Locus 2049

Sequence ID	3L_DroMel_CAF1
Location	5,639,439 – 5,639,568
Length	129
Max. P	0.968987

overview

Window 6

Location	5,639,439 – 5,639,537
Length	98
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.69
Mean single sequence MFE	-21.05
Consensus MFE	-12.06
Energy contribution	-13.40
Covariance contribution	1.34
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.57
SVM decision value	0.23
SVM RNA-class probability	0.645028
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5639439 98 + 23771897
---CCUGUUCUAUUAUUUAACUGCUUUCAACGUCAGCACCA---CGUUCAACCCGACGAAAGUCGAUUGAAAGCCGCCUUCAACGGC-------C-ACAGCAUCCCUCUCUC
---.((((..............(((((((((((.......)---)))......((((....))))..))))))).(((......)))-------.-))))............ ( -23.60)
>DroVir_CAF1 17303 90 + 1
CUGCCUGUUCUAUUAUUUAACUGCUUACAACAGA-----CG---UUUUCAACUUGACGAAAGCUGAUUGAAAGCCGCUUUCAACA-----------ACAGCAUCCAUCG---
....(((((.((.............)).))))).-----((---((........))))...((((.(((((((...)))))))..-----------.))))........--- ( -15.02)
>DroPse_CAF1 10210 103 + 1
---CCUGUUCUAUUAUUUAACUGCUUUCAACGUUAGC---G---UGUUCAACUUGACGAAAGUCGAUUGAAAGCCGCCUUCAACGGCAUCCAGCCACCAGCAUCCCUUUCUC
---.(((...............((((((((((....)---)---).......(((((....))))).))))))).(((......)))...)))................... ( -23.20)
>DroMoj_CAF1 15850 90 + 1
CUGCCUGUUCUAUUAUUUAACUGCUUACAACAGA-----CG---UUUUCAACUGGACGAAAGCUGAUUGAAAGCCGCUUUCAACA-----------GCAGCAUCCGUCG---
((((.((((...........(((.......))).-----.(---(((((((..((.(....)))..)))))))).......))))-----------)))).........--- ( -19.50)
>DroAna_CAF1 9788 99 + 1
---CCUGUUCUAUUAUUUAACUGCUUUCAACGUCAGCACAGCGCCGUUCAACUUGACGAAAGUCGAUUGAAAGCCGCCUUCAACGGC-------C--CAGCAUCCCUUUG-C
---...................((((((((.....((.....))........(((((....))))))))))))).(((......)))-------.--..(((......))-) ( -21.80)
>DroPer_CAF1 10335 103 + 1
---CCUGUUCUAUUAUUUAACUGCUUUCAACGUUAGC---G---UGUUCAACUUGACGAAAGUCGAUUGAAAGCCGCCUUCAACGGCAUCCAGCCACCAGCAUCCCUUUCUC
---.(((...............((((((((((....)---)---).......(((((....))))).))))))).(((......)))...)))................... ( -23.20)
>consensus
___CCUGUUCUAUUAUUUAACUGCUUUCAACGUAAGC__CG___UGUUCAACUUGACGAAAGUCGAUUGAAAGCCGCCUUCAACGGC_______C_ACAGCAUCCCUCUC_C
.....................((((.....................(((((.(((((....)))))))))).((((.......))))...........)))).......... (-12.06 = -13.40 +   1.34)

alignment

secondary structure

dotplot

Window 7

Location	5,639,474 – 5,639,568
Length	94
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.16
Mean single sequence MFE	-17.98
Consensus MFE	-9.24
Energy contribution	-9.77
Covariance contribution	0.53
Combinations/Pair	1.08
Mean z-score	-2.57
Structure conservation index	0.51
SVM decision value	1.63
SVM RNA-class probability	0.968987
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5639474 94 + 23771897
CCACGUUCAAC-CCGACGAAAGUCGAUUGAAAGCCGCCU-UCAACGGCCACAGCAUCCCUCUCUCUCUCUCUCUCUCAGCAAACACA--A-----AAAACAAA
.....(((((.-.((((....)))).))))).((((...-....)))).......................................--.-----........ ( -16.20)
>DroSec_CAF1 12478 85 + 1
CCGCGUUCAACCCCGACGAAAGUCGAUUGAAAGCCGCCU-UCAACGGCCACAGCAUCCCUCU----------CUCUCAGCAAACACA--A-----AAAACAAA
..((.(((((...((((....)))).))))).((((...-....))))....))........----------...............--.-----........ ( -18.00)
>DroSim_CAF1 13089 84 + 1
CCGCGUUCAAC-CCGACGAAAGUCGAUUGAAAGCCGCCU-UCAACGGCCACAGCAUCCCUCU----------CUCUCAGCAAACACA--A-----AAAACAAA
..((.(((((.-.((((....)))).))))).((((...-....))))....))........----------...............--.-----........ ( -18.90)
>DroEre_CAF1 12659 81 + 1
CCUCGUUCAAC-CCGACGAAAGUCGAUUGAAAGCCGCCU-UCAACGGACACAGCAUCCCUCU------------CUCAGCAAACACA--C------AAAAUAA
....((((...-.((((....)))).(((((.......)-)))).))))...((........------------....)).......--.------....... ( -13.70)
>DroYak_CAF1 12407 88 + 1
GCACGUUCAAC-CCGACGAAAGUCGAUUGAAAGCCGCCUUUCAACGGACCCAGCAUCCCUCU------------CUCAGCACACACA--UCACAAAAAAGUAA
((..((((...-.((((....)))).(((((((....))))))).))))...))........------------.............--.............. ( -17.90)
>DroMoj_CAF1 15884 81 + 1
-CGUUUUCAAC-UGGACGAAAGCUGAUUGAAAGCCGCUU-UCAACA---GCAGCAUCCGUCG------------UUCAC-UAAUACUCGACG---CGAGGGAG
-(((((.....-.)))))...((((.(((((((...)))-))))))---))....(((.(((------------(((..-........)).)---))).))). ( -23.20)
>consensus
CCGCGUUCAAC_CCGACGAAAGUCGAUUGAAAGCCGCCU_UCAACGGCCACAGCAUCCCUCU____________CUCAGCAAACACA__A_____AAAACAAA
.....(((((...((((....)))).)))))..(((........)))........................................................ ( -9.24 =  -9.77 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:13 2006