Locus 6163

Sequence ID	2L_DroMel_CAF1
Location	17,169,311 – 17,169,452
Length	141
Max. P	0.950194

overview

Window 0

Location	17,169,311 – 17,169,425
Length	114
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	72.63
Mean single sequence MFE	-25.24
Consensus MFE	-9.68
Energy contribution	-10.00
Covariance contribution	0.32
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.38
SVM decision value	1.14
SVM RNA-class probability	0.922003
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17169311 114 + 22407834
UAAGUACUGGAAUCAGACGUCAUAAAGA---AUUUGUGGAUACUAGACUACUAGUUUGACCUUCGAAA-CAAAACAGGCCUUUAUUUGCCUGUCUGUUUUGUAUUUAAUCCUUUUCCA
(((((((.(((.((((((.((((((...---..))))))....(((....)))))))))..)))((((-((..((((((........)))))).)))))))))))))........... ( -25.60)
>DroSec_CAF1 14790 114 + 1
UAAAGACUUGAAUCAGACUGCAUAAAGA---AUUUGUGGAAACUAGACAUCUAGUUAUACCUUUGAAA-CAGAACAGGCCUUUAUGUGCCUGUCUGUUUUGUUUUUUAUCCUUUUCCA
.((((((.....((((((..((......---...))..).((((((....)))))).....)))))((-((((.((((((.....).)))))))))))..))))))............ ( -28.00)
>DroSim_CAF1 14768 103 + 1
UAAAG-----------ACUGCAUAAAGA---AUUUGUGGAAACUAGACAUCUAGUUAUACGUUUGAAA-CAAAACAGGCCUUUAUGUGCCUGUCUGUUUUGUUUUUUAUUCUUUUCCA
.((((-----------(....(((((((---((..(((..((((((....)))))).)))....((((-((..(((((((.....).)))))).)))))))))))))))))))).... ( -25.60)
>DroEre_CAF1 14915 105 + 1
UCAGGACUGGAAUCAGACUUCAUAAAGAAAACUUUGUGAAUACAAGAC------UU-------UGUAAUCUAAGCAGGCCUUUUUGUGCCUGUUCGAUUGGUAUUUUACCAUUUUCCA
...(((....(((((((.(((((((((....)))))))))(((((...------.)-------)))).))).((((((((.....).))))))).))))((((...))))....))). ( -27.10)
>DroYak_CAF1 15845 112 + 1
UUAAGACGGAAAUCAGAAAGCAUGAAAAAAAAUUGGUGAAUACUAGAG------UUCUACCUCCGAAAUCAAAACAGGCCUUUUUGUGAAUGUCUGAUUGGUAUUUUAAUAUUUUCCA
.......((((((((((...((..((((......(((((((......)------))).))).((............))..))))..))....)))))))(((((....))))).))). ( -19.90)
>consensus
UAAAGACUGGAAUCAGACUGCAUAAAGA___AUUUGUGGAUACUAGAC__CUAGUUAUACCUUUGAAA_CAAAACAGGCCUUUAUGUGCCUGUCUGUUUUGUAUUUUAUCCUUUUCCA
....................((((((......))))))(((((.((((................(....)...((((((........))))))..)))).)))))............. ( -9.68 = -10.00 +   0.32)

alignment

secondary structure

dotplot

Window 1

Location	17,169,311 – 17,169,425
Length	114
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	72.63
Mean single sequence MFE	-24.20
Consensus MFE	-9.44
Energy contribution	-11.32
Covariance contribution	1.88
Combinations/Pair	1.18
Mean z-score	-2.10
Structure conservation index	0.39
SVM decision value	1.40
SVM RNA-class probability	0.950194
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17169311 114 - 22407834
UGGAAAAGGAUUAAAUACAAAACAGACAGGCAAAUAAAGGCCUGUUUUG-UUUCGAAGGUCAAACUAGUAGUCUAGUAUCCACAAAU---UCUUUAUGACGUCUGAUUCCAGUACUUA
(((((..((((...((((.((((((((((((........))))).))))-))).)..((....(((((....)))))..))......---....)))...))))..)))))....... ( -28.30)
>DroSec_CAF1 14790 114 - 1
UGGAAAAGGAUAAAAAACAAAACAGACAGGCACAUAAAGGCCUGUUCUG-UUUCAAAGGUAUAACUAGAUGUCUAGUUUCCACAAAU---UCUUUAUGCAGUCUGAUUCAAGUCUUUA
..(((..((((........((((((((((((........))))).))))-)))....((...((((((....)))))).))......---..........))))..)))......... ( -29.00)
>DroSim_CAF1 14768 103 - 1
UGGAAAAGAAUAAAAAACAAAACAGACAGGCACAUAAAGGCCUGUUUUG-UUUCAAACGUAUAACUAGAUGUCUAGUUUCCACAAAU---UCUUUAUGCAGU-----------CUUUA
....(((((((........((((((((((((........))))).))))-))).....((..((((((....))))))...))..))---))))).......-----------..... ( -24.00)
>DroEre_CAF1 14915 105 - 1
UGGAAAAUGGUAAAAUACCAAUCGAACAGGCACAAAAAGGCCUGCUUAGAUUACA-------AA------GUCUUGUAUUCACAAAGUUUUCUUUAUGAAGUCUGAUUCCAGUCCUGA
(((((..(((((...)))))......(((((........))))).((((((((((-------(.------...)))))((((.((((....)))).)))))))))))))))....... ( -25.00)
>DroYak_CAF1 15845 112 - 1
UGGAAAAUAUUAAAAUACCAAUCAGACAUUCACAAAAAGGCCUGUUUUGAUUUCGGAGGUAGAA------CUCUAGUAUUCACCAAUUUUUUUUCAUGCUUUCUGAUUUCCGUCUUAA
.(((((.............(((((((((..(........)..)).)))))))((((((((((((------....(((........)))....))).))).)))))))))))....... ( -14.70)
>consensus
UGGAAAAGGAUAAAAUACAAAACAGACAGGCACAUAAAGGCCUGUUUUG_UUUCAAAGGUAUAACUAG__GUCUAGUAUCCACAAAU___UCUUUAUGCAGUCUGAUUCCAGUCUUUA
((((...................((((((((........))))))))................(((((....))))).)))).................................... ( -9.44 = -11.32 +   1.88)

alignment

secondary structure

dotplot

Window 2

Location	17,169,348 – 17,169,452
Length	104
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	73.67
Mean single sequence MFE	-20.71
Consensus MFE	-7.02
Energy contribution	-7.86
Covariance contribution	0.84
Combinations/Pair	1.18
Mean z-score	-1.87
Structure conservation index	0.34
SVM decision value	0.59
SVM RNA-class probability	0.791093
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17169348 104 + 22407834
UACUAGACUACUAGUUUGACCUUCGAAA-CAAAACAGGCCUUUAUUUGCCUGUCUGUUUUGUAUUUAAUCCUUUUCCAUAAGCUAGAUCAUAAAAUGU-------------CUUGCUA
.(((((....)))))((((....(((((-((..((((((........)))))).)))))))...))))............(((.((((........))-------------)).))). ( -22.30)
>DroSec_CAF1 14827 104 + 1
AACUAGACAUCUAGUUAUACCUUUGAAA-CAGAACAGGCCUUUAUGUGCCUGUCUGUUUUGUUUUUUAUCCUUUUCCAUAAGCUAGAGCAUAAAAUGU-------------CUUACUA
((((((....))))))........((((-((((.((((((.....).)))))))))))))...((((((.((((..(....)..)))).))))))...-------------....... ( -26.00)
>DroSim_CAF1 14794 104 + 1
AACUAGACAUCUAGUUAUACGUUUGAAA-CAAAACAGGCCUUUAUGUGCCUGUCUGUUUUGUUUUUUAUUCUUUUCCAUAAGCUAGAGCAUAAAAUGU-------------CUUACUA
((((((....))))))..((((((((((-((((((((((............))))))))))))))................((....))...))))))-------------....... ( -23.60)
>DroEre_CAF1 14955 105 + 1
UACAAGAC------UU-------UGUAAUCUAAGCAGGCCUUUUUGUGCCUGUUCGAUUGGUAUUUUACCAUUUUCCAUAAGCUAGAAUAUAAAAUGUUCCUCUAAAAAGACUCACUA
........------((-------((((.((((((((((((.....).))))))).((.(((((...)))))...)).......)))).))))))........................ ( -19.10)
>DroYak_CAF1 15885 112 + 1
UACUAGAG------UUCUACCUCCGAAAUCAAAACAGGCCUUUUUGUGAAUGUCUGAUUGGUAUUUUAAUAUUUUCCAAAAGCUAGAAUAUAAAAUGUACUUCUAAAAAGUCUUACUA
.......(------(((((.((............(((((.(((....))).))))).((((..............)))).)).))))))............................. ( -12.54)
>consensus
UACUAGAC__CUAGUUAUACCUUUGAAA_CAAAACAGGCCUUUAUGUGCCUGUCUGUUUUGUAUUUUAUCCUUUUCCAUAAGCUAGAACAUAAAAUGU_____________CUUACUA
..((((.......................((((((((((............)))))))))).........(((......)))))))................................ ( -7.02 =  -7.86 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	17,169,348 – 17,169,452
Length	104
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	73.67
Mean single sequence MFE	-22.52
Consensus MFE	-9.00
Energy contribution	-9.52
Covariance contribution	0.52
Combinations/Pair	1.17
Mean z-score	-1.86
Structure conservation index	0.40
SVM decision value	0.47
SVM RNA-class probability	0.748405
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17169348 104 - 22407834
UAGCAAG-------------ACAUUUUAUGAUCUAGCUUAUGGAAAAGGAUUAAAUACAAAACAGACAGGCAAAUAAAGGCCUGUUUUG-UUUCGAAGGUCAAACUAGUAGUCUAGUA
..((.((-------------(((((...((((((..(((......))).........(.((((((((((((........))))).))))-))).).))))))....))).)))).)). ( -24.10)
>DroSec_CAF1 14827 104 - 1
UAGUAAG-------------ACAUUUUAUGCUCUAGCUUAUGGAAAAGGAUAAAAAACAAAACAGACAGGCACAUAAAGGCCUGUUCUG-UUUCAAAGGUAUAACUAGAUGUCUAGUU
.....((-------------(((((((((((((((.....))))...............((((((((((((........))))).))))-))).....))))))...))))))).... ( -27.90)
>DroSim_CAF1 14794 104 - 1
UAGUAAG-------------ACAUUUUAUGCUCUAGCUUAUGGAAAAGAAUAAAAAACAAAACAGACAGGCACAUAAAGGCCUGUUUUG-UUUCAAACGUAUAACUAGAUGUCUAGUU
.....((-------------(((((((((((((((.....))))...............((((((((((((........))))).))))-))).....))))))...))))))).... ( -25.60)
>DroEre_CAF1 14955 105 - 1
UAGUGAGUCUUUUUAGAGGAACAUUUUAUAUUCUAGCUUAUGGAAAAUGGUAAAAUACCAAUCGAACAGGCACAAAAAGGCCUGCUUAGAUUACA-------AA------GUCUUGUA
..(..((.((((.....((...(((((((.(((((.....)))))....))))))).))((((...(((((........)))))....))))..)-------))------).))..). ( -21.60)
>DroYak_CAF1 15885 112 - 1
UAGUAAGACUUUUUAGAAGUACAUUUUAUAUUCUAGCUUUUGGAAAAUAUUAAAAUACCAAUCAGACAUUCACAAAAAGGCCUGUUUUGAUUUCGGAGGUAGAA------CUCUAGUA
..(((...((....))...)))........(((((.((((((((....(((((((((((...................))..))))))))))))))))))))))------........ ( -13.41)
>consensus
UAGUAAG_____________ACAUUUUAUGCUCUAGCUUAUGGAAAAGGAUAAAAUACAAAACAGACAGGCACAUAAAGGCCUGUUUUG_UUUCAAAGGUAUAACUAG__GUCUAGUA
...............................((((.....))))...................((((((((........))))))))............................... ( -9.00 =  -9.52 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:08 2006