Locus 4197

Sequence ID	X_DroMel_CAF1
Location	11,014,473 – 11,014,638
Length	165
Max. P	0.932662

overview

Window 8

Location	11,014,473 – 11,014,582
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-30.74
Consensus MFE	-27.22
Energy contribution	-27.06
Covariance contribution	-0.16
Combinations/Pair	1.16
Mean z-score	-1.89
Structure conservation index	0.89
SVM decision value	1.09
SVM RNA-class probability	0.913268
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11014473 109 - 22224390
UUUGUCGUAUCACAGGGCGUGGCUGAUUGUCACAGUGAUGAGAUGGCAAUUUCUCAACACGCUAACGAGAUGCACUUACAAAAAAAUGGGUAUGCCCAUU--GGGAAAUUA
(((.(((((((.(..((((((((.....))))).(((.(((((........))))).))))))...).)))))...........((((((....))))))--)).)))... ( -34.60)
>DroSec_CAF1 7337 108 - 1
UUUGUCGUAUCAAGGGGCGUGGCUGGUUGUCACAGUGAUGAGACGGCAAUUUCUCAACACGCUAACAAGAUGCACUCAAAA-AAAAUGGGUAUACUCAUU--CAGAAAUUA
((((..(((((....((((((((.....))))).(((.(((((........))))).)))))).....)))))...)))).-..((((((....))))))--......... ( -29.30)
>DroSim_CAF1 2398 109 - 1
UUUGUCGUAUCAAGGGGCGUGGCUGGUUGUCACAGUGAUGAGACGGCAAUUUCUCAACACGCUAACAAGAUGCACUCAAAAAAAAAUGGGUAUACCCAUU--CGGAAAUUA
((((..(((((....((((((((.....))))).(((.(((((........))))).)))))).....)))))...))))....((((((....))))))--......... ( -32.30)
>DroEre_CAF1 1039 98 - 1
UUUGUCGCAUCAAGGGGCGUGACCGACUGUCACAGUGGUGAGAUGGCAAUUUCUCAACACGCUAACAAGAUGCACUGAAAA--ACGGUGCUAUUUUUAAC-----------
......(((((....((((((((.....))))).(((.(((((........))))).)))))).....)))))((((....--.))))............----------- ( -28.80)
>DroYak_CAF1 2345 109 - 1
UUUGUCGUAUCAAGGGGCGUGACUGGUUGUCACAGUGAUGAGACGGCAAUUUCUCAACACGCUAGCAAGAUGCACUGCAAG--AAAUGGGUAUUCUUAACGCCAAAAUCUA
(((((.(((((....((((((((.....))))).(((.(((((........))))).)))))).....)))))...)))))--...(((((.......)).)))....... ( -28.70)
>consensus
UUUGUCGUAUCAAGGGGCGUGGCUGGUUGUCACAGUGAUGAGACGGCAAUUUCUCAACACGCUAACAAGAUGCACUCAAAA_AAAAUGGGUAUACUCAUU__CAGAAAUUA
......(((((....((((((((.....))))).(((.(((((........))))).)))))).....))))).............((((....))))............. (-27.22 = -27.06 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	11,014,511 – 11,014,618
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.38
Mean single sequence MFE	-34.60
Consensus MFE	-17.44
Energy contribution	-18.98
Covariance contribution	1.53
Combinations/Pair	1.22
Mean z-score	-2.11
Structure conservation index	0.50
SVM decision value	0.43
SVM RNA-class probability	0.734059
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11014511 107 + 22224390
AUCUCGUUAGCGUGU-------UGAGAAAU-UGCCAUCUCAUCACUGUGACAAUCAGCCACGCCCUGU-GAUACGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUUAGAAAC
.(((..((((((((.-------(((((...-.....))))).)))....(((((..(((.((((((.(-(......))...))))))...))))))----))....)).)))..)))... ( -32.70)
>DroSec_CAF1 7374 107 + 1
AUCUUGUUAGCGUGU-------UGAGAAAU-UGCCGUCUCAUCACUGUGACAACCAGCCACGCCCCUU-GAUACGACAAAAGGGGCGGCGGGCGUU----GUAUUUGCUUAGUUAGAUAC
((((....((((((.-------(((((...-.....))))).)))....(((((..(((.((((((((-..........))))))))...))))))----))....))).....)))).. ( -39.00)
>DroSim_CAF1 2436 107 + 1
AUCUUGUUAGCGUGU-------UGAGAAAU-UGCCGUCUCAUCACUGUGACAACCAGCCACGCCCCUU-GAUACGACAAAAGGGGCGGCGGGCGUU----GUAUUUGCUUAGUUAGAAAC
.(((....((((((.-------(((((...-.....))))).)))....(((((..(((.((((((((-..........))))))))...))))))----))....))).....)))... ( -38.30)
>DroEre_CAF1 1066 107 + 1
AUCUUGUUAGCGUGU-------UGAGAAAU-UGCCAUCUCACCACUGUGACAGUCGGUCACGCCCCUU-GAUGCGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUUAGCAAC
...(((((((((((.-------(((((...-.....))))).))).(((((.....)))))(((((((-..........))))))).(((((....----...)))))...)))))))). ( -37.60)
>DroYak_CAF1 2383 107 + 1
AUCUUGCUAGCGUGU-------UGAGAAAU-UGCCGUCUCAUCACUGUGACAACCAGUCACGCCCCUU-GAUACGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUCGCAAAC
..((((((...(((.-------(((((...-.....))))).))).(((((.....)))))(((((((-..........)))))))))))))....----...(((((......))))). ( -38.20)
>DroAna_CAF1 1088 110 + 1
AGAUUUCUAGCGUGUCUGGUGGUCACAAAUCCGCCAACUCAUCUCCCGGGCAAUCAGUCAUCCCCCUACCCUACCCCACUA----------UCUUUAUAAAUAUUAGCAUAGUUGGGAUC
.((((((..(.(((..((((((........))))))...)))...)..)).))))..................(((.((((----------(((...........)).))))).)))... ( -21.80)
>consensus
AUCUUGUUAGCGUGU_______UGAGAAAU_UGCCAUCUCAUCACUGUGACAACCAGCCACGCCCCUU_GAUACGACAAAAGGGGCGGCAGGCGUU____GUAUUUGCAUAGUUAGAAAC
.(((..(((((.(((.......(((((.........)))))........)))....(((.((((((((...........))))))))...))).............)).)))..)))... (-17.44 = -18.98 +   1.53)

alignment

secondary structure

dotplot

Window 0

Location	11,014,543 – 11,014,638
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	67.86
Mean single sequence MFE	-28.47
Consensus MFE	-12.62
Energy contribution	-13.52
Covariance contribution	0.89
Combinations/Pair	1.35
Mean z-score	-1.96
Structure conservation index	0.44
SVM decision value	1.22
SVM RNA-class probability	0.932662
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11014543 95 + 22224390
AUCACUGUGACAAUCAGCCACGCCCUGU-GAUACGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUUAGAAAC------GAUGAAACUUG--UAUUGUUU-U-----------
...((((((.(((.(((((.((((((.(-(......))...))))))...)))..)----)...)))))))))..(((((------((((.......--))))))))-)----------- ( -27.90)
>DroSec_CAF1 7406 96 + 1
AUCACUGUGACAACCAGCCACGCCCCUU-GAUACGACAAAAGGGGCGGCGGGCGUU----GUAUUUGCUUAGUUAGAUAC------GAUGAAACUUAU-UGUUUUUU-A-----------
........(((((...(((.((((((((-..........))))))))...)))(((----(((((((......)))))))------)))........)-))))....-.----------- ( -30.60)
>DroSim_CAF1 2468 97 + 1
AUCACUGUGACAACCAGCCACGCCCCUU-GAUACGACAAAAGGGGCGGCGGGCGUU----GUAUUUGCUUAGUUAGAAAC------GAUGAAACUUUUGUUUUUUUU-U-----------
...((((..(((((..(((.((((((((-..........))))))))...))))))----)).......)))).((((((------((........))))))))...-.----------- ( -29.00)
>DroEre_CAF1 1098 104 + 1
ACCACUGUGACAGUCGGUCACGCCCCUU-GAUGCGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUUAGCAAC------GU--CAGUUUU--UAUUGUUU-UUGGCCAAGCAG
....(((((.....)(((((((((((((-..........))))))))...((((((----((.............)))))------))--)......--........-.)))))..)))) ( -33.42)
>DroYak_CAF1 2415 105 + 1
AUCACUGUGACAACCAGUCACGCCCCUU-GAUACGACAAAAGGGGCGGCAGGCGUU----GUAUUUGCAUAGUCGCAAAC------GA--AAGUUUU--UCUUGUUUUUUGGCCAAGUAC
...((((((((.....)))))(((((((-..........)))))))(((..(((.(----((....)))....)))((((------..--..)))).--............))).))).. ( -33.70)
>DroAna_CAF1 1128 96 + 1
AUCUCCCGGGCAAUCAGUCAUCCCCCUACCCUACCCCACUA----------UCUUUAUAAAUAUUAGCAUAGUUGGGAUCUGAAAACAAAAGGCCCU--CAUUAUUU-U-----------
.......((((..((((..(((((.(((..(((........----------.............)))..)))..)))))))))...(....))))).--........-.----------- ( -16.20)
>consensus
AUCACUGUGACAACCAGCCACGCCCCUU_GAUACGACAAAAGGGGCGGCAGGCGUU____GUAUUUGCAUAGUUAGAAAC______GAUGAAACUUU__UAUUGUUU_U___________
.......((((.....(((.((((((((...........))))))))...))).......((....))...))))............................................. (-12.62 = -13.52 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:56 2006