Locus 2972

Sequence ID	3R_DroMel_CAF1
Location	7,931,609 – 7,931,762
Length	153
Max. P	0.999821

overview

Window 3

Location	7,931,609 – 7,931,723
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.35
Mean single sequence MFE	-27.58
Consensus MFE	-24.78
Energy contribution	-25.34
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.92
Structure conservation index	0.90
SVM decision value	4.16
SVM RNA-class probability	0.999821
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931609 114 + 27905053
GUUCUUUUUUU------UCCUUUUUGUGGGGAAUUUAUUGCCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUGACAUCACUUGUACAGAGCAAC
.........((------((((......))))))....................((((((((...(((....)))(((..((((((.....))))))..)))........))))))))... ( -28.20)
>DroSec_CAF1 63190 112 + 1
GCUCUUUUUUU------UCC--UUUGUUGGGAAUUUAUUGCCUUAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGUCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAAC
(((((......------..(--((((((((((....(((((...((((.....)))).))))).)))))))))))....((((((.....))))))..((((.....)))).)))))... ( -26.50)
>DroSim_CAF1 65261 112 + 1
GCUCUUUUUUU------CCU--UUUGUUGGGAAUUUAUUGCCUUAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAAC
(((((....((------(((--......)))))..........(((((....((((((((.........))))))))..((((((.....))))))........)))))...)))))... ( -27.80)
>DroEre_CAF1 64108 115 + 1
GCUCUUUUUUUUUUG-----CUUUUGUUUGGAAUUUAUUGCCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUGCGGAGCAAA
(((((.........(-----((((...((((((...(((((..(((((.....)))))))))).)))))).)))))...((((((.....))))))..((((.....)))).)))))... ( -26.90)
>DroYak_CAF1 65513 120 + 1
GCUCUUUUUCUUUUCUUUCCUUUUUUUUUGGAAUUUAUUGCCUGAAGCUAUUUGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUGCAGAGCAAA
((((............((((.........)))).....(((..(((((.....)))))................((...((((((.....))))))...)).........)))))))... ( -28.50)
>consensus
GCUCUUUUUUU______UCC_UUUUGUUGGGAAUUUAUUGCCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAAC
(((((.................((((((((((....(((((..(((((.....)))))))))).))))))))))((...((((((.....))))))...))...........)))))... (-24.78 = -25.34 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	7,931,609 – 7,931,723
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.35
Mean single sequence MFE	-25.00
Consensus MFE	-19.62
Energy contribution	-20.42
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-3.58
Structure conservation index	0.78
SVM decision value	2.97
SVM RNA-class probability	0.997951
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931609 114 - 27905053
GUUGCUCUGUACAAGUGAUGUCAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGGCAAUAAAUUCCCCACAAAAAGGA------AAAAAAAGAAC
(((((.(((....(((..(((...((((((.....))))))....((((....))))...)))..)))........))))))))...((((.........)))------).......... ( -24.40)
>DroSec_CAF1 63190 112 - 1
GUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGACAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUAAGGCAAUAAAUUCCCAACAAA--GGA------AAAAAAAGAGC
...(((((.....(((..(((((.(.((((.....)))).)....((((....)))).)))))..)))...................((((.......--)))------).....))))) ( -20.20)
>DroSim_CAF1 65261 112 - 1
GUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUAAGGCAAUAAAUUCCCAACAAA--AGG------AAAAAAAGAGC
...(((((.....(((..(((((.((((((.....))))))....((((....)))).)))))..)))...................((((.......--.))------))....))))) ( -27.60)
>DroEre_CAF1 64108 115 - 1
UUUGCUCCGCACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGGCAAUAAAUUCCAAACAAAAG-----CAAAAAAAAAAGAGC
((((((.(((....))).(((((.((((((.....))))))....((((....)))).)))))..(((..........))).................))-----))))........... ( -23.50)
>DroYak_CAF1 65513 120 - 1
UUUGCUCUGCACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCAAAUAGCUUCAGGCAAUAAAUUCCAAAAAAAAAGGAAAGAAAAGAAAAAGAGC
...(((((((....(((((.....((((((.....))))))....((((....))))))))).((((.....))))...))......((((.........))))...........))))) ( -29.30)
>consensus
GUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGGCAAUAAAUUCCCAACAAAA_GGA______AAAAAAAGAGC
...(((((......(((((.....((((((.....))))))....((((....)))))))))...(((..........)))..................................))))) (-19.62 = -20.42 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	7,931,643 – 7,931,762
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.35
Mean single sequence MFE	-28.17
Consensus MFE	-21.80
Energy contribution	-22.08
Covariance contribution	0.28
Combinations/Pair	1.14
Mean z-score	-2.61
Structure conservation index	0.77
SVM decision value	1.88
SVM RNA-class probability	0.981147
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931643 119 + 27905053
CCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUGACAUCACUUGUACAGAGCAACAAUGAUUU-UAGUUUUUGCCAUCAACUGAGUAAACAUUCU
.(((((((((((.((((((((...(((....)))(((..((((((.....))))))..)))........))))))))...))))))))-)))..(((((((.....)).)))))...... ( -32.40)
>DroSec_CAF1 63222 101 + 1
CCUUAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGUCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAACAAUGAUUU-UAGUUA---GCAACAA---------------
.((.((((((((.((((((((.........((((((((..((......))..)))))))).........))))))))...))))))))-.))...---.......--------------- ( -23.57)
>DroSim_CAF1 65293 120 + 1
CCUUAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAACAAUGAUUUUUAGUUUUUGCCAUCAACUGAGUAAACAUUCU
.((.((((((((.((((((((..((((....))))....((((((.....)))))).............))))))))...))))))))..))..(((((((.....)).)))))...... ( -25.90)
>DroEre_CAF1 64143 119 + 1
CCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUGCGGAGCAAAAUUGAUUU-UGGUUUUGGCCAUCAGUUGUGUAAAUAUUUU
.((((........((((((((..((((....))))....((((((.....)))))).............))))))))...........-((((....))))))))............... ( -27.80)
>DroYak_CAF1 65553 119 + 1
CCUGAAGCUAUUUGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUGCAGAGCAAAAUUGAUUU-UAGUUUUGCCCAUCAAUUGUGUAAAUAUUUU
...(((((.....))))).............((((((((((..((((((((((((((((.(((.....))).)))))(((((((....-))))))).))))))))))).))))).))))) ( -31.20)
>consensus
CCUGAAGUUAUUAGCUUUGUAAUCUUUUAAUAAAGUUUUGCCCCAAUUGAUGGGGCUUUACAUCACUUGUACAGAGCAACAAUGAUUU_UAGUUUUGGCCAUCAACUGAGUAAACAUUCU
.(((((((((((.((((((((..((((....))))....((((((.....)))))).............))))))))...)))))))).)))............................ (-21.80 = -22.08 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	7,931,643 – 7,931,762
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.35
Mean single sequence MFE	-24.82
Consensus MFE	-16.66
Energy contribution	-18.02
Covariance contribution	1.36
Combinations/Pair	1.04
Mean z-score	-2.44
Structure conservation index	0.67
SVM decision value	0.68
SVM RNA-class probability	0.821019
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931643 119 - 27905053
AGAAUGUUUACUCAGUUGAUGGCAAAAACUA-AAAUCAUUGUUGCUCUGUACAAGUGAUGUCAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGG
..........((.(((((.((((........-......((((........))))(((((.....((((((.....))))))....((((....)))))))))...)))).)))))..)). ( -26.50)
>DroSec_CAF1 63222 101 - 1
---------------UUGUUGC---UAACUA-AAAUCAUUGUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGACAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUAAGG
---------------(((((((---(.....-..((((((((........)).))))))((((.(.((((.....)))).)....((((....)))).))))..))).)))))....... ( -15.90)
>DroSim_CAF1 65293 120 - 1
AGAAUGUUUACUCAGUUGAUGGCAAAAACUAAAAAUCAUUGUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUAAGG
.............(((((.((((...........((((((((........)).))))))((((.((((((.....))))))....((((....)))).))))...)))).)))))..... ( -27.30)
>DroEre_CAF1 64143 119 - 1
AAAAUAUUUACACAACUGAUGGCCAAAACCA-AAAUCAAUUUUGCUCCGCACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGG
...............(((((((......)))-.((((...(((((..(((....)))..)))))((((((.....))))))...............))))...............)))). ( -26.10)
>DroYak_CAF1 65553 119 - 1
AAAAUAUUUACACAAUUGAUGGGCAAAACUA-AAAUCAAUUUUGCUCUGCACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCAAAUAGCUUCAGG
......((((((((.(((..((((((((...-.......))))))))....))).)).))))))((((((.....))))))....((((....))))......((((.....)))).... ( -28.30)
>consensus
AAAAUAUUUACACAAUUGAUGGCAAAAACUA_AAAUCAUUGUUGCUCUGUACAAGUGAUGUAAAGCCCCAUCAAUUGGGGCAAAACUUUAUUAAAAGAUUACAAAGCUAAUAACUUCAGG
...................((((...........((((((..(((...)))..))))))((((.((((((.....))))))....((((....)))).))))...))))........... (-16.66 = -18.02 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:10 2006