Locus 7659

Sequence ID	X_DroMel_CAF1
Location	19,074,341 – 19,074,476
Length	135
Max. P	0.993917

overview

Window 2

Location	19,074,341 – 19,074,438
Length	97
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-29.05
Consensus MFE	-21.46
Energy contribution	-22.02
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.74
SVM decision value	0.44
SVM RNA-class probability	0.738641
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19074341 97 + 22224390
AAGCAAAGCCCAGUGACUAUGGAUCCAUCGAUAAGGUGAUAAGAUUGCGAUGGGCAGCGUGGUUACAUGUGGCUCUGGAGUGGAAGCCACAUAUUUG
...((((.....(((((((((..(((((((.(((..(....)..))))))))))...)))))))))((((((((((.....)).)))))))).)))) ( -32.60)
>DroSec_CAF1 25935 87 + 1
AAGCAAAGCCCAGUGACUAUGGAUCCAUCGAUAAGGUGAUAAGAUUGC----------GUGGUUACAUGUGGCUCUGGAGUGGAAGCCACAUAUUUG
...((((.....(((((((((((((((((.....))))....)))).)----------))))))))((((((((((.....)).)))))))).)))) ( -27.70)
>DroSim_CAF1 27865 87 + 1
AAGCAAAGCCCAGUGACUAGGGAUCCAUCGAUAAGGUGAUAAGAUUGC----------GUGGUUACAUGUGGCUCUGGAGUGGAAGCCACAUAUUUG
...((((.....((((((((.((((((((.....))))....)))).)----------.)))))))((((((((((.....)).)))))))).)))) ( -26.50)
>DroYak_CAF1 28417 97 + 1
AAGCAAAGCCCAGUGACUGUGGAUCCAUCGAUAAGGUGAUAAGAUUGCGAUGAGGAGCGUGGUUACAUGUGGCUCUCGAGUGGAAGCCACAUAUUUG
...((((.....(((((..((..(((((((.(((..(....)..)))))))).))..))..)))))((((((((..(....)..)))))))).)))) ( -29.40)
>consensus
AAGCAAAGCCCAGUGACUAUGGAUCCAUCGAUAAGGUGAUAAGAUUGC__________GUGGUUACAUGUGGCUCUGGAGUGGAAGCCACAUAUUUG
...((((.....(((((((((((((((((.....))))....))))...........)))))))))((((((((((.....)).)))))))).)))) (-21.46 = -22.02 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	19,074,341 – 19,074,438
Length	97
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-24.18
Consensus MFE	-21.77
Energy contribution	-21.77
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.83
Structure conservation index	0.90
SVM decision value	2.44
SVM RNA-class probability	0.993917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19074341 97 - 22224390
CAAAUAUGUGGCUUCCACUCCAGAGCCACAUGUAACCACGCUGCCCAUCGCAAUCUUAUCACCUUAUCGAUGGAUCCAUAGUCACUGGGCUUUGCUU
...(((((((((((........)))))))))))......((.(((((.........((((........))))(((.....)))..)))))...)).. ( -27.40)
>DroSec_CAF1 25935 87 - 1
CAAAUAUGUGGCUUCCACUCCAGAGCCACAUGUAACCAC----------GCAAUCUUAUCACCUUAUCGAUGGAUCCAUAGUCACUGGGCUUUGCUU
...(((((((((((........)))))))))))......----------(((((((.(((........)))))).....((((....)))))))).. ( -21.90)
>DroSim_CAF1 27865 87 - 1
CAAAUAUGUGGCUUCCACUCCAGAGCCACAUGUAACCAC----------GCAAUCUUAUCACCUUAUCGAUGGAUCCCUAGUCACUGGGCUUUGCUU
...(((((((((((........)))))))))))......----------(((((((.(((........))))))..(((((...)))))..)))).. ( -23.70)
>DroYak_CAF1 28417 97 - 1
CAAAUAUGUGGCUUCCACUCGAGAGCCACAUGUAACCACGCUCCUCAUCGCAAUCUUAUCACCUUAUCGAUGGAUCCACAGUCACUGGGCUUUGCUU
...((((((((((..(....)..))))))))))......((((..(((((.................)))))(((.....)))...))))....... ( -23.73)
>consensus
CAAAUAUGUGGCUUCCACUCCAGAGCCACAUGUAACCAC__________GCAAUCUUAUCACCUUAUCGAUGGAUCCAUAGUCACUGGGCUUUGCUU
...(((((((((((........)))))))))))................(((((((.(((........)))))).....((((....)))))))).. (-21.77 = -21.77 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	19,074,369 – 19,074,476
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.40
Mean single sequence MFE	-28.46
Consensus MFE	-13.69
Energy contribution	-15.42
Covariance contribution	1.72
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.48
SVM decision value	0.62
SVM RNA-class probability	0.801594
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19074369 107 - 22224390
AAUCGA-AUCAUUGGCUAUCUGGGGGC-ACAGCUGGUAGCCAAAUAUGUGGCUUCCACUC--CAGA--------GCCACAUGUAACCACGCUGCCCAUCGCAAUCUUAUCA-CCUUAUCG
...(((-....(((((((((((.....-.)))...))))))))(((((((((((......--..))--------)))))))))......((........))..........-.....))) ( -29.40)
>DroPse_CAF1 29050 111 - 1
-AUCCACCACAUGGGCUAUCUGGGAGCCCCAGCUGGUGGCACAAUAU-UGGCAACAAGUCACCAAAACGUUGCCACCCCAUGUAAAGG-------CAUCGCAAUCUUAUCAUCGUUAUCG
-..((...((((((((((((((((...)))))...))))).......-(((((((.............)))))))..))))))...))-------......................... ( -28.82)
>DroSec_CAF1 25963 97 - 1
AAUCGA-AUCAUUGGCUAUCUGGGGGC-ACAGCUGGUAGCCAAAUAUGUGGCUUCCACUC--CAGA--------GCCACAUGUAACCAC----------GCAAUCUUAUCA-CCUUAUCG
...(((-....(((((((((((.....-.)))...))))))))(((((((((((......--..))--------)))))))))......----------............-.....))) ( -28.60)
>DroSim_CAF1 27893 97 - 1
AAUCGA-AUCAUUGGCUAUCUGGGGGC-ACAGCUGGUAGCCAAAUAUGUGGCUUCCACUC--CAGA--------GCCACAUGUAACCAC----------GCAAUCUUAUCA-CCUUAUCG
...(((-....(((((((((((.....-.)))...))))))))(((((((((((......--..))--------)))))))))......----------............-.....))) ( -28.60)
>DroYak_CAF1 28445 92 - 1
----GA-GUCAUUG-----------GC-ACAGCUGGUAGCCAAAUAUGUGGCUUCCACUC--GAGA--------GCCACAUGUAACCACGCUCCUCAUCGCAAUCUUAUCA-CCUUAUCG
----((-((..(((-----------((-((.....)).)))))((((((((((..(....--)..)--------)))))))))......))))..................-........ ( -25.80)
>DroPer_CAF1 30083 111 - 1
-AUCCACCACAUGGGCUAUCUGGGAGCCCCAGCUGGUGGCACAAUAU-UGGCAACAAGUCACCAAAACGUUGCCGACCCAUGUAAAGG-------CAUCGCAAUCUUAUCAUCCUUAUCG
-..((...((((((((((((((((...)))))...)))))......(-(((((((.............)))))))).))))))...))-------......................... ( -29.52)
>consensus
_AUCGA_AUCAUUGGCUAUCUGGGGGC_ACAGCUGGUAGCCAAAUAUGUGGCUUCCACUC__CAGA________GCCACAUGUAACCAC______CAUCGCAAUCUUAUCA_CCUUAUCG
...........(((((((((....(((....))))))))))))(((((((((......................)))))))))..................................... (-13.69 = -15.42 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:32 2006