Locus 7234

Sequence ID	3R_DroMel_CAF1
Location	19,068,454 – 19,068,545
Length	91
Max. P	0.994314

overview

Window 2

Location	19,068,454 – 19,068,545
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	76.72
Mean single sequence MFE	-35.50
Consensus MFE	-22.61
Energy contribution	-23.34
Covariance contribution	0.73
Combinations/Pair	1.22
Mean z-score	-3.24
Structure conservation index	0.64
SVM decision value	2.47
SVM RNA-class probability	0.994314
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19068454 91 + 27905053
AGAGUUGGGCCCAAGUGCU-----CGAUAAGUGGGUCUU-GGGAUUGGCAUGUAGGAUUACCGCUGCCAUCGAU------UUCAAUGGCAUUGGGUUCAACUG
..((((((((((((.((((-----.(((......)))((-(..(((((((.((.((....)))))))))...))------..))).)))))))))))))))). ( -34.30)
>DroSec_CAF1 82888 91 + 1
AGAGUUGGGCCCAAGUGCU-----CGAUAAGUGGGUCUU-GGGAUUGGCAUGUGGGGUUACCGCUGCCAUCGAU------UUCAAUGGCAUUGGGUUCAACUG
..((((((((((((.((((-----.(((......)))((-(..(((((((.((((.....)))))))))...))------..))).)))))))))))))))). ( -39.40)
>DroSim_CAF1 85316 91 + 1
AGAGUUGGGCCCAAGUGCU-----CGAUAAGUGGGUCUU-GGGAUUGGCAUGUGGGGUUACCGCUGCCAUCGAU------UUCAAUGGCAUUGGGUUCAACUG
..((((((((((((.((((-----.(((......)))((-(..(((((((.((((.....)))))))))...))------..))).)))))))))))))))). ( -39.40)
>DroEre_CAF1 92503 82 + 1
AGAGUUGGGCCCAAGUGCUCGGCUCGCUAAGUGGGUCUU-GGGAUGGGCAU--------------GCCAUCGAU------UUGAAUGGCAUUGGGUUCAACUG
..(((((((((((((((((((..((.(((((.....)))-)))))))))))--------------(((((....------....))))).)))))))))))). ( -36.70)
>DroYak_CAF1 87706 95 + 1
AGAGUUGCGCCCAAGUGCUGGACUCGUUAAGUGGGUCUU-GGGAUUGGCAUGUG-GUUUAGCGCUGCCAUCGAU------UUGAUUGGCAUUGGGCUCAACUG
..(((((.(((((((((((((((((((...((.((((..-..)))).))))).)-)))))))))(((((((...------..)).))))))))))).))))). ( -41.30)
>DroPer_CAF1 88183 93 + 1
AAAGUUCAGCUCGAGUGGU-----UAACCAGAGAGGGUUAAGGCUGUGCAUAGGG-GUUA----AGCAAUCGAUACCAGUAUGAAUGGCAUUGGGAUCAACUC
..((((...(((((....(-----(((((......)))))).(((((.((((..(-((..----..........)))..)))).))))).)))))...)))). ( -21.90)
>consensus
AGAGUUGGGCCCAAGUGCU_____CGAUAAGUGGGUCUU_GGGAUUGGCAUGUGGGGUUACCGCUGCCAUCGAU______UUCAAUGGCAUUGGGUUCAACUG
..((((((((((((................((.((((.....)))).))................(((((..............))))).)))))))))))). (-22.61 = -23.34 +   0.73)

alignment

secondary structure

dotplot

Window 3

Location	19,068,454 – 19,068,545
Length	91
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	76.72
Mean single sequence MFE	-25.12
Consensus MFE	-12.32
Energy contribution	-13.54
Covariance contribution	1.22
Combinations/Pair	1.04
Mean z-score	-3.01
Structure conservation index	0.49
SVM decision value	2.30
SVM RNA-class probability	0.991922
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19068454 91 - 27905053
CAGUUGAACCCAAUGCCAUUGAA------AUCGAUGGCAGCGGUAAUCCUACAUGCCAAUCCC-AAGACCCACUUAUCG-----AGCACUUGGGCCCAACUCU
.(((((..(((((((((((((..------..))))))))((((((........))))......-(((.....)))....-----.))..)))))..))))).. ( -28.40)
>DroSec_CAF1 82888 91 - 1
CAGUUGAACCCAAUGCCAUUGAA------AUCGAUGGCAGCGGUAACCCCACAUGCCAAUCCC-AAGACCCACUUAUCG-----AGCACUUGGGCCCAACUCU
.(((((..(((((((((((((..------..))))))))((((((........))))......-(((.....)))....-----.))..)))))..))))).. ( -28.40)
>DroSim_CAF1 85316 91 - 1
CAGUUGAACCCAAUGCCAUUGAA------AUCGAUGGCAGCGGUAACCCCACAUGCCAAUCCC-AAGACCCACUUAUCG-----AGCACUUGGGCCCAACUCU
.(((((..(((((((((((((..------..))))))))((((((........))))......-(((.....)))....-----.))..)))))..))))).. ( -28.40)
>DroEre_CAF1 92503 82 - 1
CAGUUGAACCCAAUGCCAUUCAA------AUCGAUGGC--------------AUGCCCAUCCC-AAGACCCACUUAGCGAGCCGAGCACUUGGGCCCAACUCU
.(((((......((((((((...------...))))))--------------))(((((....-(((.....))).((.......))...))))).))))).. ( -22.80)
>DroYak_CAF1 87706 95 - 1
CAGUUGAGCCCAAUGCCAAUCAA------AUCGAUGGCAGCGCUAAAC-CACAUGCCAAUCCC-AAGACCCACUUAACGAGUCCAGCACUUGGGCGCAACUCU
.(((((.(((((((((((.((..------...)))))))((((.....-.....)).......-..(((.(.......).)))..))..)))))).))))).. ( -26.50)
>DroPer_CAF1 88183 93 - 1
GAGUUGAUCCCAAUGCCAUUCAUACUGGUAUCGAUUGCU----UAAC-CCCUAUGCACAGCCUUAACCCUCUCUGGUUA-----ACCACUCGAGCUGAACUUU
(((((((((...((((((.......)))))).))))((.----....-......)).(((((((((((......)))))-----)......).))))))))). ( -16.20)
>consensus
CAGUUGAACCCAAUGCCAUUCAA______AUCGAUGGCAGCGGUAACCCCACAUGCCAAUCCC_AAGACCCACUUAUCG_____AGCACUUGGGCCCAACUCU
.(((((..((((((((................(((((((..............)))).)))...(((.....)))..........))).)))))..))))).. (-12.32 = -13.54 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:56 2006