Locus 6310

Sequence ID	2L_DroMel_CAF1
Location	17,584,121 – 17,584,256
Length	135
Max. P	0.979399

overview

Window 2

Location	17,584,121 – 17,584,228
Length	107
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.60
Mean single sequence MFE	-27.36
Consensus MFE	-20.54
Energy contribution	-20.32
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-2.70
Structure conservation index	0.75
SVM decision value	0.96
SVM RNA-class probability	0.889961
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17584121 107 + 22407834
CUAUCAUUUUCCAUA---CCUUUUUCUAGCUUAUG--CCUUUGCCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAGCUUUGAACAAUGCGAUACCAUAAUU
.((((..........---..........((.((((--((.............-......)))))).))........(((((((((.......)))))))))))))........ ( -23.01)
>DroPse_CAF1 106862 109 + 1
CUCUCAUGGGCAAUA---CCCCUUCAAAGCGUGUGAGAAA-ACCCACCGAAAUAUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAACUUUGAACAAUGCGAUACCAUAAUU
.(((((((.((....---..........)).)))))))..-...........((((..((((....))))..))))(((((((((.......)))))))))............ ( -29.64)
>DroEre_CAF1 99213 107 + 1
CGAUCAUUUUCCAUG---CCUUUCUCCAGCGUAUG--CCUUUGCCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAGCUUUGAACAAUGCGAUACCAUAAUU
...........((((---((.........(((..(--(....))..)))...-......)))))).......(((.(((((((((.......))))))))).)))........ ( -25.67)
>DroYak_CAF1 101843 106 + 1
CGAUCAUUUUCCAUA---CCUUUUUCUAGCGUAUG--CCU-UGCCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAGCUUUGAACAAUGCGAUACCAUAAUU
..(((......((((---(((......)).)))))--...-...........-(((..((((....))))..))).(((((((((.......))))))))))))......... ( -24.50)
>DroAna_CAF1 105625 108 + 1
CUAG--AUUUCAAAAGGUCCUUCUUCUAGGGUAUG--CGCUAGGCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAAGUUGGAACAAUGCGAUACCAUAGUU
((((--(.................)))))(((((.--(....(....)....-(((..((((....))))..))).((((((((((.....))))))))))))))))...... ( -33.23)
>DroPer_CAF1 107298 109 + 1
CUCUCAUGGGCAAUA---CCCCUUCAAAGUGUGUGAGAAA-ACCCACCGAAAUAUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAACUUUGAACAAUGCGAUACCAUAAUU
.(((((((.((....---..........)).)))))))..-...........((((..((((....))))..))))(((((((((.......)))))))))............ ( -28.14)
>consensus
CUAUCAUUUUCAAUA___CCUUUUUCUAGCGUAUG__CCU_AGCCAACGAAA_AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAACUUUGAACAAUGCGAUACCAUAAUU
...............................((((.......................((((....))))..(((.(((((((((.......))))))))).))).))))... (-20.54 = -20.32 +  -0.22)

alignment

secondary structure

dotplot

Window 3

Location	17,584,121 – 17,584,228
Length	107
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	82.60
Mean single sequence MFE	-29.18
Consensus MFE	-18.58
Energy contribution	-18.92
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.64
SVM decision value	0.37
SVM RNA-class probability	0.710797
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17584121 107 - 22407834
AAUUAUGGUAUCGCAUUGUUCAAAGCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGGCAAAGG--CAUAAGCUAGAAAAAGG---UAUGGAAAAUGAUAG
........(((((((((((((.......)))))))))((((..((((....))))....(-(((((((.((....)--)...)))..)))))...---))))......)))). ( -25.70)
>DroPse_CAF1 106862 109 - 1
AAUUAUGGUAUCGCAUUGUUCAAAGUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAUAUUUCGGUGGGU-UUUCUCACACGCUUUGAAGGGG---UAUUGCCCAUGAGAG
..(((((.(((.(((((((((.......))))))))).)))...((((.(((((..........(((((((.-...))))).)).........))---))))))))))))... ( -33.21)
>DroEre_CAF1 99213 107 - 1
AAUUAUGGUAUCGCAUUGUUCAAAGCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGGCAAAGG--CAUACGCUGGAGAAAGG---CAUGGAAAAUGAUCG
..(((((.....(((((((((.......)))))))))))))).((((....))))..(((-((((((..((....)--)..))(((.......))---)...))))))).... ( -26.90)
>DroYak_CAF1 101843 106 - 1
AAUUAUGGUAUCGCAUUGUUCAAAGCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGGCA-AGG--CAUACGCUAGAAAAAGG---UAUGGAAAAUGAUCG
..(((((.....(((((((((.......)))))))))))))).((((....))))..(((-(((((....).-...--(((((.((......)))---))))))))))).... ( -26.60)
>DroAna_CAF1 105625 108 - 1
AACUAUGGUAUCGCAUUGUUCCAACUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGCCUAGCG--CAUACCCUAGAAGAAGGACCUUUUGAAAU--CUAG
..(((.((((.(((((((((((.....))))))))))......((((....)))).....-....).)))))))..--......(((((.((((....))))....)--)))) ( -30.00)
>DroPer_CAF1 107298 109 - 1
AAUUAUGGUAUCGCAUUGUUCAAAGUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAUAUUUCGGUGGGU-UUUCUCACACACUUUGAAGGGG---UAUUGCCCAUGAGAG
..(((((.(((.(((((((((.......))))))))).)))...((((.(((((............(((((.-...)))))............))---))))))))))))... ( -32.65)
>consensus
AAUUAUGGUAUCGCAUUGUUCAAAGCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU_UUUCGUUGGCA_AGG__CAUACGCUAGAAAAAGG___UAUGGAAAAUGAUAG
...((((.(((.(((((((((.......))))))))).)))..((((....)))).......................))))............................... (-18.58 = -18.92 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	17,584,154 – 17,584,256
Length	102
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	78.63
Mean single sequence MFE	-26.47
Consensus MFE	-16.11
Energy contribution	-15.83
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-2.84
Structure conservation index	0.61
SVM decision value	1.84
SVM RNA-class probability	0.979399
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17584154 102 + 22407834
CUUUGCCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAGC-UUUGAACAA-UGCGAUACCAUAAUUUCCAGGCAACUCGCAAACGCACAAACUC-----------
..(((((...((((-(((..((((....))))..))).(((((((((....-...))))))-)))..........))))..)))))...((....))........----------- ( -28.10)
>DroPse_CAF1 106897 113 + 1
AA-ACCCACCGAAAUAUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAAC-UUUGAACAA-UGCGAUACCAUAAUUUCCAGGCAGCUCUCUCUCGAACAAAUACAUAGGACACCA
..-..((.((....((((..((((....))))..))))(((((((((....-...))))))-)))................))..(.((......)).).........))...... ( -22.80)
>DroEre_CAF1 99246 102 + 1
CUUUGCCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAGC-UUUGAACAA-UGCGAUACCAUAAUUUUCAGGCAACUCGCAAGCGCACAAACGC-----------
..(((((...((((-((...((((....))))..(((.(((((((((....-...))))))-))).))).....)))))).))))).......(((......)))----------- ( -29.90)
>DroWil_CAF1 167665 103 + 1
-------AAUGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAACAUCUGAACAAUUGCGAUACCAUAAUUUUCAGGCA-CACACCAACACACAAUCAA----GCAUCCA
-------..(((..-....((((..((((((.......(((((((((........)))))).)))((...........)).))))-))..)))).......))).----....... ( -22.62)
>DroAna_CAF1 105659 102 + 1
GCUAGGCAACGAAA-AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAAG-UUGGAACAA-UGCGAUACCAUAGUUUCCAGGCAACUCUUGAGCGCACACACUC-----------
(((.((.(((....-(((..((((....))))..))).((((((((((...-..)))))))-))).........))).)).))).......(((.(....).)))----------- ( -32.70)
>DroPer_CAF1 107333 111 + 1
AA-ACCCACCGAAAUAUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAAC-UUUGAACAA-UGCGAUACCAUAAUUUCCAGGCAGCUCU--CUCGAACAAAUACAUAGGACACCA
..-.....((....((((..((((....))))..))))(((((((((....-...))))))-)))...........(((.(((......)--)).)))..........))...... ( -22.70)
>consensus
AA_AGCCAACGAAA_AUAUUUGGCAUGUGCCAUUUAUGGCAUUGUUCCAAC_UUUGAACAA_UGCGAUACCAUAAUUUCCAGGCAACUCUCAAACGCACAAACAC___________
.........((.........((((....))))..(((.(((((((((........)))))).))).))).........................)).................... (-16.11 = -15.83 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	17,584,154 – 17,584,256
Length	102
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	78.63
Mean single sequence MFE	-31.63
Consensus MFE	-19.06
Energy contribution	-18.87
Covariance contribution	-0.19
Combinations/Pair	1.09
Mean z-score	-2.30
Structure conservation index	0.60
SVM decision value	1.28
SVM RNA-class probability	0.939239
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17584154 102 - 22407834
-----------GAGUUUGUGCGUUUGCGAGUUGCCUGGAAAUUAUGGUAUCGCA-UUGUUCAAA-GCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGGCAAAG
-----------...(((((......)))))(((((..((((.(((..(((.(((-((((((...-....))))))))).)))..((((....)))).))).-))))...))))).. ( -29.30)
>DroPse_CAF1 106897 113 - 1
UGGUGUCCUAUGUAUUUGUUCGAGAGAGAGCUGCCUGGAAAUUAUGGUAUCGCA-UUGUUCAAA-GUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAUAUUUCGGUGGGU-UU
......(((((......((((......))))......(((((.(((.(((.(((-((((((...-....))))))))).)))..((((....))))..)))))))).))))).-.. ( -28.60)
>DroEre_CAF1 99246 102 - 1
-----------GCGUUUGUGCGCUUGCGAGUUGCCUGAAAAUUAUGGUAUCGCA-UUGUUCAAA-GCUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGGCAAAG
-----------((((....)))).......((((((((((((.....(((.(((-((((((...-....))))))))).)))..((((....))))...))-)))))..))))).. ( -32.40)
>DroWil_CAF1 167665 103 - 1
UGGAUGC----UUGAUUGUGUGUUGGUGUG-UGCCUGAAAAUUAUGGUAUCGCAAUUGUUCAGAUGUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCAUU-------
.......----.(((..((((.((((((((-((((......(((((((((......(((((........))))))))))))))..))))))))))))))))-..)))..------- ( -34.90)
>DroAna_CAF1 105659 102 - 1
-----------GAGUGUGUGCGCUCAAGAGUUGCCUGGAAACUAUGGUAUCGCA-UUGUUCCAA-CUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU-UUUCGUUGCCUAGC
-----------(((((....)))))....(.((((.(....)...)))).)(((-(((((((..-...))))))))))......((((....)))).....-.............. ( -34.20)
>DroPer_CAF1 107333 111 - 1
UGGUGUCCUAUGUAUUUGUUCGAG--AGAGCUGCCUGGAAAUUAUGGUAUCGCA-UUGUUCAAA-GUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAUAUUUCGGUGGGU-UU
......(((((......((((...--.))))......(((((.(((.(((.(((-((((((...-....))))))))).)))..((((....))))..)))))))).))))).-.. ( -30.40)
>consensus
___________GUGUUUGUGCGAUUGAGAGUUGCCUGGAAAUUAUGGUAUCGCA_UUGUUCAAA_GUUGGAACAAUGCCAUAAAUGGCACAUGCCAAAUAU_UUUCGUUGGCU_AG
...................................(((((.(((((((((......(((((........)))))))))))))).((((....))))......)))))......... (-19.06 = -18.87 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:58 2006