Locus 4990

Sequence ID	3L_DroMel_CAF1
Location	13,749,117 – 13,749,213
Length	96
Max. P	0.874658

overview

Window 1

Location	13,749,117 – 13,749,213
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.14
Mean single sequence MFE	-29.27
Consensus MFE	-14.69
Energy contribution	-16.72
Covariance contribution	2.03
Combinations/Pair	1.20
Mean z-score	-2.33
Structure conservation index	0.50
SVM decision value	0.89
SVM RNA-class probability	0.874658
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13749117 96 + 23771897
AAAUGAAUCC-------------------GUGCCCAAGUUUCCUACCUGCGUAAC-UUUACAAGUGUUGAAAGCAGGUAAGGAAUGGGCUUGAGCAGAUAGUGCAGGCGAACCAUA----
.........(-------------------(((((((...(((((((((((.((((-.........))))...)))))).))))))))))....(((.....)))..))).......---- ( -31.20)
>DroPse_CAF1 158115 114 + 1
AAAUGAAUCAAAACUUCAAACAGCAUCAGGCGGCAAAGUUA---AGCCAUCUAACAUACACAUGUGUUGAAAGCUCGAAAGGAGUGGAA--GGGCAGGAAGCU-GGGAACGCCAUAUAUA
..............(((...((((.((..(((((.......---.))).(((((((((....))))))....((((.....))))))).--..))..)).)))-).)))........... ( -24.50)
>DroSec_CAF1 155840 96 + 1
AAAUGAAUCC-------------------GUGCCCAAGUUUCCUACCUGCGUAAC-UUUACAAGUGUUGAAAGCAGGUAAGGAAUGGGCUUGAGCAGAUAGUGCAGGCGGACCAUA----
..(((..(((-------------------(((((((...(((((((((((.((((-.........))))...)))))).))))))))))....(((.....)))..))))).))).---- ( -36.10)
>DroSim_CAF1 167638 96 + 1
AAAUGAAUCC-------------------GUGCCCAAGUUUCCUACCUGCGUAAC-UUUACAAGUGUUGAAAGCAGGUAAGGAAUGGGCUUGAGCAGAUAGUGCAGACGGACCAUA----
..(((..(((-------------------(((((((...(((((((((((.((((-.........))))...)))))).))))))))))....(((.....)))..))))).))).---- ( -35.80)
>DroEre_CAF1 162718 96 + 1
AAAUGAAUCC-------------------GUGCCCAAGUUUCCUACCUGCGUAAC-UUUACAAGUGUUGAAAGCUGGUAAGGAAUGGGCUUGAGCAGAUAGUACAGGCGUAUAAUA----
..........-------------------(((((((...((((((((.((.((((-.........))))...)).))).))))))))(((((.((.....)).)))))))))....---- ( -25.10)
>DroYak_CAF1 167023 96 + 1
AAAUGAAUCC-------------------GUGUCCAAGUUUCCUACCUGCGUAAC-UUUACAAGUGUUGAAAGCAGCUAAGGAAUGUGCUUGAGCAGAUAGUGCAGGAGGACCAUA----
..........-------------------(.((((....(((((..((((.((((-.........))))...))))...)))))((..((.........))..))...)))))...---- ( -22.90)
>consensus
AAAUGAAUCC___________________GUGCCCAAGUUUCCUACCUGCGUAAC_UUUACAAGUGUUGAAAGCAGGUAAGGAAUGGGCUUGAGCAGAUAGUGCAGGCGGACCAUA____
..............................(((.((((((((((((((((.((((.((....)).))))...)))))).)))))...))))).)))........................ (-14.69 = -16.72 +   2.03)

alignment

secondary structure

dotplot

Window 2

Location	13,749,117 – 13,749,213
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.14
Mean single sequence MFE	-25.92
Consensus MFE	-12.13
Energy contribution	-14.72
Covariance contribution	2.58
Combinations/Pair	1.16
Mean z-score	-2.20
Structure conservation index	0.47
SVM decision value	0.39
SVM RNA-class probability	0.717362
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13749117 96 - 23771897
----UAUGGUUCGCCUGCACUAUCUGCUCAAGCCCAUUCCUUACCUGCUUUCAACACUUGUAAA-GUUACGCAGGUAGGAAACUUGGGCAC-------------------GGAUUCAUUU
----.((((((((...(((.....)))....((((((((((.((((((....(((.........-)))..)))))))))))...))))).)-------------------))).)))).. ( -28.50)
>DroPse_CAF1 158115 114 - 1
UAUAUAUGGCGUUCCC-AGCUUCCUGCCC--UUCCACUCCUUUCGAGCUUUCAACACAUGUGUAUGUUAGAUGGCU---UAACUUUGCCGCCUGAUGCUGUUUGAAGUUUUGAUUCAUUU
((((((((..(((...-(((((.......--.............)))))...))).)))))))).(((((.((((.---.......)))).)))))......((((.......))))... ( -20.75)
>DroSec_CAF1 155840 96 - 1
----UAUGGUCCGCCUGCACUAUCUGCUCAAGCCCAUUCCUUACCUGCUUUCAACACUUGUAAA-GUUACGCAGGUAGGAAACUUGGGCAC-------------------GGAUUCAUUU
----.((((((((...(((.....)))....((((((((((.((((((....(((.........-)))..)))))))))))...))))).)-------------------))).)))).. ( -31.40)
>DroSim_CAF1 167638 96 - 1
----UAUGGUCCGUCUGCACUAUCUGCUCAAGCCCAUUCCUUACCUGCUUUCAACACUUGUAAA-GUUACGCAGGUAGGAAACUUGGGCAC-------------------GGAUUCAUUU
----.(((((((((..(((.....)))....((((((((((.((((((....(((.........-)))..)))))))))))...)))))))-------------------))).)))).. ( -32.60)
>DroEre_CAF1 162718 96 - 1
----UAUUAUACGCCUGUACUAUCUGCUCAAGCCCAUUCCUUACCAGCUUUCAACACUUGUAAA-GUUACGCAGGUAGGAAACUUGGGCAC-------------------GGAUUCAUUU
----.................(((((.....((((((((((.(((((((((((.....)).)))-))).....))))))))...))))).)-------------------))))...... ( -20.30)
>DroYak_CAF1 167023 96 - 1
----UAUGGUCCUCCUGCACUAUCUGCUCAAGCACAUUCCUUAGCUGCUUUCAACACUUGUAAA-GUUACGCAGGUAGGAAACUUGGACAC-------------------GGAUUCAUUU
----....((((.......((((((((...(((..........)))(((((((.....)).)))-))...)))))))).......))))..-------------------.......... ( -21.94)
>consensus
____UAUGGUCCGCCUGCACUAUCUGCUCAAGCCCAUUCCUUACCUGCUUUCAACACUUGUAAA_GUUACGCAGGUAGGAAACUUGGGCAC___________________GGAUUCAUUU
........................((((((((....(((((.((((((......................))))))))))).)))))))).............................. (-12.13 = -14.72 +   2.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:50 2006