Locus 5539

Sequence ID	3L_DroMel_CAF1
Location	15,212,414 – 15,212,574
Length	160
Max. P	0.989573

overview

Window 2

Location	15,212,414 – 15,212,534
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.75
Mean single sequence MFE	-20.54
Consensus MFE	-17.00
Energy contribution	-17.60
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-2.27
Structure conservation index	0.83
SVM decision value	2.17
SVM RNA-class probability	0.989573
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15212414 120 + 23771897
AAGAUUAAAUUUAUUAAACUGAUUUUGAAACAACGAAGACAAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUAAAAUUUUUU
....(((((((((((...(((.(((((......))))).........(((.((((......)))).)))..((((((((((....))))))))))..))).)))))))))))........ ( -21.90)
>DroSec_CAF1 101802 118 + 1
AAGAUUAAAUUUAUUAAACUGAUUUCGAAACAACCAAGACAAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAUUGCUUGUUGACGCAGCAAUAAAUUUAAA--UUUUU
....(((((((((((...(((..........................(((.((((......)))).)))..((((((((((....))))))))))..))).))))))))))).--..... ( -21.90)
>DroSim_CAF1 107317 118 + 1
AAGAUUAAAUUUAUUAAACUGAUUCCGAAACAACCAAGACAAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUUAA--UUUUU
(((((((((((((((...(((..........................(((.((((......)))).)))..((((((((((....))))))))))..))).)))))).)))))--)))). ( -20.90)
>DroEre_CAF1 102293 117 + 1
AAGAUUAAGUUUAUUAAACUGAUUUCCCGACAA-CAAGACAAACCAUAUUUAUGCAAAACAGCGUCAAUCUUUAACAAGCAUGAAUGCUUGUUGACGCAGCUAUAAAUCUCAG--UAUUU
.................(((((...........-..........(((....))).......((((((.......(((((((....)))))))))))))...........))))--).... ( -20.01)
>DroYak_CAF1 106513 118 + 1
AAGAUUAAAUUUAUUAAACUGAUUUCCAAACAACCAAGACAAACCAUAUUUAUGCAAAGCAGCGCCAAUCUUUAACAAGCAUGAAUGCUUGUUGACGCAGCUAUAAAUCUUCA--UUUUU
((((((......................................(((....)))...(((.(((.......((((((((((....))))))))))))).)))...))))))..--..... ( -18.01)
>consensus
AAGAUUAAAUUUAUUAAACUGAUUUCGAAACAACCAAGACAAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUAAA__UUUUU
......(((((((((...(((..........................(((.((((......)))).)))..((((((((((....))))))))))..))).))))))))).......... (-17.00 = -17.60 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	15,212,414 – 15,212,534
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.75
Mean single sequence MFE	-25.03
Consensus MFE	-21.79
Energy contribution	-21.03
Covariance contribution	-0.76
Combinations/Pair	1.15
Mean z-score	-1.44
Structure conservation index	0.87
SVM decision value	0.74
SVM RNA-class probability	0.839002
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15212414 120 - 23771897
AAAAAAUUUUAAAUUUAUUGCUGCGUCAACAAGCAUUCGUGCUUGUUAAAGAUUGAUGCUGUUUUGCAUAAAUAUGGUUUGUCUUCGUUGUUUCAAAAUCAGUUUAAUAAAUUUAAUCUU
........(((((((((((((((((((((((((((....))))))).......)))))).((((((....(((..((.....))..)))....)))))).)))..))))))))))).... ( -23.81)
>DroSec_CAF1 101802 118 - 1
AAAAA--UUUAAAUUUAUUGCUGCGUCAACAAGCAAUCGUGCUUGUUAAAGAUUGAUGCUGUUUUGCAUAAAUAUGGUUUGUCUUGGUUGUUUCGAAAUCAGUUUAAUAAAUUUAAUCUU
.....--.(((((((((((((((..((((((((((....)))))))).(((((.(((..(((((.....)))))..))).))))).........))...))))..))))))))))).... ( -25.50)
>DroSim_CAF1 107317 118 - 1
AAAAA--UUAAAAUUUAUUGCUGCGUCAACAAGCAUUCGUGCUUGUUAAAGAUUGAUGCUGUUUUGCAUAAAUAUGGUUUGUCUUGGUUGUUUCGGAAUCAGUUUAAUAAAUUUAAUCUU
.....--...(((((((((((((..((((((((((....)))))))).(((((.(((..(((((.....)))))..))).)))))..........))..))))..)))))))))...... ( -23.70)
>DroEre_CAF1 102293 117 - 1
AAAUA--CUGAGAUUUAUAGCUGCGUCAACAAGCAUUCAUGCUUGUUAAAGAUUGACGCUGUUUUGCAUAAAUAUGGUUUGUCUUG-UUGUCGGGAAAUCAGUUUAAUAAACUUAAUCUU
.....--.((((.((((((((.(((((((((((((....))))))).......)))))).))).....(((((.((((((.((...-.....)).))))))))))))))))))))..... ( -26.61)
>DroYak_CAF1 106513 118 - 1
AAAAA--UGAAGAUUUAUAGCUGCGUCAACAAGCAUUCAUGCUUGUUAAAGAUUGGCGCUGCUUUGCAUAAAUAUGGUUUGUCUUGGUUGUUUGGAAAUCAGUUUAAUAAAUUUAAUCUU
.....--...(((((((((((.(((((((((((((....))))))).......)))))).))).....(((((.((((((.((..........)))))))))))))))))))))...... ( -25.51)
>consensus
AAAAA__UUAAAAUUUAUUGCUGCGUCAACAAGCAUUCGUGCUUGUUAAAGAUUGAUGCUGUUUUGCAUAAAUAUGGUUUGUCUUGGUUGUUUCGAAAUCAGUUUAAUAAAUUUAAUCUU
..........((((((((.((.(((((((((((((....))))))).......)))))).))......(((((.((((((...............)))))))))))))))))))...... (-21.79 = -21.03 +  -0.76)

alignment

secondary structure

dotplot

Window 4

Location	15,212,454 – 15,212,574
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.92
Mean single sequence MFE	-23.04
Consensus MFE	-19.18
Energy contribution	-18.94
Covariance contribution	-0.24
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.83
SVM decision value	1.76
SVM RNA-class probability	0.975887
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15212454 120 + 23771897
AAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUAAAAUUUUUUGCAAGAUUUAUUCAACGUGUUGACAAUGUUUUAGAAACCG
...........((((......))))...(((..((((.(((....)))((((..((((.((((.((((.....)))).))))..((.....))...))))..))))))))..)))..... ( -25.10)
>DroSec_CAF1 101842 118 + 1
AAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAUUGCUUGUUGACGCAGCAAUAAAUUUAAA--UUUUUGCAAGAUUUAUUCAACCUGUUGACAACGUUUUAAAAACCA
...............(((((......(((((((((((((((....)))))))))).((((.(((........)--)).)))).)))))...((((....))))....)))))........ ( -20.10)
>DroSim_CAF1 107357 118 + 1
AAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUUAA--UUUUUGCAAGAUUUAUUCAACCUGUUGACAACGUUUUAAAAACCG
...............(((((......(((((((((((((((....)))))))))).((((.(((........)--)).)))).)))))...((((....))))....)))))........ ( -20.00)
>DroEre_CAF1 102332 118 + 1
AAACCAUAUUUAUGCAAAACAGCGUCAAUCUUUAACAAGCAUGAAUGCUUGUUGACGCAGCUAUAAAUCUCAG--UAUUUGCAAGAUUUAUUCCACCUGCUGACAACGUUUUAGAAACCG
...............(((((...((((....((((((((((....)))))))))).((((..((((((((..(--(....)).)))))))).....))))))))...)))))........ ( -26.50)
>DroYak_CAF1 106553 118 + 1
AAACCAUAUUUAUGCAAAGCAGCGCCAAUCUUUAACAAGCAUGAAUGCUUGUUGACGCAGCUAUAAAUCUUCA--UUUUUGCCAGAUUUAUUCAACCUGCUGACAACGUUUUAGAAACCG
...............(((((...........((((((((((....)))))))))).((((..((((((((.((--....))..)))))))).....)))).......)))))........ ( -23.50)
>consensus
AAACCAUAUUUAUGCAAAACAGCAUCAAUCUUUAACAAGCACGAAUGCUUGUUGACGCAGCAAUAAAUUUAAA__UUUUUGCAAGAUUUAUUCAACCUGUUGACAACGUUUUAGAAACCG
...............(((((...........((((((((((....)))))))))).((((((((((((((.............))))))))......))))).)...)))))........ (-19.18 = -18.94 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:46 2006