Locus 2385

Sequence ID	2R_DroMel_CAF1
Location	8,618,599 – 8,618,758
Length	159
Max. P	0.782958

overview

Window 6

Location	8,618,599 – 8,618,693
Length	94
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	71.49
Mean single sequence MFE	-32.84
Consensus MFE	-13.78
Energy contribution	-14.58
Covariance contribution	0.80
Combinations/Pair	1.33
Mean z-score	-1.75
Structure conservation index	0.42
SVM decision value	0.22
SVM RNA-class probability	0.641524
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8618599 94 + 20766785
AAUUGCAAUUGGAGGACUCUGCAGAUGCAAUUGGCAGUGCAUCGUAGGA---C----CCUCCAAUGAAGUU----UCCGAAACUGAGUGUCCUAUAUACGACAGA---------------
((((...((((((((..(((((.((((((........))))))))))).---.----))))))))..))))----.......(((.((((.....))))..))).--------------- ( -29.60)
>DroSec_CAF1 20890 107 + 1
AAUUGUAAUUGGAGGACUCUGCAGAUGCAA-UGGCAGUGCAUCGGAGGA---C----CCUCCAAUGAAGUU----UCCGAAAGUGAGUGUCCUAUAUACGAAGAAUCUCGCUCACUGAG-
((((...((((((((..(((.(.((((((.-......))))))).))).---.----))))))))..))))----......((((((((...................))))))))...- ( -32.81)
>DroSim_CAF1 18180 107 + 1
AAUUGUAAUUGGAGGACUCUGCAGAUGGAA-UGGCAGUGCAUCGGAGGA---C----CCUCCAAUGAAGUU----UGCGAAACUGAGUGUCCUAUAUACGACGAUUCUCGCACACUGAG-
.......((((((((.(((((((..((...-...)).)))...))))..---.----))))))))..(((.----(((((....(((((((........))).))))))))).)))...- ( -30.20)
>DroEre_CAF1 18634 115 + 1
AACUGUAAUUGGAAGUCCCUGCAGCUGGCUGUCCUUGUCAGUUGGAGGAGAGCCCUGCCAUCAUUGGAGUGCUGCACCAGCACUCAAUUUUUGAUAAACGAAA---CCCG--CACCGGGA
.......((..(((((....((((..((((.(((((........))))).))))))))........((((((((...)))))))).)))))..))........---((((--...)))). ( -39.90)
>DroYak_CAF1 14396 104 + 1
AACUGUAAUUCGAGGACUCUGCAGAUGCAACUGCCAGUGCAUCGGAGGA---C----CCUUCAAUGAAGUU----UCCGAAACUGAGUGUCCUAUAUACGAAG---CUCG--CACUCAGU
........((((..((((...((((((((........))))))((((..---.----.))))..)).))))----..))))(((((((((.((........))---...)--)))))))) ( -31.70)
>consensus
AAUUGUAAUUGGAGGACUCUGCAGAUGCAA_UGGCAGUGCAUCGGAGGA___C____CCUCCAAUGAAGUU____UCCGAAACUGAGUGUCCUAUAUACGAAG___CUCG__CACUGAG_
............(((((.((...((((((........))))))(((((.........))))).......................)).)))))........................... (-13.78 = -14.58 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	8,618,599 – 8,618,693
Length	94
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.49
Mean single sequence MFE	-31.12
Consensus MFE	-8.05
Energy contribution	-9.77
Covariance contribution	1.72
Combinations/Pair	1.21
Mean z-score	-1.65
Structure conservation index	0.26
SVM decision value	-0.03
SVM RNA-class probability	0.515875
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8618599 94 - 20766785
---------------UCUGUCGUAUAUAGGACACUCAGUUUCGGA----AACUUCAUUGGAGG----G---UCCUACGAUGCACUGCCAAUUGCAUCUGCAGAGUCCUCCAAUUGCAAUU
---------------..((((........)))).........(..----..)...((((((((----(---..((.(((((((........)))))).).))..)))))))))....... ( -26.60)
>DroSec_CAF1 20890 107 - 1
-CUCAGUGAGCGAGAUUCUUCGUAUAUAGGACACUCACUUUCGGA----AACUUCAUUGGAGG----G---UCCUCCGAUGCACUGCCA-UUGCAUCUGCAGAGUCCUCCAAUUACAAUU
-...((((((.(...((((........))))).))))))...(..----..)...((((((((----(---..(((.((((((......-.)))))).).))..)))))))))....... ( -31.80)
>DroSim_CAF1 18180 107 - 1
-CUCAGUGUGCGAGAAUCGUCGUAUAUAGGACACUCAGUUUCGCA----AACUUCAUUGGAGG----G---UCCUCCGAUGCACUGCCA-UUCCAUCUGCAGAGUCCUCCAAUUACAAUU
-....((((((((......))))))))(((((.(((((....(((----.....((((((((.----.---..))))))))...)))..-......))).)).)))))............ ( -30.20)
>DroEre_CAF1 18634 115 - 1
UCCCGGUG--CGGG---UUUCGUUUAUCAAAAAUUGAGUGCUGGUGCAGCACUCCAAUGAUGGCAGGGCUCUCCUCCAACUGACAAGGACAGCCAGCUGCAGGGACUUCCAAUUACAGUU
......((--..((---(..(...(((((......((((((((...))))))))...)))))((((((((.((((..........)))).))))..)))).)..)))..))......... ( -35.90)
>DroYak_CAF1 14396 104 - 1
ACUGAGUG--CGAG---CUUCGUAUAUAGGACACUCAGUUUCGGA----AACUUCAUUGAAGG----G---UCCUCCGAUGCACUGGCAGUUGCAUCUGCAGAGUCCUCGAAUUACAGUU
(((((((.--((((---.(((((((..(((((..(((((...(..----..)...)))))...----)---))))...))))....((((......)))).)))..)))).))).)))). ( -31.10)
>consensus
_CUCAGUG__CGAG___CUUCGUAUAUAGGACACUCAGUUUCGGA____AACUUCAUUGGAGG____G___UCCUCCGAUGCACUGCCA_UUGCAUCUGCAGAGUCCUCCAAUUACAAUU
.....................(((...(((((..........(((........((......))........)))...((((((........))))))......))))).....))).... ( -8.05 =  -9.77 +   1.72)

alignment

secondary structure

dotplot

Window 8

Location	8,618,668 – 8,618,758
Length	90
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	80.66
Mean single sequence MFE	-25.88
Consensus MFE	-15.61
Energy contribution	-17.55
Covariance contribution	1.94
Combinations/Pair	1.14
Mean z-score	-2.08
Structure conservation index	0.60
SVM decision value	0.56
SVM RNA-class probability	0.782958
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8618668 90 + 20766785
AACUGAGUGUCCUAUAUACGACAGA---------------UGACAGAUUUUCCACAAAUAUCAACAGCCUGGCCCUCAUUCGUGGGCCAUGGUUA----CUCAUAUGUU
...((((((((........)))...---------------.........................((((((((((........)))))).)))))----))))...... ( -23.40)
>DroSec_CAF1 20958 108 + 1
AAGUGAGUGUCCUAUAUACGAAGAAUCUCGCUCACUGAG-UUGCGGAUUUUCCGCAAAUAUCAACAGCCUGGCUCUCAUUCGUGAGCCAUGGUUACUCUCUCAUAUAUU
.((((((((...................))))))))(((-((((((.....))))))........((((((((((........)))))).)))).....)))....... ( -35.91)
>DroSim_CAF1 18248 104 + 1
AACUGAGUGUCCUAUAUACGACGAUUCUCGCACACUGAG-UUGCGGAUUUUCCGCAAAUAUCAACAGCCUGGCUAUCAUUCGUGGGCCAUGGUUC----CUCAUAUAUU
...((((((((........))))............(((.-((((((.....))))))...)))..(((((((((..........))))).)))).----))))...... ( -25.70)
>DroYak_CAF1 14465 100 + 1
AACUGAGUGUCCUAUAUACGAAG---CUCG--CACUCAGUUCACAGAUUUUCCGCAAAUAUCAACAAACUGGCUCUCAUUCGUCGGCCAUGGUUA----CUCAUAUAUU
((((((((((.((........))---...)--))))))))).....................(((....(((((..(....)..)))))..))).----.......... ( -18.50)
>consensus
AACUGAGUGUCCUAUAUACGAAGAA_CUCG__CACUGAG_UUACAGAUUUUCCGCAAAUAUCAACAGCCUGGCUCUCAUUCGUGGGCCAUGGUUA____CUCAUAUAUU
...((((.................................((((((.....))))))........((((((((((.(....).)))))).)))).....))))...... (-15.61 = -17.55 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:46 2006