Locus 4804

Sequence ID	2R_DroMel_CAF1
Location	15,776,144 – 15,776,341
Length	197
Max. P	0.794465

overview

Window 6

Location	15,776,144 – 15,776,242
Length	98
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	81.91
Mean single sequence MFE	-17.13
Consensus MFE	-11.11
Energy contribution	-11.14
Covariance contribution	0.03
Combinations/Pair	1.20
Mean z-score	-1.66
Structure conservation index	0.65
SVM decision value	0.07
SVM RNA-class probability	0.569466
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15776144 98 - 20766785
AUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGAAGCUACAUACAUACGUAUCCUAU-------ACUUAGU
((((((((((........(((((....))))).........))))))...((((((((....))-------...)))))).........)))).....-------....... ( -18.33)
>DroPse_CAF1 14470 91 - 1
AUAUAUGUAAUAAAUGUUGCAUGUUUACAUGCUUCCAAUACUUGAAUAAUUGGCUUGCUUAUCC-------UAAAAGCCUUA-ACCUACGUAUC-UAU-------A-----U
..(((((((.........(((((....)))))...................(((((........-------...)))))...-...))))))).-...-------.-----. ( -16.20)
>DroSec_CAF1 6185 105 - 1
AUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGAAGCUACAUACAUACGUAUCCUAUCCAUCCUACUUAGU
((((((((((........(((((....))))).........))))))...((((((((....))-------...)))))).........))))................... ( -18.33)
>DroSim_CAF1 6185 98 - 1
AUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGAAGCUACAUACAUACGUAUCCUAU-------ACUUAGU
((((((((((........(((((....))))).........))))))...((((((((....))-------...)))))).........)))).....-------....... ( -18.33)
>DroYak_CAF1 13742 97 - 1
AUACAUUUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGAUUGCUUAUGCUUGCUUUUAAGAGCUACA--------UAUCCUAU-------ACUUAGU
..................(((((....))))).(((((...........)))))..(..((((...((((....))))..))--------))..)...-------....... ( -15.40)
>DroPer_CAF1 13305 91 - 1
AUAUAUGUAAUAAAUAUUGCAUGUUUACAUGCUUCCAAUACUUGAAUAAUUGGCUUGCUUAUCC-------UAAAAGCCUUA-ACCUACGUAUC-UAU-------A-----U
..(((((((.........(((((....)))))...................(((((........-------...)))))...-...))))))).-...-------.-----. ( -16.20)
>consensus
AUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC_______UAAAAGCUACA_ACAUACGUAUCCUAU_______ACUUAGU
....(((((.........(((((....)))))...................(((((..................))))).......)))))..................... (-11.11 = -11.14 +   0.03)

alignment

secondary structure

dotplot

Window 7

Location	15,776,174 – 15,776,274
Length	100
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-23.22
Consensus MFE	-14.01
Energy contribution	-15.40
Covariance contribution	1.39
Combinations/Pair	1.04
Mean z-score	-2.19
Structure conservation index	0.60
SVM decision value	0.44
SVM RNA-class probability	0.737712
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15776174 100 + 20766785
UCUA-------GCAUAAGCAAGCCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUACAUGUAUUUACAUACGAUUAAUGCUCUUGAAUGCAGGCA
....-------((....))..(((..(((((.((((((((...(((((....)))))..((.....)))).)))))).)))))......(((........)))))). ( -24.10)
>DroSec_CAF1 6222 100 + 1
UCUA-------GCAUAAGCAAGCCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUACAUGUAUUUACAUACGAUUAAUGCUCUUGAAUGCAGGCA
....-------((....))..(((..(((((.((((((((...(((((....)))))..((.....)))).)))))).)))))......(((........)))))). ( -24.10)
>DroSim_CAF1 6215 100 + 1
UCUA-------GCAUAAGCAAGCCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUACAUGUAUUUACAUACGAUUAAUGCUCUUGAAUGCAGGCA
....-------((....))..(((..(((((.((((((((...(((((....)))))..((.....)))).)))))).)))))......(((........)))))). ( -24.10)
>DroEre_CAF1 7357 93 + 1
CUUAAAAGCAAG----------CCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUACAUAUACUU----ACGAUUAAUGCUCUUGAAUGCAGGCA
...........(----------(((((((((..((((...((.(((((....))))).))...))))...)))))))----........(((........)))))). ( -22.10)
>DroYak_CAF1 13764 103 + 1
CUUAAAAGCAAGCAUAAGCAAUCCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUAAAUGUAUUU----ACGAAUUAUGCUCUUGAAUGCAGGCA
.......(((..((..((((.(((((.(((....)))))))).(((((....)))))....................----........))))..))..)))..... ( -24.00)
>DroPer_CAF1 13328 100 + 1
UUUA-------GGAUAAGCAAGCCAAUUAUUCAAGUAUUGGAAGCAUGUAAACAUGCAAUAUUUAUUACAUAUAUGUAUGUACAAUGUACAAAAUAUGUUCCAGGCA
....-------((((((.........))))))..((.(((((((((((....))))).((((((..((((....))))(((((...))))))))))).)))))))). ( -20.90)
>consensus
UCUA_______GCAUAAGCAAGCCAAGUAUGCAAGUAUUGGAAGCGUGUAAACACGCAUUAUUUAUUACAUGUAUUUACAUACGAUUAAUGCUCUUGAAUGCAGGCA
.....................(((....(((((.(((.((((.(((((....)))))....)))).))).)))))..............(((........)))))). (-14.01 = -15.40 +   1.39)

alignment

secondary structure

dotplot

Window 8

Location	15,776,174 – 15,776,274
Length	100
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	81.40
Mean single sequence MFE	-22.28
Consensus MFE	-12.61
Energy contribution	-12.45
Covariance contribution	-0.16
Combinations/Pair	1.24
Mean z-score	-2.05
Structure conservation index	0.57
SVM decision value	0.09
SVM RNA-class probability	0.577658
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15776174 100 - 20766785
UGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGA
...((((((....((((.......((((....))))((((((........(((((....))))).........)))))).....))))....))))-------.)). ( -23.73)
>DroSec_CAF1 6222 100 - 1
UGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGA
...((((((....((((.......((((....))))((((((........(((((....))))).........)))))).....))))....))))-------.)). ( -23.73)
>DroSim_CAF1 6215 100 - 1
UGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC-------UAGA
...((((((....((((.......((((....))))((((((........(((((....))))).........)))))).....))))....))))-------.)). ( -23.73)
>DroEre_CAF1 7357 93 - 1
UGCCUGCAUUCAAGAGCAUUAAUCGU----AAGUAUAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGG----------CUUGCUUUUAAG
(((((.......)).)))((((..((----((((.(((((((........(((((....))))).........)))))))....)----------)))))..)))). ( -22.53)
>DroYak_CAF1 13764 103 - 1
UGCCUGCAUUCAAGAGCAUAAUUCGU----AAAUACAUUUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGAUUGCUUAUGCUUGCUUUUAAG
.....(((..((.(((((........----....................(((((....))))).(((((...........))))).))))).))..)))....... ( -21.20)
>DroPer_CAF1 13328 100 - 1
UGCCUGGAACAUAUUUUGUACAUUGUACAUACAUAUAUGUAAUAAAUAUUGCAUGUUUACAUGCUUCCAAUACUUGAAUAAUUGGCUUGCUUAUCC-------UAAA
.(((((((((((((..(((((...))))).....))))))..........(((((....))))).))))..............)))..........-------.... ( -18.73)
>consensus
UGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUCCAAUACUUGCAUACUUGGCUUGCUUAUGC_______UAAA
.((((((........)))..................((((((........(((((....))))).........))))))....)))..................... (-12.61 = -12.45 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	15,776,207 – 15,776,304
Length	97
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	79.88
Mean single sequence MFE	-21.87
Consensus MFE	-13.13
Energy contribution	-11.17
Covariance contribution	-1.97
Combinations/Pair	1.42
Mean z-score	-1.74
Structure conservation index	0.60
SVM decision value	0.25
SVM RNA-class probability	0.654006
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15776207 97 - 20766785
UUUUGCAACAAAGAGCUUUAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUC
..(((((.......(((((....((((((......)))))).))))).......((((....)))).)))))........(((((....)))))... ( -22.40)
>DroPse_CAF1 14526 97 - 1
CUUUACAUUAAAUGACUCUUAGCGAGUUUGUGCCUGGAACAUAUUUUGUACAUUGUACAUACAUAUAUGUAAUAAAUGUUGCAUGUUUACAUGCUUC
..((((((...(((((((.....)))).(((((...(.(((.....))).)...)))))..)))..))))))........(((((....)))))... ( -19.70)
>DroSim_CAF1 6248 97 - 1
UUUUGCAACAAAGAGCUCUUAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUC
..(((((.......((((((...((((((......)))))))))))).......((((....)))).)))))........(((((....)))))... ( -26.20)
>DroEre_CAF1 7387 93 - 1
UUUUGCAACAAAGAGCUCGAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGU----AAGUAUAUGUAAUAAAUAAUGCGUGUUUACACGCUUC
..(((((.......((((.....((((((......))))))..))))......(..----..)....)))))........(((((....)))))... ( -21.20)
>DroYak_CAF1 13804 93 - 1
UUUUGCAACAAAGAGCUCGAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUAAUUCGU----AAAUACAUUUAAUAAAUAAUGCGUGUUUACACGCUUC
....((........))..(((((((((.(((((((.......)).)))))))))((----((((((..(((.....)))...))))))))..))))) ( -22.00)
>DroPer_CAF1 13361 97 - 1
CUUUACAUUAAAUGACUCUUAGCGAGUUUGUGCCUGGAACAUAUUUUGUACAUUGUACAUACAUAUAUGUAAUAAAUAUUGCAUGUUUACAUGCUUC
..((((((...(((((((.....)))).(((((...(.(((.....))).)...)))))..)))..))))))........(((((....)))))... ( -19.70)
>consensus
UUUUGCAACAAAGAGCUCUAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUAAAUCGUA__UAAAUACAUGUAAUAAAUAAUGCGUGUUUACACGCUUC
..(((((.((....((((.....))))...))..(((........)))...................)))))........(((((....)))))... (-13.13 = -11.17 +  -1.97)

alignment

secondary structure

dotplot

Window 0

Location	15,776,242 – 15,776,341
Length	99
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	82.98
Mean single sequence MFE	-29.66
Consensus MFE	-20.83
Energy contribution	-21.50
Covariance contribution	0.67
Combinations/Pair	1.21
Mean z-score	-2.52
Structure conservation index	0.70
SVM decision value	0.60
SVM RNA-class probability	0.794465
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15776242 99 - 20766785
A--UAAGUACUCGUUCCGUAUGAGGCACAUAGUCGGGA-GUUUUGCAACAAAGAGCUUUAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAA
.--.............(((((((((((((((.((((((-(((((.......))))))))...))).))))))))(((........)))....)))))))... ( -30.60)
>DroSec_CAF1 6290 101 - 1
AUAUAAGUACUCGUUCCGUAUGAGGCACAUAGUCGGGA-GUUUUGCAACAAAGAGCUCUAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAA
................(((((((((((((((.((((((-(((((.......))))))))...))).))))))))(((........)))....)))))))... ( -33.30)
>DroSim_CAF1 6283 101 - 1
AUAUAAGUACUCGUUCCGUAUGAGGCACAUAGUCGGGA-GUUUUGCAACAAAGAGCUCUUAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAA
................(((((((((((((((.((((((-(((((.......))))))))...))).))))))))(((........)))....)))))))... ( -33.30)
>DroEre_CAF1 7422 97 - 1
AUAUAAGUACUCGAUCCGUAUGAGGCACAUAGUCGGGA-GUUUUGCAACAAAGAGCUCGAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGU----AA
.....(((.(((.......((((((((((((.(((.((-(((((.......)))))))....))).))))))))).)))....))).)))......----.. ( -29.20)
>DroYak_CAF1 13839 97 - 1
AUAUAAGUACUCGAUCCGUAUGAGGCACAUAGUCGGGA-GUUUUGCAACAAAGAGCUCGAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUAAUUCGU----AA
.........(((.......((((((((((((.(((.((-(((((.......)))))))....))).))))))))).)))....)))..........----.. ( -28.70)
>DroPer_CAF1 13396 102 - 1
AUACAUUUAUAUGCAUCGUAUCAGGCACAUAUUCGGCACGCUUUACAUUAAAUGACUCUUAGCGAGUUUGUGCCUGGAACAUAUUUUGUACAUUGUACAUAC
.................((.(((((((((.....(((.((((..................)))).)))))))))))).))......(((((...)))))... ( -22.87)
>consensus
AUAUAAGUACUCGUUCCGUAUGAGGCACAUAGUCGGGA_GUUUUGCAACAAAGAGCUCUAAGCGAGUGUGUGCCUGCAUUCAAGAGCAUUAAUCGUAUGUAA
.....(((.(((.......((((((((((((.((((((.(((((.......))))))))...))).))))))))).)))....))).)))............ (-20.83 = -21.50 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:40 2006