1
--UGG-AGACCUCCUUGGCGCCUAUCUUGAGCGCCUUUUGACGAGCUGCCUCAAAGUCCUCCUGCUGACCCACAUCGGCCAGCACGCAGAUGACCUCAUAGCGCUGCUCCAGCAGCCACU
--.((-((..((....((((((......).))))).......(((....)))..))..))))(((((.((......)).))))).((..(((....))).))(((((....))))).... ( -36.90)
>DroPse_CAF1 28720 120 + 1
GUUAUCUCACCUUAUUGGCGCCGAUAUUGAGAGCCUUCUUUUCGGCCGCUGCAAAGUCCUCUUUCUGGCCAACAUCAGCCAAGACACAGAUGACGUUGUACUGCUGGUCCAGUAGCCAUU
(((((((.......((((((((((....(((......))).))))).((((.((((....)))).))))........))))).....)))))))......((((((...))))))..... ( -33.60)
>DroMoj_CAF1 14403 118 + 1
--UAACCCACCUCCUUGGCUCCGAUUUUGAGCGCCUUCUGGCGGGCUGCCUCAAAGUUCUCCUGCUGGCCAACAUCGGCCAGCACACAGAUAACCUCAUAGCGCUGCUCCAGCAGCCAUU
--...(((.........((((.......))))(((....))))))..((......(((.((.((((((((......))))))))....)).)))......))(((((....))))).... ( -40.70)
>DroAna_CAF1 10718 113 + 1
-------UACCUUCUUGGCUCCUAUUUUCAGAGCCUUUUUCUCGGCCGCCACAAAGUCCUCUUUUUGGCCCACAUCAGCCAGAACACAGAUUACCUCGUACUUUUGGUCCAGCAACCACU
-------.........(((((.........)))))........((..((((.((((....)))).))))........(((((((....((.....))....))))))).......))... ( -22.40)
>DroPer_CAF1 27512 120 + 1
GUUAUCUCACCUUAUUGGCGCCGAUAUUGAGAGCCUUCUUUUCGGCCGCUACAAAGUCCUCUUUCUGGCCAACAUCAGCCAAGACACAGAUGACGUUGUACUGCUGGUCCAGUAGCCAUU
(((((((.......((((((((((....(((......))).))))).((((.((((....)))).))))........))))).....)))))))......((((((...))))))..... ( -34.90)
>consensus
__UAGCCCACCUUCUUGGCGCCGAUAUUGAGAGCCUUCUUCUCGGCCGCCACAAAGUCCUCCUUCUGGCCAACAUCAGCCAGGACACAGAUGACCUCAUACUGCUGGUCCAGCAGCCACU
...............((((.............(((........))).........(((.((.(((((((........)))))))....)).)))........((((...)))).)))).. (-16.09 = -16.95 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,469,927 – 2,470,047
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.40
Mean single sequence MFE -42.17
Consensus MFE -30.45
Energy contribution -28.98
Covariance contribution -1.47
Combinations/Pair 1.55
Mean z-score -2.25
Structure conservation index 0.72
SVM decision value 2.07
SVM RNA-class probability 0.987187
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469927 120 - 27905053
AGUGGUUGCUGGACAAGCAGUAUGAGGUCAUUUGCGUCCUGGCCGAUGUAGGCCAGAAGGAAGAUUUCACCGCCGCCGAGAAGAAGGCUCUUAAGAUUGGCGCAAAAAAGGUUGUCCAAC
.........(((((((.(....(((((((.(((...((.(((((......))))))).))).)))))))..((.(((((.((((....))))....)))))))......).))))))).. ( -41.00)
>DroVir_CAF1 23181 117 - 1
AGUGGCUGCUGGAGCAGCGCUAUGAGGUCAUCUGCGUGCUGGCCGAUGUGGGUCAGCAGGAGGACUUUGAGGCAGCUCGUCAAAAGGCGCUCAAGAUAGGCGCCAAGGAGGUCU-CCA--
(((.(((((....)))))(((.(((((((.....(.((((((((......)))))))).)..))))))).))).)))........((((((.......))))))..(((....)-)).-- ( -49.70)
>DroPse_CAF1 28720 120 - 1
AAUGGCUACUGGACCAGCAGUACAACGUCAUCUGUGUCUUGGCUGAUGUUGGCCAGAAAGAGGACUUUGCAGCGGCCGAAAAGAAGGCUCUCAAUAUCGGCGCCAAUAAGGUGAGAUAAC
..(((((((((......)))))((((((((.(((.....))).))))))))))))...........(((.((.((((........)))))))))((((..((((.....)))).)))).. ( -35.50)
>DroMoj_CAF1 14403 118 - 1
AAUGGCUGCUGGAGCAGCGCUAUGAGGUUAUCUGUGUGCUGGCCGAUGUUGGCCAGCAGGAGAACUUUGAGGCAGCCCGCCAGAAGGCGCUCAAAAUCGGAGCCAAGGAGGUGGGUUA--
....(((((....)))))(((.(((((((.(((...(((((((((....)))))))))))).))))))).)))((((((((.....(.((((.......))))).....)))))))).-- ( -54.70)
>DroAna_CAF1 10718 113 - 1
AGUGGUUGCUGGACCAAAAGUACGAGGUAAUCUGUGUUCUGGCUGAUGUGGGCCAAAAAGAGGACUUUGUGGCGGCCGAGAAAAAGGCUCUGAAAAUAGGAGCCAAGAAGGUA-------
..((((((((..((.....))(((((((..(((...((.(((((......))))))).)))..))))))))))))))).......((((((.......)))))).........------- ( -35.30)
>DroPer_CAF1 27512 120 - 1
AAUGGCUACUGGACCAGCAGUACAACGUCAUCUGUGUCUUGGCUGAUGUUGGCCAGAAAGAGGACUUUGUAGCGGCCGAAAAGAAGGCUCUCAAUAUCGGCGCCAAUAAGGUGAGAUAAC
.((((((((((......)))))....)))))...((((((.((((((((((((.(.((((....)))).).))((((........))))..))))))))))(((.....))))))))).. ( -36.80)
>consensus
AAUGGCUGCUGGACCAGCAGUACGAGGUCAUCUGUGUCCUGGCCGAUGUUGGCCAGAAAGAGGACUUUGAGGCGGCCGAAAAGAAGGCUCUCAAAAUCGGCGCCAAGAAGGUGAGAUA__
...((((((((.((.....)).(((((((.(((.....((((((......))))))..))).)))))))))))))))........(((.((.......)).)))................ (-30.45 = -28.98 +  -1.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,469,967 – 2,470,087
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.67
Mean single sequence MFE -41.80
Consensus MFE -20.29
Energy contribution -21.72
Covariance contribution 1.42
Combinations/Pair 1.37
Mean z-score -2.55
Structure conservation index 0.49
SVM decision value 1.02
SVM RNA-class probability 0.901232
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469967 120 + 27905053
CUCGGCGGCGGUGAAAUCUUCCUUCUGGCCUACAUCGGCCAGGACGCAAAUGACCUCAUACUGCUUGUCCAGCAACCACUUGAGGACGCAACUAGUGUCCAGGCCACCGGAGUAAGCCAA
.((((.((((((.............(((((......)))))(((((((.(((....)))..)))..))))....)))......((((((.....))))))..))).)))).......... ( -41.80)
>DroVir_CAF1 23218 120 + 1
ACGAGCUGCCUCAAAGUCCUCCUGCUGACCCACAUCGGCCAGCACGCAGAUGACCUCAUAGCGCUGCUCCAGCAGCCACUUUAGUAUGCAGCUCGUAUCCAGGCCACCCGAAUAGGCCAA
(((((((((..((((((.....(((((.((......)).))))).((..(((....))).))(((((....))))).))))).)...))))))))).....((((.........)))).. ( -44.10)
>DroPse_CAF1 28760 120 + 1
UUCGGCCGCUGCAAAGUCCUCUUUCUGGCCAACAUCAGCCAAGACACAGAUGACGUUGUACUGCUGGUCCAGUAGCCAUUUAAGAAUGCAGCUGGUGUCCAAUCCGCCGGAAUAGGCCAA
...((((((((((..(((.(((.((((((........))).)))...))).)))......((((((...))))))...........))))))(((((.......))))).....)))).. ( -39.70)
>DroGri_CAF1 15192 120 + 1
UCUUGCUGCCUCAAAGUUCUCCUGCUGACCGACAUCGGCCAGCACGCAGAUGACCUCGUAGCGCUGCUCCAGCAACCACUUGAGUAUGCAGCUUGUGUCGAGGCCACCGGAGUAGGCCAA
.(((((((((((.....((((.(((((.(((....))).))))).).))).(((..((.((((((((((.((......)).))))).)).))))).))))))))......)))))).... ( -40.80)
>DroMoj_CAF1 14441 120 + 1
GCGGGCUGCCUCAAAGUUCUCCUGCUGGCCAACAUCGGCCAGCACACAGAUAACCUCAUAGCGCUGCUCCAGCAGCCAUUUGAGUAUGCAGCUCGUAUCCAGGCCACCCGAAUAGGCCAA
(((((((((((((((..(((..((((((((......))))))))...)))..........(.(((((....)))))).))))))...))))))))).....((((.........)))).. ( -53.30)
>DroAna_CAF1 10751 120 + 1
CUCGGCCGCCACAAAGUCCUCUUUUUGGCCCACAUCAGCCAGAACACAGAUUACCUCGUACUUUUGGUCCAGCAACCACUUGAGGAUACAGCUCGUAUCCAGGCCCCCAGAGUAGGCUAA
...((((.......((((....(((((((........)))))))....))))......((((((.((.((..(((....))).((((((.....)))))).))..)).)))))))))).. ( -31.10)
>consensus
CCCGGCUGCCUCAAAGUCCUCCUGCUGGCCAACAUCGGCCAGCACACAGAUGACCUCAUACCGCUGCUCCAGCAACCACUUGAGUAUGCAGCUCGUAUCCAGGCCACCGGAAUAGGCCAA
...(((.((......(((.((.((((((((......))))))))....)).)))((((....((((......))))....))))...)).)))........((((.........)))).. (-20.29 = -21.72 +   1.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,469,967 – 2,470,087
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.67
Mean single sequence MFE -48.12
Consensus MFE -34.13
Energy contribution -33.00
Covariance contribution -1.13
Combinations/Pair 1.63
Mean z-score -1.98
Structure conservation index 0.71
SVM decision value 1.25
SVM RNA-class probability 0.935548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469967 120 - 27905053
UUGGCUUACUCCGGUGGCCUGGACACUAGUUGCGUCCUCAAGUGGUUGCUGGACAAGCAGUAUGAGGUCAUUUGCGUCCUGGCCGAUGUAGGCCAGAAGGAAGAUUUCACCGCCGCCGAG
(((((....(((((..(((.((((.(.....).))))......)))..)))))...((.((..((((((.(((...((.(((((......))))))).))).)))))))).)).))))). ( -45.60)
>DroVir_CAF1 23218 120 - 1
UUGGCCUAUUCGGGUGGCCUGGAUACGAGCUGCAUACUAAAGUGGCUGCUGGAGCAGCGCUAUGAGGUCAUCUGCGUGCUGGCCGAUGUGGGUCAGCAGGAGGACUUUGAGGCAGCUCGU
..((((.........)))).....(((((((((.......((((.((((....))))))))..((((((.....(.((((((((......)))))))).)..))))))...))))))))) ( -55.20)
>DroPse_CAF1 28760 120 - 1
UUGGCCUAUUCCGGCGGAUUGGACACCAGCUGCAUUCUUAAAUGGCUACUGGACCAGCAGUACAACGUCAUCUGUGUCUUGGCUGAUGUUGGCCAGAAAGAGGACUUUGCAGCGGCCGAA
((((((...(((((....))))).....((((((.((((...(((((((((......)))))((((((((.(((.....))).)))))))))))).....))))...)))))))))))). ( -46.10)
>DroGri_CAF1 15192 120 - 1
UUGGCCUACUCCGGUGGCCUCGACACAAGCUGCAUACUCAAGUGGUUGCUGGAGCAGCGCUACGAGGUCAUCUGCGUGCUGGCCGAUGUCGGUCAGCAGGAGAACUUUGAGGCAGCAAGA
...((((.((((((((((((((......(((((....((.(((....))).)))))))....))))))))))....(((((((((....))))))))))))).......))))....... ( -53.30)
>DroMoj_CAF1 14441 120 - 1
UUGGCCUAUUCGGGUGGCCUGGAUACGAGCUGCAUACUCAAAUGGCUGCUGGAGCAGCGCUAUGAGGUUAUCUGUGUGCUGGCCGAUGUUGGCCAGCAGGAGAACUUUGAGGCAGCCCGC
..((((.........))))......((.(((((...(((.....(((((....))))).....((((((.(((...(((((((((....)))))))))))).)))))))))))))).)). ( -49.90)
>DroAna_CAF1 10751 120 - 1
UUAGCCUACUCUGGGGGCCUGGAUACGAGCUGUAUCCUCAAGUGGUUGCUGGACCAAAAGUACGAGGUAAUCUGUGUUCUGGCUGAUGUGGGCCAAAAAGAGGACUUUGUGGCGGCCGAG
(..(((...((..(.((((.((((((.....))))))......)))).)..))......(((((((((..(((...((.(((((......))))))).)))..))))))).)))))..). ( -38.60)
>consensus
UUGGCCUACUCCGGUGGCCUGGACACGAGCUGCAUACUCAAGUGGCUGCUGGACCAGCACUACGAGGUCAUCUGCGUGCUGGCCGAUGUGGGCCAGAAGGAGGACUUUGAGGCAGCCGAA
..((((.........)))).........(((((...........((((......))))....(((((((.(((....(((((((......))))))).))).)))))))..))))).... (-34.13 = -33.00 +  -1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:36 2006