Locus 2333

Sequence ID	X_DroMel_CAF1
Location	6,262,069 – 6,262,331
Length	262
Max. P	0.800335

overview

Window 3

Location	6,262,069 – 6,262,175
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.04
Mean single sequence MFE	-24.14
Consensus MFE	-18.55
Energy contribution	-18.30
Covariance contribution	-0.25
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.77
SVM decision value	0.07
SVM RNA-class probability	0.567586
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6262069 106 - 22224390
AAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUCCGGCCAACAAUACAGAAGCCGCAAUAUUCACACUUUUACAGCUGACUGGGCAC----ACACAUCCAGGCA----------
..((.((((((((((((..((((((....))))))(((((.(..........).)))))...........)))))))...(((.....)))..----.....))))))).---------- ( -26.80)
>DroSec_CAF1 3734 97 - 1
AAGCUCUGGAAAAAGUGCAGAGCAUAAAAAUGUUUGCUUCCGGCCAACAAUACAGAAGCCGCAAUAUUCACACUUUUACAGCUGACUGGGCAC----ACAC-------------------
..((((((.(.....).)))))).......(((.((((..((((.............)))).................(((....))))))).----))).------------------- ( -21.12)
>DroSim_CAF1 3668 105 - 1
AAGCUCUGGAAAAAGUGCAGAGCAUAAAAAUGUUUGCUUCCGGCCAACAAUACAGAAGCCGCAAUAUUCACACUUUUACAGCUGACUGGGCAC----ACACAUCCCGAC-----------
..((((((.(.....).)))))).......(((.((((..((((.............)))).................(((....))))))).----))).........----------- ( -21.12)
>DroYak_CAF1 3205 120 - 1
AAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUCCGGCCAACAAUACAGAAGCCGCAAUAUUCACACUUUUACAGCUGACUGGGCAGACGCACACAUCCAGGCAUAUUCAGACA
..((.(((((....((((.((((((....))))))(((..((((.............)))).................(((....))))))....))))...)))))))........... ( -27.52)
>consensus
AAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUCCGGCCAACAAUACAGAAGCCGCAAUAUUCACACUUUUACAGCUGACUGGGCAC____ACACAUCCAGGC___________
..((((.((.(((((((..((((((....))))))(((((.(..........).)))))...........)))))))....))....))))............................. (-18.55 = -18.30 +  -0.25)

alignment

secondary structure

dotplot

Window 4

Location	6,262,135 – 6,262,254
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.54
Mean single sequence MFE	-30.85
Consensus MFE	-24.62
Energy contribution	-25.12
Covariance contribution	0.50
Combinations/Pair	1.21
Mean z-score	-1.63
Structure conservation index	0.80
SVM decision value	0.34
SVM RNA-class probability	0.696314
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6262135 119 + 22224390
GAAGCAAACAUUUUUAUGUUCUGCACUUUUUCCAGAGCUUCUUCAUCUUCGCUCCAUACCCCUAUAU-AUCGUAAGGACGAAAAGGACGAGGUAGUUGGGCAUUUGAUUAAGCCCGGCUC
...((((((((....))))).)))(((((.(((.(((....)))...((((.(((.(((........-...))).)))))))..))).)))))((((((((..........)))))))). ( -31.70)
>DroSec_CAF1 3791 120 + 1
GAAGCAAACAUUUUUAUGCUCUGCACUUUUUCCAGAGCUUCUUCAUCUUCGCUCCAUACCAGUAUACCGCCCUAAGGACGAAAAGGACCAUCUAGCUGAGCAUUUGAUUAAGCCCGGCUC
..(((......((..((((((.((......(((.((((............)))).............((((....)).))....))).......)).))))))..)).........))). ( -21.08)
>DroSim_CAF1 3733 120 + 1
GAAGCAAACAUUUUUAUGCUCUGCACUUUUUCCAGAGCUUCUUCGUCUUCGCUCCAUACCAGUAUACCGCCCUAAGGACGAAAGGGACGAGGUAGCUGGGCAUUUGAUUAAGCCCGGCUC
.................((((((.........))))))..(((((((((((.(((.((...((.....))..)).))))))...)))))))).((((((((..........)))))))). ( -35.40)
>DroYak_CAF1 3285 108 + 1
GAAGCAAACAUUUUUAUGUUCUGCACUUUUUCCAGAGCUUCUUCAUCUUU-CUCC----CCCCAA-------AAGGGACAAAAAGGAUGAAGUAGCUGGGCAUUUGAUUAAGCCCGGUUC
...((((((((....))))).))).......((..((((.((((((((((-.(((----(.....-------..))))....)))))))))).))))((((..........))))))... ( -35.20)
>consensus
GAAGCAAACAUUUUUAUGCUCUGCACUUUUUCCAGAGCUUCUUCAUCUUCGCUCCAUACCACUAUAC_GCCCUAAGGACGAAAAGGACGAGGUAGCUGGGCAUUUGAUUAAGCCCGGCUC
.................((((((.........))))))..(((((((((((.(((....................))))))...)))))))).((((((((..........)))))))). (-24.62 = -25.12 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	6,262,135 – 6,262,254
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.54
Mean single sequence MFE	-35.83
Consensus MFE	-23.61
Energy contribution	-23.43
Covariance contribution	-0.19
Combinations/Pair	1.15
Mean z-score	-2.05
Structure conservation index	0.66
SVM decision value	0.49
SVM RNA-class probability	0.755220
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6262135 119 - 22224390
GAGCCGGGCUUAAUCAAAUGCCCAACUACCUCGUCCUUUUCGUCCUUACGAU-AUAUAGGGGUAUGGAGCGAAGAUGAAGAAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUC
...((((((((..(((..((((((..((((((.......((((....)))).-.....))))))))).)))....)))..)))).)))).......(((((.(((....))))))))... ( -33.02)
>DroSec_CAF1 3791 120 - 1
GAGCCGGGCUUAAUCAAAUGCUCAGCUAGAUGGUCCUUUUCGUCCUUAGGGCGGUAUACUGGUAUGGAGCGAAGAUGAAGAAGCUCUGGAAAAAGUGCAGAGCAUAAAAAUGUUUGCUUC
...((((((((..(((..(((((.(((((((.(((((..........))))).))...)))))...)))))....)))..)))).)))).......(((((.(((....))))))))... ( -34.60)
>DroSim_CAF1 3733 120 - 1
GAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCCUUUCGUCCUUAGGGCGGUAUACUGGUAUGGAGCGAAGACGAAGAAGCUCUGGAAAAAGUGCAGAGCAUAAAAAUGUUUGCUUC
.(((.((((..........)))).))).(.(((((...(((((((....(.(((....))).)..))).))))))))).)..((((((.(.....).))))))................. ( -35.80)
>DroYak_CAF1 3285 108 - 1
GAACCGGGCUUAAUCAAAUGCCCAGCUACUUCAUCCUUUUUGUCCCUU-------UUGGGG----GGAG-AAAGAUGAAGAAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUC
...((((((..........))))((((.(((((((.(((((.((((..-------..))))----.)))-)).))))))).))))..)).......(((((.(((....))))))))... ( -39.90)
>consensus
GAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCUUUUCGUCCUUAGGGC_GUAUACGGGUAUGGAGCGAAGAUGAAGAAGCUCUGGAAAAAGUGCAGAACAUAAAAAUGUUUGCUUC
.(((.((((..........)))).)))...(((((...(((((((....................))).))))))))).(((((((((.(.....).))))((((....))))..))))) (-23.61 = -23.43 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	6,262,175 – 6,262,294
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.67
Mean single sequence MFE	-39.55
Consensus MFE	-29.12
Energy contribution	-28.50
Covariance contribution	-0.62
Combinations/Pair	1.17
Mean z-score	-1.56
Structure conservation index	0.74
SVM decision value	0.17
SVM RNA-class probability	0.617145
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6262175 119 - 22224390
GCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAACUACCUCGUCCUUUUCGUCCUUACGAU-AUAUAGGGGUAUGGAGCGAAGAUGAAG
..((((..(((((((((((((.......)))).)))))))))...((((..........))))......))))((.(((((((((.(((...-........))).))).)))))).)).. ( -37.50)
>DroSec_CAF1 3831 120 - 1
GCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCUCAGCUAGAUGGUCCUUUUCGUCCUUAGGGCGGUAUACUGGUAUGGAGCGAAGAUGAAG
(((..(..(((((((((((((.......)))).)))))))))..).)))...(((...(((((.(((((((.(((((..........))))).))...)))))...)))))..))).... ( -38.50)
>DroSim_CAF1 3773 120 - 1
GCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCCUUUCGUCCUUAGGGCGGUAUACUGGUAUGGAGCGAAGACGAAG
...(((..(((((((((((((.......)))).)))))))))((.((((..........)))).))...)))(((...(((((((....(.(((....))).)..))).))))))).... ( -39.30)
>DroYak_CAF1 3325 108 - 1
GCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCAAGCUGGGAACCGGGCUUAAUCAAAUGCCCAGCUACUUCAUCCUUUUUGUCCCUU-------UUGGGG----GGAG-AAAGAUGAAG
((......(((((((((((((.......)))).)))))))))...((((..........)))).))..(((((((.(((((.((((..-------..))))----.)))-)).))))))) ( -42.90)
>consensus
GCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCUUUUCGUCCUUAGGGC_GUAUACGGGUAUGGAGCGAAGAUGAAG
.....(..(((((((((((((.......)))).)))))))))..)((((..........)))).......(((((...(((((((....................))).))))))))).. (-29.12 = -28.50 +  -0.62)

alignment

secondary structure

dotplot

Window 7

Location	6,262,214 – 6,262,331
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.55
Mean single sequence MFE	-39.88
Consensus MFE	-32.11
Energy contribution	-32.30
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-2.02
Structure conservation index	0.81
SVM decision value	0.61
SVM RNA-class probability	0.800335
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6262214 117 - 22224390
AACCGG---GCACUGGCAGCACACUUUGCAUUCCAGCAAUGCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAACUACCUCGUCCUUUU
....((---((...(((......(((.(((((.....))))).)))..(((((((((((((.......)))).))))))))))))((((..........)))).........)))).... ( -39.80)
>DroSec_CAF1 3871 117 - 1
AACCGG---GCACUGGCAGCACACUUUGCAUUCCGGCAAUGCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCUCAGCUAGAUGGUCCUUUU
....((---((.(((((.((..........(((((((...)))).)))(((((((((((((.......)))).))))))))))).((((..........)))).)))))...)))).... ( -40.40)
>DroSim_CAF1 3813 117 - 1
AACCGG---GCACUGGCAGCACACUUUGCAUUCCGGCAAUGCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCCUUU
....((---((.((.(((((.....(((((((.((((...)))).(((.......))))))))))...))))).))..((((((.((((..........)))).))).))).)))).... ( -42.90)
>DroYak_CAF1 3353 120 - 1
AACCAGGCGGCAAUGGGAGCACACUUUGCAUUCUGGCAAUGCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCAAGCUGGGAACCGGGCUUAAUCAAAUGCCCAGCUACUUCAUCCUUUU
....((((((((.((((((((.....))).)))))....))))).((((((((((((((((.......)))).)))))))))...((((..........))))......)))..)))... ( -36.40)
>consensus
AACCGG___GCACUGGCAGCACACUUUGCAUUCCGGCAAUGCCGAGAAUCUCAGUUUCAGUGCAAUUAGCUGCGAGCUGGGAGCCGGGCUUAAUCAAAUGCCCAGCUACCUCGUCCUUUU
.........((...(((.(((.....))).(((((((...)))).)))(((((((((((((.......)))).))))))))))))((((..........)))).)).............. (-32.11 = -32.30 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:53 2006