Locus 9570

Sequence ID	3R_DroMel_CAF1
Location	25,279,367 – 25,279,537
Length	170
Max. P	0.995460

overview

Window 2

Location	25,279,367 – 25,279,471
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	82.69
Mean single sequence MFE	-29.02
Consensus MFE	-14.81
Energy contribution	-15.97
Covariance contribution	1.16
Combinations/Pair	1.12
Mean z-score	-2.39
Structure conservation index	0.51
SVM decision value	0.32
SVM RNA-class probability	0.688760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25279367 104 - 27905053
AGUAGAGCUUCUCCCAAAGCAAACCCGAUUACUCGGUAUUAUCCUGAUUUGAGCUAAUGCUCGUUUGUGAACCCAACCUCCGCAUGGCCUUCGGGCCAACAAAU
.(..(((...........((((((((((....))))..............((((....)))))))))).........)))..).(((((....)))))...... ( -31.15)
>DroSec_CAF1 136246 99 - 1
AGUAGAGCUGCUCCCA-----AACACGAUUACUCGGCAUUAUCCUGAUUUGAGCUAAUGCUCGUUUGCGAAUCCAGCCUCCGCAUGGCCUUCGGGCCAACAAAU
.(..((((((.((.((-----(((.(((....)))...............((((....))))))))).))...))).)))..).(((((....)))))...... ( -33.30)
>DroSim_CAF1 135976 104 - 1
AGUAGAGCUGCUCCCAAAGCAAACCCGAUUACUCGGCAUUAUCCUGAUUUGAGUUAAUGCUCGUUUGCGAAUCCAACCUCCGCAUGGCCUUCGGGCCAACAAAU
.(..(((...........((((((((((....))))..............((((....)))))))))).........)))..).(((((....)))))...... ( -30.45)
>DroEre_CAF1 153632 86 - 1
AGUAAAGCAGCUCCAAUCGCAAACCCGAUUACUCGGCAUUAUCCUGAUUUGAGCUAAUGCU------------------CCGGAUGGCCUUCCGGGCAACAAAU
........(((((.(((((.....((((....))))........))))).)))))..(((.------------------(((((......))))))))...... ( -25.72)
>DroYak_CAF1 141592 104 - 1
AGUGAAGCUUCUCCAUGAGCAAACCCGAUUACUUGGCAUUAUCCUGAUUUGAGCUAAUGCUCGUUUGGAAACCCAACCUCCGAAUGGCCUUCCGGGCAACAAAU
......((((......))))...((((.......(((.............((((....))))(((((((.........))))))).)))...))))........ ( -24.50)
>consensus
AGUAGAGCUGCUCCCAAAGCAAACCCGAUUACUCGGCAUUAUCCUGAUUUGAGCUAAUGCUCGUUUGCGAACCCAACCUCCGCAUGGCCUUCGGGCCAACAAAU
....((((.((((...........((((....))))..............))))....))))......................(((((....)))))...... (-14.81 = -15.97 +   1.16)

alignment

secondary structure

dotplot

Window 3

Location	25,279,431 – 25,279,537
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.40
Mean single sequence MFE	-34.64
Consensus MFE	-17.00
Energy contribution	-17.72
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.77
Structure conservation index	0.49
SVM decision value	2.58
SVM RNA-class probability	0.995460
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25279431 106 + 27905053
AAUACCGAGUAAUCGGGUUUGCUUUGGGAGAAGCUCUACUUUCAGUAGAGCAUUUGCAUUCCAAAUGGAAACAUUAGCUAGCCAGGUGAUUCGGCAUGG--------------UUUUGUU
....((((((.(((.((((.(((.(((((((((((((((.....))))))).)))...)))))((((....))))))).)))).))).)))))).....--------------....... ( -36.80)
>DroSec_CAF1 136310 99 + 1
AAUGCCGAGUAAUCGUGUU-----UGGGAGCAGCUCUACUUUCAGUAGA--CUUUGCAUUCCAAAUGGAAACAUUAGUUAGCAAGGUGAUUCGGCAUGG--------------UUUUCUU
.(((((((((.(((.((((-----(((((((((.(((((.....)))))--..)))).)))))((((....))))....)))).))).)))))))))..--------------....... ( -35.60)
>DroSim_CAF1 136040 104 + 1
AAUGCCGAGUAAUCGGGUUUGCUUUGGGAGCAGCUCUACUUUCAGUAGA--CUUUGCAUUCCAAAUGGAAACAUUAGUUAGCAAGGUGAUUCGGCAUGG--------------UUUUGUU
.(((((((((.(((..(((.(((.(((((((((.(((((.....)))))--..)))).)))))((((....))))))).)))..))).)))))))))..--------------....... ( -38.20)
>DroEre_CAF1 153678 113 + 1
AAUGCCGAGUAAUCGGGUUUGCGAUUGGAGCUGCUUUACUACCAGUAGA--GUUUGCAUUCCGAAUUGAAACAUCAGUUAGCAAGGUGAUUCGGGAUGAUUCCCUCGCAAUGUU-C----
....((((....))))..(((((((((((((.(((((((.....)))))--))..))..)))))...(((.((((.........)))).)))((((....))))))))))....-.---- ( -36.50)
>DroYak_CAF1 141656 118 + 1
AAUGCCAAGUAAUCGGGUUUGCUCAUGGAGAAGCUUCACUUUCUGUGGA--AUUUGCAUUCCAAAUUGAAACAUUAGUUAGCAAGGUGAUUCGAGAGGGAUGCCUUACUAUGAUUUUGUU
........((((......))))((((((.(((..(((((.....)))))--.)))(((((((...(((((.((((.........)))).)))))..)))))))....))))))....... ( -26.10)
>consensus
AAUGCCGAGUAAUCGGGUUUGCUUUGGGAGCAGCUCUACUUUCAGUAGA__AUUUGCAUUCCAAAUGGAAACAUUAGUUAGCAAGGUGAUUCGGCAUGG______________UUUUGUU
....((((((.(((..(((.((....((((..(((((((.....)))))......)).)))).((((....)))).)).)))..))).)))))).......................... (-17.00 = -17.72 +   0.72)

alignment

secondary structure

dotplot

Window 4

Location	25,279,431 – 25,279,537
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.40
Mean single sequence MFE	-24.93
Consensus MFE	-14.40
Energy contribution	-14.56
Covariance contribution	0.16
Combinations/Pair	1.22
Mean z-score	-2.07
Structure conservation index	0.58
SVM decision value	1.06
SVM RNA-class probability	0.908387
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25279431 106 - 27905053
AACAAAA--------------CCAUGCCGAAUCACCUGGCUAGCUAAUGUUUCCAUUUGGAAUGCAAAUGCUCUACUGAAAGUAGAGCUUCUCCCAAAGCAAACCCGAUUACUCGGUAUU
.......--------------..(((((((.......((...(((..(((((((....)))).)))...(((((((.....))))))).........)))...)).......))))))). ( -27.34)
>DroSec_CAF1 136310 99 - 1
AAGAAAA--------------CCAUGCCGAAUCACCUUGCUAACUAAUGUUUCCAUUUGGAAUGCAAAG--UCUACUGAAAGUAGAGCUGCUCCCA-----AACACGAUUACUCGGCAUU
.......--------------..((((((((((....((..(((....)))..))(((((...(((...--(((((.....)))))..)))..)))-----))...)))...))))))). ( -24.00)
>DroSim_CAF1 136040 104 - 1
AACAAAA--------------CCAUGCCGAAUCACCUUGCUAACUAAUGUUUCCAUUUGGAAUGCAAAG--UCUACUGAAAGUAGAGCUGCUCCCAAAGCAAACCCGAUUACUCGGCAUU
.......--------------..((((((((((...((((((((....))).....((((...(((...--(((((.....)))))..)))..)))))))))....)))...))))))). ( -25.30)
>DroEre_CAF1 153678 113 - 1
----G-AACAUUGCGAGGGAAUCAUCCCGAAUCACCUUGCUAACUGAUGUUUCAAUUCGGAAUGCAAAC--UCUACUGGUAGUAAAGCAGCUCCAAUCGCAAACCCGAUUACUCGGCAUU
----.-....((((((((((....))))........((((...((((.........))))...))))..--.....(((.(((......)))))).))))))..((((....)))).... ( -26.70)
>DroYak_CAF1 141656 118 - 1
AACAAAAUCAUAGUAAGGCAUCCCUCUCGAAUCACCUUGCUAACUAAUGUUUCAAUUUGGAAUGCAAAU--UCCACAGAAAGUGAAGCUUCUCCAUGAGCAAACCCGAUUACUUGGCAUU
..(((((((.((((((((..((......))....))))))))......((((((...((((((....))--)))).......))))))..................))))..)))..... ( -21.30)
>consensus
AACAAAA______________CCAUGCCGAAUCACCUUGCUAACUAAUGUUUCCAUUUGGAAUGCAAAG__UCUACUGAAAGUAGAGCUGCUCCCAAAGCAAACCCGAUUACUCGGCAUU
.......................((((((((((...((((...((((.........))))...))))....(((((.....)))))....................)))...))))))). (-14.40 = -14.56 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:23 2006