Locus 1168

Sequence ID	3L_DroMel_CAF1
Location	3,362,426 – 3,362,706
Length	280
Max. P	0.997614

overview

Window 8

Location	3,362,426 – 3,362,546
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.83
Mean single sequence MFE	-47.38
Consensus MFE	-43.52
Energy contribution	-43.44
Covariance contribution	-0.08
Combinations/Pair	1.16
Mean z-score	-1.73
Structure conservation index	0.92
SVM decision value	2.19
SVM RNA-class probability	0.989896
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3362426 120 + 23771897
GCUGCCGGACAUCGAGUCCGUGGCGGAGGCAUUGCGCUUUGUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGCUUCCACAAGCCGCACAUUAAUUUCCGGUU
...((((((.((..(....(((((((((((.....((((((((....))))))))...((..((((((((......))))))))..)).))))))....)))))...)..)).)))))). ( -49.10)
>DroSec_CAF1 29584 120 + 1
GCUGCCGGACAUUGAGUCCGUGGCGGAGGCACUGCGCUUUGUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUCCUGGCCAUGGGUUUCCACAAGCCGCACAUUAAUUUCCGGUU
...((((((.(((((....(((((((((((.....((((((((....))))))))...((..((((((((......))))))))..)).))))))....)))))...))))).)))))). ( -52.20)
>DroSim_CAF1 27285 120 + 1
GCUGCCGGACAUAGAGUCCGUGGCGGAGGCACUGCGCUUUGUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGCUUCCACAAGCCGCACAUUAAUUUCCGGUU
...(((((((.....))))(((((((((((.....((((((((....))))))))...((..((((((((......))))))))..)).))))))....)))))............))). ( -48.60)
>DroEre_CAF1 28382 120 + 1
GCUGCCGGACAUCGAGUCCGUGGCGGAGGCACUGCGCUUCGUGGAGUCACGGAGCACGCACAACCAGGAACCAUUUUUUCUGGCCAUGGGUUUCCACAAGCCACACAUUAAUUUCCGAUU
((..(.((((.....)))))..))((((((..(((((((((((....))))))))..)))....((((((......))))))))).(((((((....))))).))........))).... ( -42.60)
>DroYak_CAF1 28167 120 + 1
ACUGCCGGACAUCGAGUCCGUGGCGGAGGCACUGCGCUUUGUGGAGUCACGGAGCACGCGGAAGCAGGAACCCUUUUUCCUGGCCAUGGGUUUUCACAAGCCUCACAUUAAUUUCCGGUU
...((((((.((..(.((((((((((.....))))((((((((....)))))))).))))))..((((((......)))))).....((((((....))))))....)..)).)))))). ( -44.40)
>consensus
GCUGCCGGACAUCGAGUCCGUGGCGGAGGCACUGCGCUUUGUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGUUUCCACAAGCCGCACAUUAAUUUCCGGUU
...(((((((.....))))(((((((((((..(((((((((((....))))))))..)))..((((((((......)))))))).....))))))....)))))............))). (-43.52 = -43.44 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	3,362,426 – 3,362,546
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-46.39
Consensus MFE	-38.90
Energy contribution	-39.46
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.95
Structure conservation index	0.84
SVM decision value	1.71
SVM RNA-class probability	0.973518
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3362426 120 - 23771897
AACCGGAAAUUAAUGUGCGGCUUGUGGAAGCCCAUGGCCAGAAAAAAUGGUUCCUGGCUGUGCCUGCUCCGUGAGCCCACAAAGCGCAAUGCCUCCGCCACGGACUCGAUGUCCGGCAGC
....(((......((((.((((..((((.((.(((((((((............)))))))))...))))))..))))))))..((.....)).)))(((..((((.....)))))))... ( -48.50)
>DroSec_CAF1 29584 120 - 1
AACCGGAAAUUAAUGUGCGGCUUGUGGAAACCCAUGGCCAGGAAAAAUGGUUCCUGGCUGUGCCUGCUCCGUGAGCCCACAAAGCGCAGUGCCUCCGCCACGGACUCAAUGUCCGGCAGC
....(((......((((.((((..((((....((((((((((((......)))))))))))).....))))..))))))))..((.....)).)))(((..((((.....)))))))... ( -52.60)
>DroSim_CAF1 27285 120 - 1
AACCGGAAAUUAAUGUGCGGCUUGUGGAAGCCCAUGGCCAGAAAAAAUGGUUCCUGGCUGUGCCUGCUCCGUGAGCCCACAAAGCGCAGUGCCUCCGCCACGGACUCUAUGUCCGGCAGC
....(((......((((.((((..((((.((.(((((((((............)))))))))...))))))..))))))))..((.....)).)))(((..((((.....)))))))... ( -48.50)
>DroEre_CAF1 28382 120 - 1
AAUCGGAAAUUAAUGUGUGGCUUGUGGAAACCCAUGGCCAGAAAAAAUGGUUCCUGGUUGUGCGUGCUCCGUGACUCCACGAAGCGCAGUGCCUCCGCCACGGACUCGAUGUCCGGCAGC
....((((.......(.(((((.((((....))))))))).)........)))).((..(..((((((.((((....)))).))))).)..)..))(((..((((.....)))))))... ( -44.76)
>DroYak_CAF1 28167 120 - 1
AACCGGAAAUUAAUGUGAGGCUUGUGAAAACCCAUGGCCAGGAAAAAGGGUUCCUGCUUCCGCGUGCUCCGUGACUCCACAAAGCGCAGUGCCUCCGCCACGGACUCGAUGUCCGGCAGU
..(((((........((((....((....))((.((((((((((......))))))....((((((((..(((....)))..))))).))).....)))).)).))))...))))).... ( -37.60)
>consensus
AACCGGAAAUUAAUGUGCGGCUUGUGGAAACCCAUGGCCAGAAAAAAUGGUUCCUGGCUGUGCCUGCUCCGUGAGCCCACAAAGCGCAGUGCCUCCGCCACGGACUCGAUGUCCGGCAGC
....(((......((((.((((..((((....(((((((((............))))))))).....))))..))))))))..((.....)).)))(((..((((.....)))))))... (-38.90 = -39.46 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	3,362,466 – 3,362,586
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-34.94
Consensus MFE	-27.88
Energy contribution	-27.80
Covariance contribution	-0.08
Combinations/Pair	1.16
Mean z-score	-1.97
Structure conservation index	0.80
SVM decision value	1.17
SVM RNA-class probability	0.925304
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3362466 120 + 23771897
GUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGCUUCCACAAGCCGCACAUUAAUUUCCGGUUCCCACGGCAAUUCCUUUCGAGAUUCAACCUUUCCCAGUUU
(((((..(.(((((....((..((((((((......))))))))..))(((((....)))))..........))))))..)))))((.(((..(....)..)))...))........... ( -33.50)
>DroSec_CAF1 29624 120 + 1
GUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUCCUGGCCAUGGGUUUCCACAAGCCGCACAUUAAUUUCCGGUUCCCACUGCAAUUCCUAUCGAGAUUCCACCUUUCCCAGUUU
((((.(((..(((((((.....((((((((......))))))))..((((........(((((............)))))))))))))...)))....)))...))))............ ( -35.00)
>DroSim_CAF1 27325 120 + 1
GUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGCUUCCACAAGCCGCACAUUAAUUUCCGGUUCCCACGGCAAUUUCUAUCGAGAUUUCACCUUUCCCAGUUU
(((((..(.(((((....((..((((((((......))))))))..))(((((....)))))..........))))))..)))))((.((((((....))))))...))........... ( -36.80)
>DroEre_CAF1 28422 120 + 1
GUGGAGUCACGGAGCACGCACAACCAGGAACCAUUUUUUCUGGCCAUGGGUUUCCACAAGCCACACAUUAAUUUCCGAUUCCCACGGCAAUUUCUAUCAAGAUUCCACCUUUCCGACUUU
((((((((..((((.((.((...(((((((......)))))))...)).))))))....(((.......................)))............))))))))............ ( -30.30)
>DroYak_CAF1 28207 120 + 1
GUGGAGUCACGGAGCACGCGGAAGCAGGAACCCUUUUUCCUGGCCAUGGGUUUUCACAAGCCUCACAUUAAUUUCCGGUUUCCACGGCAAUUUCUGUCAAGAUUCCACCUCUCCCAGUUU
((((((((..((((.((.((((((((((((......)))))).....((((((....))))))........))))))))))))..((((.....))))..))))))))............ ( -39.10)
>consensus
GUGGGCUCACGGAGCAGGCACAGCCAGGAACCAUUUUUUCUGGCCAUGGGUUUCCACAAGCCGCACAUUAAUUUCCGGUUCCCACGGCAAUUUCUAUCGAGAUUCCACCUUUCCCAGUUU
(((((....(((((....((..((((((((......))))))))..))(((((....)))))..........)))))...)))))................................... (-27.88 = -27.80 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	3,362,586 – 3,362,706
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.58
Mean single sequence MFE	-40.84
Consensus MFE	-37.50
Energy contribution	-38.10
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	0.92
SVM decision value	0.43
SVM RNA-class probability	0.731650
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3362586 120 + 23771897
UACAAUUACACGGAGGAUAGCCUGAAGCCGCCGGAUAUGCCGGCAGUGGCCUGGAAUCCUUACACAGAUGUGCGGGCCAGGGAUGACUUCAAGCACUCCAACAUAUCCUUUCCCUACGGA
...........((((....((.((((((((((((.....)))))..(((((((.((((........))).).))))))).))....))))).)).))))...........(((....))) ( -38.10)
>DroSec_CAF1 29744 120 + 1
UACAACUACACGGAGGACAGCCUGAAGCCGCCGGACAUGCCGGCAGUGGCCUGGAAUCCCUACACGGAUGUGCGGGCCAGGGAUGACUUCAAGCACUCCAACAUAUCCUUUCCCUACGGA
...........((((....((.((((((((((((.....)))))..(((((((.(((((......)))).).))))))).))....))))).)).))))...........(((....))) ( -41.50)
>DroSim_CAF1 27445 120 + 1
UACAACUACACGGAGGACAGCCUGAAGCCGCCGGACAUGCCGGCAGUGGCCUGGAAUCCCUACACGGAUGUGCGGGCCAGAGAUGACUUCAAGCACUCCAACAUAUCCUUUCCCUACGGA
...........((((....((.(((((.((((((.....)))))..(((((((.(((((......)))).).))))))).....).))))).)).))))...........(((....))) ( -41.40)
>DroEre_CAF1 28542 120 + 1
UACAACUACACGGAGGACAGCCUGAAGCCGCCGGAUAUGCCGGCAGUAGCCUGGAAUCCGUACACGGAUGUGCGGGCCAGGGAUGACUUCAAGCACUCCAAUAUAUCGUUUCCCUACGGA
...........((((....((.(((((.((((((.....))))).....(((((...(((((((....))))))).)))))...).))))).)).))))......((((......)))). ( -45.00)
>DroYak_CAF1 28327 120 + 1
UACAACUACACGGAGGACAGCCUGAAGCCGCCGGAUAUGCCGGCAGUGGCCUGGAAUCCCUACACGGAUGUGCGGGCCAGGGAUGACUUCAAGCACACCAAUAUAUCGUUUCCCUACGGC
..............((...((.((((((((((((.....)))))..(((((((.(((((......)))).).))))))).))....))))).))...))......((((......)))). ( -38.20)
>consensus
UACAACUACACGGAGGACAGCCUGAAGCCGCCGGAUAUGCCGGCAGUGGCCUGGAAUCCCUACACGGAUGUGCGGGCCAGGGAUGACUUCAAGCACUCCAACAUAUCCUUUCCCUACGGA
...........((((....((.(((((.((((((.....)))))..(((((((.(((((......)))).).))))))).....).))))).)).))))..................... (-37.50 = -38.10 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	3,362,586 – 3,362,706
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-48.88
Consensus MFE	-44.32
Energy contribution	-45.36
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.08
Structure conservation index	0.91
SVM decision value	2.89
SVM RNA-class probability	0.997614
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3362586 120 - 23771897
UCCGUAGGGAAAGGAUAUGUUGGAGUGCUUGAAGUCAUCCCUGGCCCGCACAUCUGUGUAAGGAUUCCAGGCCACUGCCGGCAUAUCCGGCGGCUUCAGGCUAUCCUCCGUGUAAUUGUA
(((....)))((..(((((..(((..((((((((((...(((((.((((((....))))..))...))))).....(((((.....)))))))))))))))..)))..)))))..))... ( -47.70)
>DroSec_CAF1 29744 120 - 1
UCCGUAGGGAAAGGAUAUGUUGGAGUGCUUGAAGUCAUCCCUGGCCCGCACAUCCGUGUAGGGAUUCCAGGCCACUGCCGGCAUGUCCGGCGGCUUCAGGCUGUCCUCCGUGUAGUUGUA
(((....)))....(((((..(((..((((((((((...((((((((((((....)))).)))...))))).....(((((.....)))))))))))))))..)))..)))))....... ( -51.10)
>DroSim_CAF1 27445 120 - 1
UCCGUAGGGAAAGGAUAUGUUGGAGUGCUUGAAGUCAUCUCUGGCCCGCACAUCCGUGUAGGGAUUCCAGGCCACUGCCGGCAUGUCCGGCGGCUUCAGGCUGUCCUCCGUGUAGUUGUA
(((....)))....(((((..(((..((((((((((...((((((((((((....)))).)))...))))).....(((((.....)))))))))))))))..)))..)))))....... ( -48.70)
>DroEre_CAF1 28542 120 - 1
UCCGUAGGGAAACGAUAUAUUGGAGUGCUUGAAGUCAUCCCUGGCCCGCACAUCCGUGUACGGAUUCCAGGCUACUGCCGGCAUAUCCGGCGGCUUCAGGCUGUCCUCCGUGUAGUUGUA
(((....))).(((((((((.((((.((((((((((...(((((.(((.(((....))).)))...))))).....(((((.....)))))))))))))))....)))))))).))))). ( -49.30)
>DroYak_CAF1 28327 120 - 1
GCCGUAGGGAAACGAUAUAUUGGUGUGCUUGAAGUCAUCCCUGGCCCGCACAUCCGUGUAGGGAUUCCAGGCCACUGCCGGCAUAUCCGGCGGCUUCAGGCUGUCCUCCGUGUAGUUGUA
.((....))..(((((((((.((...((((((((((...((((((((((((....)))).)))...))))).....(((((.....)))))))))))))))...))...)))).))))). ( -47.60)
>consensus
UCCGUAGGGAAAGGAUAUGUUGGAGUGCUUGAAGUCAUCCCUGGCCCGCACAUCCGUGUAGGGAUUCCAGGCCACUGCCGGCAUAUCCGGCGGCUUCAGGCUGUCCUCCGUGUAGUUGUA
(((....)))....(((((..(((..((((((((((...((((((((((((....)))).)))...))))).....(((((.....)))))))))))))))..)))..)))))....... (-44.32 = -45.36 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:57 2006