Locus 1515

Sequence ID	X_DroMel_CAF1
Location	4,432,916 – 4,433,260
Length	344
Max. P	0.994656

overview

Window 2

Location	4,432,916 – 4,433,036
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-37.28
Consensus MFE	-37.76
Energy contribution	-37.28
Covariance contribution	-0.48
Combinations/Pair	1.09
Mean z-score	-1.77
Structure conservation index	1.01
SVM decision value	2.50
SVM RNA-class probability	0.994656
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4432916 120 - 22224390
AGGCCAGAGACCAUAUCACGCGCCUUCGUUUGGCGGGGGGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAACCAAAGCCCAGAGACAACAGCAAGAGGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) ( -37.00)
>DroSec_CAF1 35273 120 - 1
AGGCCAGAGACCAUAUCACGCGCCUUCGUUUGGCGGGGGGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAACCAAAGCCCAGAGACAACAGCAAGAGGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) ( -37.00)
>DroSim_CAF1 36631 120 - 1
AGGCCAGAGACCAUAUCACGCGCCUUCGUUUGGCGGGGGGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAACCAAAGCCCAGAGACAACAGCAAGAGGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) ( -37.00)
>DroEre_CAF1 36211 120 - 1
AGGCCAGAGACCGUAUCACGCGCCUUCGUUUGGCGAGGGGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAACCAAAGCCCAGAGACAACAGCAAGAAGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) ( -37.60)
>DroYak_CAF1 35410 120 - 1
AGGCCAGAGACCAUAUCACGCGCCUUCGUUUGGCGGGGAGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAAGCAAAGCCCAGAGACAACAGCAAAAGGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) ( -37.80)
>consensus
AGGCCAGAGACCAUAUCACGCGCCUUCGUUUGGCGGGGGGCUUAAAAAUCGCUUCCAGCGUCUUUGAUACUUUGGAACCAAAGCCCAGAGACAACAGCAAGAGGCUCCACAGAUAUAUCU
.......(((..(((((...((((.......)))).(((((((.......((.....))(((((((...(((((....)))))..))))))).........)))))))...))))).))) (-37.76 = -37.28 +  -0.48)

alignment

secondary structure

dotplot

Window 3

Location	4,433,036 – 4,433,144
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.06
Mean single sequence MFE	-18.78
Consensus MFE	-17.16
Energy contribution	-17.56
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.91
SVM decision value	1.88
SVM RNA-class probability	0.981215
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4433036 108 + 22224390
UCCUCCGAUCAAUUCCCAUUCCC------------AUUGCCAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUC
.......................------------................(((..((....))..)))...((((((((....)))))))).........((((((...)))))).... ( -19.10)
>DroSec_CAF1 35393 120 + 1
UCCUCCGAUCAAUUCCCAUUCCCAUUCCCAUUCUCAUUGCCAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUC
...................................................(((..((....))..)))...((((((((....)))))))).........((((((...)))))).... ( -19.10)
>DroSim_CAF1 36751 114 + 1
UCCUCCGAUCAAUUCCCAUUCCCAUUCCC------AUUGCCAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUC
.............................------................(((..((....))..)))...((((((((....)))))))).........((((((...)))))).... ( -19.10)
>DroEre_CAF1 36331 114 + 1
UCCUCCGAUCAAUUCCCAUUCCCAUUUCC------AUUGCCAUUCCCAUUCCGAUUUCGAUAGAUUUCGCCUUAUGUGAUCGCAAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUC
.............................------(((((...((.(((..(((..((....))..)))....))).))..)))))...............((((((...)))))).... ( -17.20)
>DroYak_CAF1 35530 108 + 1
UCCUCCGAUCGAUUCCCAUUCCC------------AUUGCCAUUUCCAUUCCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGGUUCAGCUUAUUC
.....................((------------(..(((..........(((..((....))..)))...((((((((....))))))))..........))))))............ ( -19.40)
>consensus
UCCUCCGAUCAAUUCCCAUUCCCAUU_CC______AUUGCCAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUC
...................................................(((..((....))..)))...((((((((....)))))))).........((((((...)))))).... (-17.16 = -17.56 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	4,433,064 – 4,433,180
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-29.92
Consensus MFE	-24.36
Energy contribution	-24.56
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-2.11
Structure conservation index	0.81
SVM decision value	1.55
SVM RNA-class probability	0.963413
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4433064 116 + 22224390
CAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUCCGGCCAGGUGACUCACCC----GCAAUCAUCACUCUUGGC
..........((((....(((.((((.((((.((((((((....)))))))).........((((((...)))))).....)))..((((...)))).----).)))))))....)))). ( -29.20)
>DroSec_CAF1 35433 120 + 1
CAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUCCGGCCAGGUGACUCACCCACCGGCAAUCAUUACUCUUGGC
............((..((....))..))(((.((((((((....))))))))..........(((((...)))))((((((((...((((...))))..)))).)))).........))) ( -32.20)
>DroSim_CAF1 36785 120 + 1
CAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUCCGGCCAGGUGACUCACCCACCGGCAAUCAUUACUCUUGGC
............((..((....))..))(((.((((((((....))))))))..........(((((...)))))((((((((...((((...))))..)))).)))).........))) ( -32.20)
>DroEre_CAF1 36365 116 + 1
CAUUCCCAUUCCGAUUUCGAUAGAUUUCGCCUUAUGUGAUCGCAAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUCCGGCCAGGUGACUCACCA----CCAAUCAUCACUCUUGGC
............((..((....))..))(((....(((((.((......))...........(((((..((....))...))))).((((......))----))....)))))....))) ( -27.20)
>DroYak_CAF1 35558 116 + 1
CAUUUCCAUUCCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGGUUCAGCUUAUUCCGGCCAGGUGACUCACUC----CCAAUCAUCACUCUUAGC
............((((..((..((..((((((((((((((....))))))))..........((((((...........)))))))))))).))..))----..))))............ ( -28.80)
>consensus
CAUUCCCAUACCGAUUUCGAUAGAUUUCGCCUUGUGUGAUCGCUAUCACGCACUCCUCCUCCGGCUGAUUCAGCUGAUUCCGGCCAGGUGACUCACCC____GCAAUCAUCACUCUUGGC
..........((((....(((.((((..(((.((((((((....)))))))).........((((((...)))))).....)))..((((...)))).......)))))))....)))). (-24.36 = -24.56 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	4,433,144 – 4,433,260
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.43
Mean single sequence MFE	-18.32
Consensus MFE	-13.44
Energy contribution	-13.45
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.73
SVM decision value	-0.06
SVM RNA-class probability	0.505189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4433144 116 + 22224390
CGGCCAGGUGACUCACCC----GCAAUCAUCACUCUUGGCGACCGAUUCCAAUUUCAACUAUUACGAUUCCCAAUAACCGAGGCCAUAUCUCACUUCCAAAUACUUAUUCACACCUUCGC
.((((.((((...)))).----.............((((.((.((...................)).)).)))).......))))................................... ( -14.11)
>DroSec_CAF1 35513 120 + 1
CGGCCAGGUGACUCACCCACCGGCAAUCAUUACUCUUGGCGACCGAUUCCAAUUCCCACUAUUACGAUUCCCAAUAACCGAGGCCAUAUCUCACUUCCAAAUACUUAUUCACACCUUCGC
.((((.((((.......))))((.((((........(((.((...........))))).......)))).)).........))))................................... ( -19.76)
>DroSim_CAF1 36865 120 + 1
CGGCCAGGUGACUCACCCACCGGCAAUCAUUACUCUUGGCGACCGAUUCCAAUUCCCACUAUUACGAUUCCCAAUAACCGAGGCCAUAUCUCAUUUCCAAAUACUUAUUCACACCUUCGC
.((((.((((.......))))((.((((........(((.((...........))))).......)))).)).........))))................................... ( -19.76)
>DroEre_CAF1 36445 100 + 1
CGGCCAGGUGACUCACCA----CCAAUCAUCACUCUUGGCGA----------------CUAUUACGAUUCCCAAUAGCCGAGGCCAUAUCUCACUGCCAAAUACUUAUUCACACUUUCGC
.((((.((((......))----))...........(((((..----------------..................)))))))))................................... ( -19.65)
>consensus
CGGCCAGGUGACUCACCC____GCAAUCAUCACUCUUGGCGACCGAUUCCAAUUCCCACUAUUACGAUUCCCAAUAACCGAGGCCAUAUCUCACUUCCAAAUACUUAUUCACACCUUCGC
.((((.((((...))))..................((((.((..........................)))))).......))))................................... (-13.44 = -13.45 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:51 2006