Locus 5115

Sequence ID 3L_DroMel_CAF1
Location 14,051,428 – 14,051,573
Length 145
Max. P 0.891968
window8101 window8102 window8103

overview

Window 1

Location 14,051,428 – 14,051,540
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 85.59
Mean single sequence MFE -24.14
Consensus MFE -16.90
Energy contribution -17.07
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.23
Structure conservation index 0.70
SVM decision value 0.36
SVM RNA-class probability 0.704551
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14051428 112 + 23771897
AAGGAAAACGGUUUAUUAUAC------GAAUGCGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAAUGCAUACAUAAAACCACACUCAAA
.........(((((....((.------(.(((((.((..........((((((((((....((.....))..)))))))))).........)).))))).).)))))))......... ( -19.81)
>DroGri_CAF1 48457 111 + 1
-----AAACGGUUUAUUAUGCUUAUGCGAAUGUGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAG--CAAUACAAUGCAUACAUAAAACCGCACACACA
-----...((((((..((((..((((((..(((.......)))....((((((((((....((.....))..))))))))))..--........))))))))))))))))........ ( -26.90)
>DroWil_CAF1 64252 102 + 1
---CGAAACGGUUUAUUAUGC------GAAUGCGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAG-------CAAUACACACAUAAAACCACACACAGG
---......(((((..((((.------(..(((..((....))....((((((((((....((.....))..)))))))))).)-------)).....).)))))))))......... ( -20.20)
>DroMoj_CAF1 54367 111 + 1
-----AAACGGUUUAUUAUGCUUAUGCGAAUGUGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAG--CAAUACAAUGCACACAUAAAACCACACACACA
-----....(((((....(((....))).(((((.............((((((((((....((.....))..)))))))))).(--((......))).))))).)))))......... ( -27.50)
>DroAna_CAF1 51413 112 + 1
UACCAGAACGGUUUAUUAUAC------GAAUACGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCGGGCCAAUACAAUGCACACAUAAAACCGCACUCACA
........((((((.((((.(------(....)))))).........((((((((((....((.....))..))))))))))......................))))))........ ( -19.90)
>DroPer_CAF1 54177 117 + 1
AAUGAGAACGGUUUAUUAUACGCGUGUGAAUGCGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCA-GCCAAUACAAUGCACACAUAAAACCGCACUCGCA
...(((..((((((.((((.(((((....))))))))).........((((((((((....((.....))..)))))))))).-....................))))))..)))... ( -30.50)
>consensus
____AAAACGGUUUAUUAUAC______GAAUGCGAUGACAACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAG__CAAUACAAUGCACACAUAAAACCACACACACA
.........(((((.................................((((((((((....((.....))..))))))))))...........(((....))).)))))......... (-16.90 = -17.07 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,051,428 – 14,051,540
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -28.53
Consensus MFE -22.58
Energy contribution -21.36
Covariance contribution -1.22
Combinations/Pair 1.25
Mean z-score -2.99
Structure conservation index 0.79
SVM decision value 0.97
SVM RNA-class probability 0.891968
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14051428 112 - 23771897
UUUGAGUGUGGUUUUAUGUAUGCAUUGUAUUGGCCUGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCGCAUUC------GUAUAAUAAACCGUUUUCCUU
...(((..((((((..((((((...(((..((((..((((((((((...............))))))))))........))))..)))..)------)))))..))))))..)))... ( -27.66)
>DroGri_CAF1 48457 111 - 1
UGUGUGUGCGGUUUUAUGUAUGCAUUGUAUUG--CUGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCACAUUCGCAUAAGCAUAAUAAACCGUUU-----
.......((((((((((((((((..(((..((--(.((((((((((...............))))))))))........).))..)))...))))..)))))..)))))))..----- ( -26.76)
>DroWil_CAF1 64252 102 - 1
CCUGUGUGUGGUUUUAUGUGUGUAUUG-------CUGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCGCAUUC------GCAUAAUAAACCGUUUCG---
.........(((((..((((((...((-------(.((((((((((...............))))))))))....((....))..)))..)------)))))..)))))......--- ( -25.56)
>DroMoj_CAF1 54367 111 - 1
UGUGUGUGUGGUUUUAUGUGUGCAUUGUAUUG--CUGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCACAUUCGCAUAAGCAUAAUAAACCGUUU-----
(((.(((((((....(((((.(((......))--).((((((((((...............)))))))))).............)))))))))))).))).............----- ( -26.26)
>DroAna_CAF1 51413 112 - 1
UGUGAGUGCGGUUUUAUGUGUGCAUUGUAUUGGCCCGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCGUAUUC------GUAUAAUAAACCGUUCUGGUA
..(.((.(((((((....(((((...((((((((..((((((((((...............))))))))))........))))..))))..------)))))..))))))).)).).. ( -26.56)
>DroPer_CAF1 54177 117 - 1
UGCGAGUGCGGUUUUAUGUGUGCAUUGUAUUGGC-UGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCGCAUUCACACGCGUAUAAUAAACCGUUCUCAUU
...(((.(((((((((((((((...(((..((((-.((((((((((...............))))))))))........))))..)))....))))))))....))))))).)))... ( -38.36)
>consensus
UGUGAGUGCGGUUUUAUGUGUGCAUUGUAUUG__CUGGCAUAAUAGACACAUUUAAUUUUACUAUUAUGCCUUUUUGUUGUCAUCGCAUUC______GCAUAAUAAACCGUUUU____
........((((((....(((((.............((((((((((...............)))))))))).......(((....))).........)))))..))))))........ (-22.58 = -21.36 +  -1.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,051,462 – 14,051,573
Length 111
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -18.59
Consensus MFE -13.20
Energy contribution -13.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.03
Structure conservation index 0.71
SVM decision value 0.88
SVM RNA-class probability 0.872936
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14051462 111 + 23771897
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAAUGCAUACAUAAAACCACACUCAAACC----UAGCAAAA---CCGAGAGCUAUACAAUCUCAAAU
.......((((((((((....((.....))..))))))))))............(((.......................----..)))...---..((((.........)))).... ( -16.91)
>DroSim_CAF1 50969 111 + 1
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAAUGCAUACAUAAAACCACACUCAAACC----UAGCAAAA---CCGAAAGCUAUACAAUCUCGAAU
.......((((((((((....((.....))..))))))))))......................................----((((....---......))))............. ( -15.20)
>DroEre_CAF1 47786 111 + 1
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAAUGCAUACAUAAAACCACACGCAAACC----UAGCAAAA---UUCAGAGCCAUACAAUCUCAAAU
.......((((((((((....((.....))..)))))))))).((((......(((....)))..........((.....----..))....---....).))).............. ( -18.80)
>DroYak_CAF1 51532 107 + 1
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAA----UACAUAAAACCACACUCAAACC----CAGCAAAA---CCGAGAGCUAUACAAUCUCAAAU
.......((((((((((....((.....))..))))))))))............----......................----........---..((((.........)))).... ( -16.80)
>DroMoj_CAF1 54402 97 + 1
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAG--CAAUACAAUGCACACAUAAAACCACACACACACA----GAGGCU-------GAUACA--------CUCACAC
.......((((((((((....((.....))..)))))))))).(--((......))).......................----(((...-------......--------))).... ( -17.90)
>DroAna_CAF1 51447 118 + 1
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCGGGCCAAUACAAUGCACACAUAAAACCGCACUCACACCCACAUAGCAGGCCAGGCAGGAGCCUUGAAAUCAUAAAU
.......((((((((((....((.....))..)))))))))).((((......(((....)))......((...............)).))))((((....))))............. ( -25.96)
>consensus
ACAAAAAGGCAUAAUAGUAAAAUUAAAUGUGUCUAUUAUGCCAGGCCAAUACAAUGCAUACAUAAAACCACACUCAAACC____UAGCAAAA___CCGAGAGCUAUACAAUCUCAAAU
.......((((((((((....((.....))..))))))))))............................................................................ (-13.20 = -13.20 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:21 2006