Locus 9592

Sequence ID	3R_DroMel_CAF1
Location	25,340,121 – 25,340,211
Length	90
Max. P	0.619293

overview

Window 4

Location	25,340,121 – 25,340,211
Length	90
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.79
Mean single sequence MFE	-27.70
Consensus MFE	-18.00
Energy contribution	-18.58
Covariance contribution	0.59
Combinations/Pair	1.12
Mean z-score	-1.99
Structure conservation index	0.65
SVM decision value	0.13
SVM RNA-class probability	0.597136
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25340121 90 + 27905053
AGCGAACAAAGCCGAACGAAACCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUCGCCGG--GUACGCAGCAGCGU--------------UC--GCUGCAUUUGGCC
.(((.((....(((..(((((((((((((............))))))))...))))).)))--)).))).(((((..--------------..--)))))........ ( -25.70)
>DroSec_CAF1 25094 90 + 1
AGCGAACAAAGCCGAACGAAACCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUCGCUGG--GUACGCAGCAGCGU--------------CC--GCUGCAUUUGGCC
.(((.((..(((.(((.....((((((((............))))))))....))))))..--)).))).(((((..--------------..--)))))........ ( -26.80)
>DroSim_CAF1 25480 92 + 1
AGCGAACAAAGCCGAACGAAACCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUCGCUGG--GUACGCAGCAGCGU--------------CCGCGCUGCAUUUGGCC
.(((.((..(((.(((.....((((((((............))))))))....))))))..--)).))).((((((.--------------...))))))........ ( -29.40)
>DroEre_CAF1 25295 91 + 1
AGCGAACAAAGCCGAACGAAUCCAAUUUAUUUUAGCCAUUUUAAAUUGGCCUUUUCGUCGG--CUACGCAGCGCAGUU-------------UC--GCUGCAGUUGGCC
.((.(((..((((((.((((.((((((((............))))))))....))))))))--))..((((((.....-------------.)--))))).))).)). ( -36.10)
>DroYak_CAF1 27770 104 + 1
AGCGAACAAAGCCGAACGAAUCCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUCGCCGG--GUACGCAGCGCAGUUUCGCUUGCCAGUUUC--GCUGCAUUUGGCC
..........((((((.(.((((((((((............))))))(((......)))))--)).)(((((((((......)))).......--))))).)))))). ( -25.41)
>DroAna_CAF1 31001 98 + 1
AGCGAACAAAACCGAACGAAACCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUUGCUGUGCGUUCGCAGUGCAC-------UGGUAGUUGU--GAUGU-UGUGGCC
.((..((((......((((.((((..........((((........)))).....(((..(((....)))..))).-------))))..))))--....)-))).)). ( -22.80)
>consensus
AGCGAACAAAGCCGAACGAAACCAAUUUAUUUUAGCCAUUUUAAAUUGGCAUUUUCGCCGG__GUACGCAGCACAGU______________UC__GCUGCAUUUGGCC
..........(((((((((((((((((((............))))))))...)))))..........(((((.......................))))).)))))). (-18.00 = -18.58 +   0.59)

alignment

secondary structure

dotplot

Window 5

Location	25,340,121 – 25,340,211
Length	90
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	82.79
Mean single sequence MFE	-28.22
Consensus MFE	-18.48
Energy contribution	-19.45
Covariance contribution	0.97
Combinations/Pair	1.12
Mean z-score	-2.03
Structure conservation index	0.65
SVM decision value	0.17
SVM RNA-class probability	0.619293
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25340121 90 - 27905053
GGCCAAAUGCAGC--GA--------------ACGCUGCUGCGUAC--CCGGCGAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGUUUCGUUCGGCUUUGUUCGCU
((((..(((((((--(.--------------....))))))))..--..((((((...(((((((((............))))))))))))))).))))......... ( -27.40)
>DroSec_CAF1 25094 90 - 1
GGCCAAAUGCAGC--GG--------------ACGCUGCUGCGUAC--CCAGCGAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGUUUCGUUCGGCUUUGUUCGCU
((((..(((((((--((--------------...)))))))))..--..((((((...(((((((((............))))))))))))))).))))......... ( -29.00)
>DroSim_CAF1 25480 92 - 1
GGCCAAAUGCAGCGCGG--------------ACGCUGCUGCGUAC--CCAGCGAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGUUUCGUUCGGCUUUGUUCGCU
((((..(((((((((..--------------..)).)))))))..--..((((((...(((((((((............))))))))))))))).))))......... ( -29.60)
>DroEre_CAF1 25295 91 - 1
GGCCAACUGCAGC--GA-------------AACUGCGCUGCGUAG--CCGACGAAAAGGCCAAUUUAAAAUGGCUAAAAUAAAUUGGAUUCGUUCGGCUUUGUUCGCU
(((.(((.(((((--(.-------------.....))))))..((--((((((((....((((((((............)))))))).)))).))))))..))).))) ( -33.30)
>DroYak_CAF1 27770 104 - 1
GGCCAAAUGCAGC--GAAACUGGCAAGCGAAACUGCGCUGCGUAC--CCGGCGAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGAUUCGUUCGGCUUUGUUCGCU
.((.....))(((--(((...(((.((((((.((.(((((.....--.))))).....((((........))))...........)).))))))..)))...)))))) ( -29.00)
>DroAna_CAF1 31001 98 - 1
GGCCACA-ACAUC--ACAACUACCA-------GUGCACUGCGAACGCACAGCAAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGUUUCGUUCGGUUUUGUUCGCU
(((.(((-(.(((--..(((.((((-------((((..(((....)))..))......((((........))))........))))))...))).))).))))..))) ( -21.00)
>consensus
GGCCAAAUGCAGC__GA______________ACGCCGCUGCGUAC__CCAGCGAAAAUGCCAAUUUAAAAUGGCUAAAAUAAAUUGGUUUCGUUCGGCUUUGUUCGCU
((((..(((((((.......................)))))))......((((((...(((((((((............))))))))))))))).))))......... (-18.48 = -19.45 +   0.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:50 2006