Locus 3154

Sequence ID	3L_DroMel_CAF1
Location	9,170,776 – 9,170,933
Length	157
Max. P	0.992016

overview

Window 9

Location	9,170,776 – 9,170,893
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.68
Mean single sequence MFE	-23.60
Consensus MFE	-12.34
Energy contribution	-11.46
Covariance contribution	-0.88
Combinations/Pair	1.36
Mean z-score	-2.29
Structure conservation index	0.52
SVM decision value	1.40
SVM RNA-class probability	0.950194
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9170776 117 - 23771897
AACAUAUUGUCUUUUCGAGCUUAUUUUAUCCUCGGAGCUUUACCAAAAUAUCCAUCUUUUAUCCAAAGCUCCAAGCUUUGCAUUGC---AAGCUUUUUCAAAGUCUUCGGUUGCGUAAAA
......(((..(..((((((((...........((((((((...((((........))))....))))))))((((((.((...))---)))))).....))))..))))..)..))).. ( -20.30)
>DroSec_CAF1 25701 110 - 1
AACAGAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCACAAUUUCCACCUUUUAUCCAAAGCUCCAAGCUUUGCUUCGC---AAGCUUUUUCAUAGUCUUCGGUC-------A
...(((((((......((((((........(((((((((((.......................)))))))))))....((...))---))))))....)))))))......-------. ( -22.40)
>DroSim_CAF1 26032 110 - 1
AACAGAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCACAGUUUCUAUCUCUUAUCCAAAGCUCCAAGCUUUGCACUGC---AAGCUUUUUCAAAGUCUUCGGUC-------G
....(((((..((((.((((((........(((((((((((.....((.........)).....)))))))))))....((...))---))))))....))))....)))))-------. ( -23.40)
>DroEre_CAF1 38549 112 - 1
AACAAAUUGUCCUUUCAAGUUUACAUUAUCCUUGGAGCUUUA--------UCCAGCUUUUAUCCGAAGCUCUUAGCAUUACUAGGAAAAAAGCUGUUCCAGAGUCUUUGGUUGUGUAAAA
...................(((((((...((..(((.((((.--------..((((((((.(((.((((.....)).))....))).))))))))....)))))))..))..))))))). ( -27.50)
>DroYak_CAF1 40144 111 - 1
AACAAAUUGUCCUUUCAAGUUCAUAUUAUCCUUGGAGCUUUA--------UGCAGCUUUUAUCCAAAGCUCUUAGCUUUACUAAGCAGAAAGCUUUUUCAGAGUCUUUGGUUGUGUAA-A
.((((...........(((((((((...((....))....))--------)).)))))....((((((((((.((((((.((....)))))))).....)))).))))))))))....-. ( -24.40)
>consensus
AACAAAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCA_A_U_UCCAGCUUUUAUCCAAAGCUCCAAGCUUUGCUAUGC___AAGCUUUUUCAAAGUCUUCGGUUG_GUAA_A
..........((....((((((...........((((((((.......................))))))))((((((...........)))))).....))).))).)).......... (-12.34 = -11.46 +  -0.88)

alignment

secondary structure

dotplot

Window 0

Location	9,170,813 – 9,170,933
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.19
Mean single sequence MFE	-27.16
Consensus MFE	-14.42
Energy contribution	-14.10
Covariance contribution	-0.32
Combinations/Pair	1.14
Mean z-score	-2.12
Structure conservation index	0.53
SVM decision value	0.33
SVM RNA-class probability	0.691500
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9170813 120 + 23771897
CAAAGCUUGGAGCUUUGGAUAAAAGAUGGAUAUUUUGGUAAAGCUCCGAGGAUAAAAUAAGCUCGAAAAGACAAUAUGUUGUGAAAUUCUCUAUUUACUUCAUUGAAGCUUUAAAUAUUU
.....((((((((((((..(((((........))))).))))))))))))((((....((((((((...(((.....)))(((((........)))))....))).)))))....)))). ( -27.30)
>DroSec_CAF1 25731 120 + 1
CAAAGCUUGGAGCUUUGGAUAAAAGGUGGAAAUUGUGGUAAAGCUCCAAGGAUAAAAUAAGCUUGAAAGGACAAUCUGUUGUGAAAUUCUCUAUUUAAGUCUUUAAAGCUUUAAACAUUU
.....((((((((((((..((...(((....))).)).))))))))))))........((((((..((((((.....((.(.(.....).).))....)))))).))))))......... ( -27.80)
>DroSim_CAF1 26062 120 + 1
CAAAGCUUGGAGCUUUGGAUAAGAGAUAGAAACUGUGGUAAAGCUCCAAGGAUAAAAUAAGCUUGAAAGGACAAUCUGUUGUGAAAUUCUCUAUUUACUUCUUUGAAGCUUUAAAAAUGU
.....((((((((((((....(.((.......)).)..))))))))))))........((((((.(((((((.....)))(((((........)))))..)))).))))))......... ( -29.00)
>DroEre_CAF1 38589 111 + 1
UAAUGCUAAGAGCUUCGGAUAAAAGCUGGA--------UAAAGCUCCAAGGAUAAUGUAAACUUGAAAGGACAAUUUGUUGUGAAAUUGCCUAUUUAUUU-UUUGAAGCUUUACAAGUUU
........(((((((((((....((((...--------...)))).((((...........))))..(((.((((((......)))))))))........-)))))))))))........ ( -24.30)
>DroYak_CAF1 40183 109 + 1
UAAAGCUAAGAGCUUUGGAUAAAAGCUGCA--------UAAAGCUCCAAGGAUAAUAUGAACUUGAAAGGACAAUUUGUUGUGAAAUUGUCUAUUUAAUA-UU--GAGCUUUGCAAGGGU
....(((...((((((.....))))))(((--------..((((((((((...........))))...(((((((((......)))))))))........-..--)))))))))...))) ( -27.40)
>consensus
CAAAGCUUGGAGCUUUGGAUAAAAGAUGGA_A_U_UGGUAAAGCUCCAAGGAUAAAAUAAGCUUGAAAGGACAAUCUGUUGUGAAAUUCUCUAUUUAAUUCUUUGAAGCUUUAAAAAUUU
((((((.....)))))).....................(((((((.((((...........)))).....((((....))))........................)))))))....... (-14.42 = -14.10 +  -0.32)

alignment

secondary structure

dotplot

Window 1

Location	9,170,813 – 9,170,933
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.19
Mean single sequence MFE	-22.68
Consensus MFE	-14.48
Energy contribution	-14.64
Covariance contribution	0.16
Combinations/Pair	1.22
Mean z-score	-2.97
Structure conservation index	0.64
SVM decision value	2.30
SVM RNA-class probability	0.992016
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9170813 120 - 23771897
AAAUAUUUAAAGCUUCAAUGAAGUAAAUAGAGAAUUUCACAACAUAUUGUCUUUUCGAGCUUAUUUUAUCCUCGGAGCUUUACCAAAAUAUCCAUCUUUUAUCCAAAGCUCCAAGCUUUG
.......((((((((..(((((((((...(((((....((((....)))).)))))....)))))))))....((((((((...((((........))))....)))))))))))))))) ( -23.00)
>DroSec_CAF1 25731 120 - 1
AAAUGUUUAAAGCUUUAAAGACUUAAAUAGAGAAUUUCACAACAGAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCACAAUUUCCACCUUUUAUCCAAAGCUCCAAGCUUUG
.........((((((.((((.........((.(((((......))))).)))))).))))))........(((((((((((.......................)))))))))))..... ( -22.50)
>DroSim_CAF1 26062 120 - 1
ACAUUUUUAAAGCUUCAAAGAAGUAAAUAGAGAAUUUCACAACAGAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCACAGUUUCUAUCUCUUAUCCAAAGCUCCAAGCUUUG
.........((((((.((((.........((.(((((......))))).)))))).))))))........(((((((((((.....((.........)).....)))))))))))..... ( -22.90)
>DroEre_CAF1 38589 111 - 1
AAACUUGUAAAGCUUCAAA-AAAUAAAUAGGCAAUUUCACAACAAAUUGUCCUUUCAAGUUUACAUUAUCCUUGGAGCUUUA--------UCCAGCUUUUAUCCGAAGCUCUUAGCAUUA
......((((((((((((.-.........((((((((......)))))))).......(....).......)))))))))))--------)..((((((.....)))))).......... ( -21.50)
>DroYak_CAF1 40183 109 - 1
ACCCUUGCAAAGCUC--AA-UAUUAAAUAGACAAUUUCACAACAAAUUGUCCUUUCAAGUUCAUAUUAUCCUUGGAGCUUUA--------UGCAGCUUUUAUCCAAAGCUCUUAGCUUUA
....(((((((((((--..-.........((((((((......))))))))....((((...........))))))))))..--------))))).........(((((.....))))). ( -23.50)
>consensus
AAAUUUUUAAAGCUUCAAAGAAGUAAAUAGAGAAUUUCACAACAAAUUGUCCUUUCAAGCUUAUUUUAUCCUUGGAGCUUUACCA_A_U_UCCAGCUUUUAUCCAAAGCUCCAAGCUUUG
.......((((((((..............((.(((((......))))).))......................((((((((.......................)))))))))))))))) (-14.48 = -14.64 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:54 2006