Locus 1312

Sequence ID	3L_DroMel_CAF1
Location	3,812,924 – 3,813,015
Length	91
Max. P	0.823953

overview

Window 2

Location	3,812,924 – 3,813,015
Length	91
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.44
Mean single sequence MFE	-14.48
Consensus MFE	-11.42
Energy contribution	-11.67
Covariance contribution	0.25
Combinations/Pair	1.06
Mean z-score	-1.20
Structure conservation index	0.79
SVM decision value	0.69
SVM RNA-class probability	0.823953
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3812924 91 + 23771897
U--------------------UUUUUGCGCAUCUUUUC---CGUUUCAGUACACUUGACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUAGCUACGAAUAUU
.--------------------.(((((.(...(((...---.(((.((((.............)))).)))...)))...).)))))......(((((....)))))....... ( -12.22)
>DroVir_CAF1 14360 88 + 1
U--------------------GUUUUG--UGUC-UUCU---CUUUGCAGUACAUUUUACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUUGCUACAAAUAUU
.--------------------((((((--((..-..((---(.(..((((.............))))..)....)))...)))))))).....(((((....)))))....... ( -20.32)
>DroGri_CAF1 13050 89 + 1
U--------------------UC--GC--CGUC-UUCUUUAUUUUGCAGUACAUUUUACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUUGCUACAAAUAUU
.--------------------..--..--.((.-..(((....(..((((.............))))..)....)))....))..........(((((....)))))....... ( -12.72)
>DroEre_CAF1 13149 111 + 1
UUGAUUGCAUUACUAACUUGGUUUUCCGGCUUCUUUUC---CGUUUCAGUACACUUGACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUAGCUACGAAUAUU
.((((..((........((((....)))).........---.(((..((....)).)))......))..))))((((...........)))).(((((....)))))....... ( -15.60)
>DroYak_CAF1 13252 79 + 1
--------------------------------UUUUUC---CUUUACAGUACACUUGACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUAGCUACGAAUAUU
--------------------------------......---..(((((((.............)))))))...((((...........)))).(((((....)))))....... ( -13.32)
>DroMoj_CAF1 14618 88 + 1
U--------------------UUUUUU--UUUU-UGCU---UUUUGCAGUACAUUUUACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUCGCUACAAAUAUU
.--------------------......--...(-(((.---....))))......(((((.....)))))...((((...........)))).(((((....)))))....... ( -12.70)
>consensus
U____________________UUUUUC__CGUC_UUCC___CUUUGCAGUACACUUGACAUAAACUGUGAUUAUGAGUUCCACAAAAUCUCAAGUAGCCCUAGCUACAAAUAUU
...........................................(((((((.............)))))))...((((...........)))).(((((....)))))....... (-11.42 = -11.67 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	3,812,924 – 3,813,015
Length	91
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.44
Mean single sequence MFE	-17.23
Consensus MFE	-12.75
Energy contribution	-12.50
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-1.08
Structure conservation index	0.74
SVM decision value	0.36
SVM RNA-class probability	0.704322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3812924 91 - 23771897
AAUAUUCGUAGCUAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUCAAGUGUACUGAAACG---GAAAAGAUGCGCAAAAA--------------------A
....(((((..(.((..(.((((((.((.((((((.........))))))...)).)))))))..)))..)))---))...............--------------------. ( -18.30)
>DroVir_CAF1 14360 88 - 1
AAUAUUUGUAGCAAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUAAAAUGUACUGCAAAG---AGAA-GACA--CAAAAC--------------------A
.......(((((....)))))......(((((((...(((.......((((.(((.....))).))))....)---))..-..))--))))).--------------------. ( -16.80)
>DroGri_CAF1 13050 89 - 1
AAUAUUUGUAGCAAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUAAAAUGUACUGCAAAAUAAAGAA-GACG--GC--GA--------------------A
.......(((((....))))).....((((((..(.((.(((((.......)))))......)).)..))))))......-....--..--..--------------------. ( -15.30)
>DroEre_CAF1 13149 111 - 1
AAUAUUCGUAGCUAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUCAAGUGUACUGAAACG---GAAAAGAAGCCGGAAAACCAAGUUAGUAAUGCAAUCAA
..((((..(((((.((((.((((((.((.((((((.........))))))...)).)))))))).......((---(........))).....)).)))))..))))....... ( -21.80)
>DroYak_CAF1 13252 79 - 1
AAUAUUCGUAGCUAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUCAAGUGUACUGUAAAG---GAAAAA--------------------------------
....(((...((.((..(.((((((.((.((((((.........))))))...)).)))))))..))))...)---))....-------------------------------- ( -15.30)
>DroMoj_CAF1 14618 88 - 1
AAUAUUUGUAGCGAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUAAAAUGUACUGCAAAA---AGCA-AAAA--AAAAAA--------------------A
....(((((((.(((..((((..........))))..)))......(((.....)))........))))))).---....-....--......--------------------. ( -15.90)
>consensus
AAUAUUCGUAGCUAGGGCUACUUGAGAUUUUGUGGAACUCAUAAUCACAGUUUAUGUAAAAUGUACUGCAAAG___AAAA_GAAG__CAAAAA____________________A
.......(((((....))))).((((.(((....)))))))......((((.(((.....))).)))).............................................. (-12.75 = -12.50 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:34 2006