Locus 9894

Sequence ID	3R_DroMel_CAF1
Location	26,424,017 – 26,424,116
Length	99
Max. P	0.845902

overview

Window 2

Location	26,424,017 – 26,424,116
Length	99
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	78.33
Mean single sequence MFE	-22.33
Consensus MFE	-16.97
Energy contribution	-17.38
Covariance contribution	0.42
Combinations/Pair	1.11
Mean z-score	-1.02
Structure conservation index	0.76
SVM decision value	0.21
SVM RNA-class probability	0.636868
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26424017 99 + 27905053
AUUCGUGUGUUCGUACAAUAUAU---CAUUUCAGACCUAUCAGAUUGACUUUGUGAUCGAUCUGCAUGCGAAUAGCAGCAUGCACGGCUGCUUUAUCUACGG
...((((((((((((.......(---(......)).....(((((((((.....).))))))))..))))))))(((((.......)))))......)))). ( -25.20)
>DroGri_CAF1 32907 82 + 1
-UUUACUUGCU-------------------GCAGACAUAUCAGAUUGAUUUUGUGAUCGAUCUGCAUGCGAAUAGCAGCAUGCACGGCUGCUUCAUCUAUGG
-......((..-------------------((((.(.....(((((((((....)))))))))((((((........))))))..).))))..))....... ( -25.90)
>DroSec_CAF1 16279 97 + 1
AUUAAU--GUUUGUACAAGAUAU---CGUUUCAGACUUAUCAGAUUGACUUUGUGAUCGAUCUGCAUGCGAAUAGCAGCAUGCACGGCUGCUUUAUCUACGG
.....(--(((((((...(((((---(......))..))))((((((((.....).)))))))...))))))))(((((.......)))))........... ( -21.80)
>DroEre_CAF1 19039 89 + 1
AUAGGU--G-----------UAUCUCCGUUUCAGACCUAUCAGAUUGACUUUGUGAUCGAUCUGCAUGCGAAUAGCAGCAUGCACGGCUGCUUUAUCUACGG
.(((((--(-----------.....((((............((((((((.....).)))))))((((((........))))))))))......))))))... ( -24.10)
>DroYak_CAF1 16644 86 + 1
AUAAAU--G-----------UAU---CGUUUCAGACCUAUCAGAUAGACUUUGUCAUCGAUCUGCACGCGAAUAGCAGCAUGCACGGCUGCUUCAUCUACGG
.....(--(-----------(((---(((..((((....((.(((.(((...))))))))))))...))))..((((((.......)))))).....)))). ( -18.10)
>DroMoj_CAF1 20028 85 + 1
-UUUACUUCCGU----------------UGACAGACCUAUCAGAUUGACUUUGUGAUUGAUCUGCACGCGAACAACAGCAUGCACGGCUGCUUCAUCUACGG
-.......((((----------------((((((.((....((((..((.....).)..))))(((.((........)).)))..)))))..)))...)))) ( -18.90)
>consensus
AUUAAU__G_U_________UAU___CGUUUCAGACCUAUCAGAUUGACUUUGUGAUCGAUCUGCAUGCGAAUAGCAGCAUGCACGGCUGCUUCAUCUACGG
...............................(((.((....(((((((........)))))))((((((........))))))..)))))............ (-16.97 = -17.38 +   0.42)

alignment

secondary structure

dotplot

Window 3

Location	26,424,017 – 26,424,116
Length	99
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	78.33
Mean single sequence MFE	-22.48
Consensus MFE	-17.54
Energy contribution	-17.43
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-1.37
Structure conservation index	0.78
SVM decision value	0.77
SVM RNA-class probability	0.845902
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26424017 99 - 27905053
CCGUAGAUAAAGCAGCCGUGCAUGCUGCUAUUCGCAUGCAGAUCGAUCACAAAGUCAAUCUGAUAGGUCUGAAAUG---AUAUAUUGUACGAACACACGAAU
.((((((...((((((.......))))))..)).(((.((((((.((((...........)))).))))))..)))---........))))........... ( -22.10)
>DroGri_CAF1 32907 82 - 1
CCAUAGAUGAAGCAGCCGUGCAUGCUGCUAUUCGCAUGCAGAUCGAUCACAAAAUCAAUCUGAUAUGUCUGC-------------------AGCAAGUAAA-
.....((...((((((.......))))))..))((.(((((((..((((...........))))..))))))-------------------))).......- ( -23.30)
>DroSec_CAF1 16279 97 - 1
CCGUAGAUAAAGCAGCCGUGCAUGCUGCUAUUCGCAUGCAGAUCGAUCACAAAGUCAAUCUGAUAAGUCUGAAACG---AUAUCUUGUACAAAC--AUUAAU
..(((((((.((((((.......))))))..(((....(((((..((((...........))))..)))))...))---))))))...))....--...... ( -20.80)
>DroEre_CAF1 19039 89 - 1
CCGUAGAUAAAGCAGCCGUGCAUGCUGCUAUUCGCAUGCAGAUCGAUCACAAAGUCAAUCUGAUAGGUCUGAAACGGAGAUA-----------C--ACCUAU
((((.((...((((((.......))))))..)).....((((((.((((...........)))).))))))..)))).....-----------.--...... ( -23.10)
>DroYak_CAF1 16644 86 - 1
CCGUAGAUGAAGCAGCCGUGCAUGCUGCUAUUCGCGUGCAGAUCGAUGACAAAGUCUAUCUGAUAGGUCUGAAACG---AUA-----------C--AUUUAU
..(((((((.((((((.......))))))..(((....((((((((((((...))).))).....))))))...))---)..-----------)--)))))) ( -22.80)
>DroMoj_CAF1 20028 85 - 1
CCGUAGAUGAAGCAGCCGUGCAUGCUGUUGUUCGCGUGCAGAUCAAUCACAAAGUCAAUCUGAUAGGUCUGUCA----------------ACGGAAGUAAA-
((((.((...((((((.......))))))..))....(((((((.((((...........)))).)))))))..----------------)))).......- ( -22.80)
>consensus
CCGUAGAUAAAGCAGCCGUGCAUGCUGCUAUUCGCAUGCAGAUCGAUCACAAAGUCAAUCUGAUAGGUCUGAAACG___AUA_________A_C__AUAAAU
...(((((..((((((.......)))))).........(((((.(((......))).)))))....)))))............................... (-17.54 = -17.43 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:25 2006