Locus 3963

Sequence ID	X_DroMel_CAF1
Location	10,520,939 – 10,521,266
Length	327
Max. P	0.853222

overview

Window 2

Location	10,520,939 – 10,521,058
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.97
Mean single sequence MFE	-23.12
Consensus MFE	-15.53
Energy contribution	-15.53
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-1.60
Structure conservation index	0.67
SVM decision value	0.01
SVM RNA-class probability	0.538771
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10520939 119 + 22224390
CAAGUUUCAAUUGCAAUUGUUGCUGCUAGUUUCUUUACUGCUCUUUUCAGUCAUUAUUUUUUUUUUUUUGUAGCUCGGUGAAAUCAAUGUGUAGGU-UUAUUUUUACUGCACAACUGGCA
..(((..((((....))))..)))((((((...(((((((..((...(((.................))).))..))))))).....(((((((..-.........))))))))))))). ( -24.83)
>DroSim_CAF1 55943 100 + 1
CAAGUUUCAAUUGCAAUUGUUGCUGCUGGUUUCUUUACU------------CA-------UUUUUUUUUUUAGCUCUGUGAAAUCAAUGUGUAGGU-UUAUUUUUACUGCACAACUGGCA
..(((..((((....))))..)))((..((...(((((.------------..-------.................))))).....(((((((..-.........)))))))))..)). ( -19.35)
>DroEre_CAF1 54358 108 + 1
CAAGUUACAAUUGCAAUUGUUGCUGCUGGUUUCUUUACGGCCCUUUUAAGUCA------------UUUUUCAGAUCGGCGAAAUCAAUGUGUAGCUUUUAUCCUUACUGCACAACUAGCA
..(((.(((((....))))).)))((((((.........(((..(((.((...------------...)).)))..)))........(((((((............))))))))))))). ( -23.00)
>DroYak_CAF1 53989 109 + 1
CCAGUUUCAAUUGCAAUUGUGGCUGCUGCUUUCUUUGCUGCUAUUUUGAGUCAG----------UUUUUUUAGCUCGGUGAAAUCAAUGUGUAGAU-UUAUUCUUACUGCACAACUGGCA
(((((((((...((((....(((....)))....)))).......(((((..((----------.....))..))))))))).....(((((((..-.........)))))))))))).. ( -25.30)
>consensus
CAAGUUUCAAUUGCAAUUGUUGCUGCUGGUUUCUUUACUGCUCUUUU_AGUCA___________UUUUUUUAGCUCGGUGAAAUCAAUGUGUAGGU_UUAUUCUUACUGCACAACUGGCA
..(((..((((....))))..)))((((((...(((((.......................................))))).....(((((((............))))))))))))). (-15.53 = -15.53 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	10,521,019 – 10,521,123
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.77
Mean single sequence MFE	-27.36
Consensus MFE	-19.97
Energy contribution	-20.65
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.73
SVM decision value	-0.04
SVM RNA-class probability	0.512251
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521019 104 - 22224390
ACGGUUAAGUUAACUUGGCCUUGCC------AGCAAUGUGUUGUAUUGGUUAUUGAUUUGGC---------CCUCCUACUUGCCAGUUGUGCAGUAAAAAUAA-ACCUACACAUUGAUUU
..(((((((....))))))).....------..((((((((..((((..((((((..(((((---------..........))))).....)))))).)))).-....)))))))).... ( -27.60)
>DroSec_CAF1 52418 104 - 1
ACGGUUAAGUUAACUUGGCCUUGCC------AGCAAUGUGUUGUAUUGGUUAUUGAUUUGGC---------CCUCCUACUUGCCAGUUGUGCAGUAAAAAUAA-ACCUACACAUUGAUUU
..(((((((....))))))).....------..((((((((..((((..((((((..(((((---------..........))))).....)))))).)))).-....)))))))).... ( -27.60)
>DroSim_CAF1 56004 104 - 1
ACGGUUAAGUUAACUUGGCCUUGCC------AGCAAUGUGUUGUAUUGGUUAUUGAUUUGGC---------CCUCCUACUUGCCAGUUGUGCAGUAAAAAUAA-ACCUACACAUUGAUUU
..(((((((....))))))).....------..((((((((..((((..((((((..(((((---------..........))))).....)))))).)))).-....)))))))).... ( -27.60)
>DroEre_CAF1 54426 101 - 1
ACGGUUAAGCUAACUUGGCCUUG----------CCAAGUGUUGUAUUGGUUAUUGAUUUGGC---------CCUCCUACUUGCUAGUUGUGCAGUAAGGAUAAAAGCUACACAUUGAUUU
..(((((((....)))))))...----------.(((((((.((...(((((......))))---------).(((((((.((.......))))).)))).....)).)))).))).... ( -25.20)
>DroYak_CAF1 54059 119 - 1
ACGGUUAAGCUAACUUGGCCUUGUGUUGUUGGCCCAAGUGUUGUAUUGGUUAUUGAUUUGCCUUGCUGCCACCUCCUACUUGCCAGUUGUGCAGUAAGAAUAA-AUCUACACAUUGAUUU
..(((((((....))))))).(((((.......((((........)))).....((((((.((((((((((.((..........)).)).))))))))..)))-))).)))))....... ( -28.80)
>consensus
ACGGUUAAGUUAACUUGGCCUUGCC______AGCAAUGUGUUGUAUUGGUUAUUGAUUUGGC_________CCUCCUACUUGCCAGUUGUGCAGUAAAAAUAA_ACCUACACAUUGAUUU
..(((((((....))))))).............((((((((..((((..((((((..(((((...................))))).....)))))).))))......)))))))).... (-19.97 = -20.65 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	10,521,123 – 10,521,226
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.47
Mean single sequence MFE	-35.78
Consensus MFE	-24.74
Energy contribution	-25.06
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-1.85
Structure conservation index	0.69
SVM decision value	0.09
SVM RNA-class probability	0.576271
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521123 103 + 22224390
UGCCCUGCGAACAGUU------GCCAAGCUGAAAAUGGACAGGUGGCGCGGGCAGGGGGAUUCCCCG----------GGGGCAAUAAAUUAACAGCCCGAUGGCAAGAGCAAAG-AAAAU
(((((.(((..((.((------((((.........))).))).)).))))))))((((....)))).----------.((((............))))....((....))....-..... ( -34.10)
>DroSec_CAF1 52522 102 + 1
UGCCCUGCGAACAGUU------GCCAAGCUGAAAAUGGACAGGUGGCGCGGGCAGG-GGAUUCCCCG----------GGGGCAAUAAAUUAACAGCCCGAUGGCGAGAGCAAAG-AAAAU
(((((.(((..((.((------((((.........))).))).)).))))))))((-((...)))).----------.((((............))))....((....))....-..... ( -35.50)
>DroSim_CAF1 56108 102 + 1
UGCCCUGCGAACAGUU------GCCAAGCUGAAAAUGGACAGGUGGCGCGGGCAGG-GGAUUCCCCG----------GGGGCAAUAAAUUAACAGCCCGAUGGCGAGAGCAAAG-AAAAU
(((((.(((..((.((------((((.........))).))).)).))))))))((-((...)))).----------.((((............))))....((....))....-..... ( -35.50)
>DroEre_CAF1 54527 108 + 1
UGCCCUGCGAACAGUUGCCGUUGCCAAGCUGAAAAUGGACAGGUGGUGCUGGAGG--GGAUUCCCCAG---------GGGGCCAUAAAUUAACAGCCCGACGGCGAGAGCGAAAGAAAA-
.((.(((....)))(((((((((....((((..(((......(((((.((...((--((...))))..---------)).)))))..)))..)))).)))))))))..)).........- ( -33.60)
>DroYak_CAF1 54178 114 + 1
UGCCCUGCGAACAGUU------GCCAGGCUGAAAAUGGACAGGUGGCGCUGGAGGGGGGAUUCCCCGGGGAAGGGGGGGGGCAAUAAAUUAACAGCCCGAUGGCGAGAGCAAAAGAAAAU
..((((.(...((((.------((((..(((........))).))))))))..).)))).((((((......))))))((((............))))....((....)).......... ( -40.20)
>consensus
UGCCCUGCGAACAGUU______GCCAAGCUGAAAAUGGACAGGUGGCGCGGGCAGG_GGAUUCCCCG__________GGGGCAAUAAAUUAACAGCCCGAUGGCGAGAGCAAAG_AAAAU
((((.(((..............((((..(((........))).)))).(((((.(...((((((((...........)))).....))))..).)))))...))).).)))......... (-24.74 = -25.06 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	10,521,123 – 10,521,226
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.47
Mean single sequence MFE	-31.62
Consensus MFE	-23.21
Energy contribution	-23.41
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.73
SVM decision value	0.47
SVM RNA-class probability	0.750899
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521123 103 - 22224390
AUUUU-CUUUGCUCUUGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCCCCCUGCCCGCGCCACCUGUCCAUUUUCAGCUUGGC------AACUGUUCGCAGGGCA
.....-...(((.(((((...(((((.((.........))...----------.((((....)))).))))).((((.(((........)))..))))------........)))))))) ( -31.80)
>DroSec_CAF1 52522 102 - 1
AUUUU-CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCC-CCUGCCCGCGCCACCUGUCCAUUUUCAGCUUGGC------AACUGUUCGCAGGGCA
.....-...(((((((((....((((.((......)).)))).----------(((((....)-))))...))((((.(((........)))..))))------........).)))))) ( -30.20)
>DroSim_CAF1 56108 102 - 1
AUUUU-CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCC-CCUGCCCGCGCCACCUGUCCAUUUUCAGCUUGGC------AACUGUUCGCAGGGCA
.....-...(((((((((....((((.((......)).)))).----------(((((....)-))))...))((((.(((........)))..))))------........).)))))) ( -30.20)
>DroEre_CAF1 54527 108 - 1
-UUUUCUUUCGCUCUCGCCGUCGGGCUGUUAAUUUAUGGCCCC---------CUGGGGAAUCC--CCUCCAGCACCACCUGUCCAUUUUCAGCUUGGCAACGGCAACUGUUCGCAGGGCA
-.........(((...(((((.(((((((......))))))).---------((((((.....--.))))))..(((.(((........)))..)))..)))))..(((....)))))). ( -34.70)
>DroYak_CAF1 54178 114 - 1
AUUUUCUUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCCCCCCCUUCCCCGGGGAAUCCCCCCUCCAGCGCCACCUGUCCAUUUUCAGCCUGGC------AACUGUUCGCAGGGCA
.........((((((.((....((((.((......)).))))............((((.....))))..(((.((((.(((........)))..))))------..)))...)))))))) ( -31.20)
>consensus
AUUUU_CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC__________CGGGGAAUCC_CCUGCCCGCGCCACCUGUCCAUUUUCAGCUUGGC______AACUGUUCGCAGGGCA
..........(((((.((...(((((.............((((...........)))).............))((((.(((........)))..))))........)))...))))))). (-23.21 = -23.41 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	10,521,157 – 10,521,266
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.75
Mean single sequence MFE	-35.16
Consensus MFE	-26.64
Energy contribution	-26.60
Covariance contribution	-0.04
Combinations/Pair	1.19
Mean z-score	-2.01
Structure conservation index	0.76
SVM decision value	0.80
SVM RNA-class probability	0.853222
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521157 109 - 22224390
GUCGGAGGGCAUCGAGAUUUCUGCCGACAUUUUCCGUGGCAUUUU-CUUUGCUCUUGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCCCCCUGCCCGCGCCACCU
...((.(((((..(.((((((..(((.........((((((....-.........)))))).((((.((......)).)))).----------))))))))).)..)))))...)).... ( -34.92)
>DroSec_CAF1 52556 108 - 1
GUCGGGGAGAAUUGAGAUUUUUGCCGACAUUUUUCCUGGCAUUUU-CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCC-CCUGCCCGCGCCACCU
(.((((((((...((((....(((((..........)))))...)-)))...))))......((((.((......)).)))).----------(((((....)-)))))))))....... ( -33.50)
>DroSim_CAF1 56142 108 - 1
GUCGGAGAGAAUUGAGAUUUUUGCCGACAUUUUCCCUGGCAUUUU-CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC----------CGGGGAAUCC-CCUGCCCGCGCCACCU
....(((((....((((....(((((..........)))))...)-)))..)))))((....((((.((......)).)))).----------(((((....)-))))...))....... ( -31.50)
>DroEre_CAF1 54567 108 - 1
GACGGGGAGAAUUGAGAUUUUUGCCGGCAUUUUUCCUGGC-UUUUCUUUCGCUCUCGCCGUCGGGCUGUUAAUUUAUGGCCCC---------CUGGGGAAUCC--CCUCCAGCACCACCU
(((((.((((...((((.....(((((........)))))-...))))....)))).)))))(((((((......))))))).---------((((((.....--.))))))........ ( -43.30)
>DroYak_CAF1 54212 120 - 1
GUUGGGGAAAUUUGAGAUUUUUGCCGACAUUUUCCCUGGCAUUUUCUUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCCCCCCCUUCCCCGGGGAAUCCCCCCUCCAGCGCCACCU
(((((((((....((((....(((((..........)))))...))))..............((((.((......)).))))......))))))((((.....))))...)))....... ( -32.60)
>consensus
GUCGGGGAGAAUUGAGAUUUUUGCCGACAUUUUCCCUGGCAUUUU_CUUUGCUCUCGCCAUCGGGCUGUUAAUUUAUUGCCCC__________CGGGGAAUCC_CCUGCCCGCGCCACCU
(((((.((((((....)))))).)))))...((((((((((........)))..........((((.((......)).))))...........))))))).................... (-26.64 = -26.60 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:01 2006