Locus 4779

Sequence ID	3R_DroMel_CAF1
Location	12,511,975 – 12,512,118
Length	143
Max. P	0.933154

overview

Window 8

Location	12,511,975 – 12,512,085
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.82
Mean single sequence MFE	-41.44
Consensus MFE	-35.42
Energy contribution	-35.34
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-1.78
Structure conservation index	0.85
SVM decision value	1.07
SVM RNA-class probability	0.910031
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12511975 110 - 27905053
--UUGGGAGGGGGCAGCUACAGCAGCGGCAGCUAAAACGCCGAUAAAAGCAACGAUGGCAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCUGAUUGCCAUUGCC--------GU
--..((.((..((((((....))..(((((((.....((((......((((((((.(((......)))))).))))).....)))).....)))))))..)))).)).))--------.. ( -41.80)
>DroSec_CAF1 1124 112 - 1
UCUUGGGAGGGGGCAGCUACAGCAGCGGCAGCUAAAACGCCGAUAAAAGCAACGAUGGCAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCUGAUUGCCAUUGCC--------GU
....((.((..((((((....))..(((((((.....((((......((((((((.(((......)))))).))))).....)))).....)))))))..)))).)).))--------.. ( -41.80)
>DroSim_CAF1 1153 111 - 1
U-UUGGGAGGGGGCAGCUACAGCAGCGGCAGCUAAAACGCCGAUAAAAGCAACGAUGGCAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCUGAUUGCCAUUGCC--------GU
.-..((.((..((((((....))..(((((((.....((((......((((((((.(((......)))))).))))).....)))).....)))))))..)))).)).))--------.. ( -41.80)
>DroAna_CAF1 2755 111 - 1
CC---------AACAGCAGCAGCAGCAGCAGCUAAAACGCCGAUAAAAGCAACGAUGGCAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCUGAUUGCCAUUGCCCGUUGUAUGU
.(---------(((.((((..(((((((((((.....((((......((((((((.(((......)))))).))))).....)))).....))))))).))))..))))..))))..... ( -43.30)
>DroPer_CAF1 3122 103 - 1
---------GGCGCGGCAGCAGCAGCGGCAGCUAAAACGCCGAUAAAAGCAACGAUGGUAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCAGAUUGCCAUUGCC--------AU
---------((((.((((((((((..(((........((((......((((((((.(((......)))))).))))).....))))))).))))))....))))..))))--------.. ( -38.50)
>consensus
__UUGGGAGGGGGCAGCUACAGCAGCGGCAGCUAAAACGCCGAUAAAAGCAACGAUGGCAGUUCAGCUUCGUUUGCUGCUCAGGCGGCCAUGUUGCUGAUUGCCAUUGCC________GU
...............((....(((((((((((.....((((......((((((((.(((......)))))).))))).....)))).....))))))).))))....))........... (-35.42 = -35.34 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	12,512,007 – 12,512,118
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.72
Mean single sequence MFE	-26.25
Consensus MFE	-21.98
Energy contribution	-21.78
Covariance contribution	-0.20
Combinations/Pair	1.11
Mean z-score	-1.05
Structure conservation index	0.84
SVM decision value	1.23
SVM RNA-class probability	0.933154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12512007 111 + 27905053
AGCAGCAAACGAAGCUGAACUGCCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCCGCUGCUGUAGCUGCCCCCUCCCAA------AAAAAAAGACUCCCCUUGGAAACCCCUUCUCA---C
.((((((..((.(((((((.((((...............)))).)))))))..)).))))))................------..........(((....)))............---. ( -23.66)
>DroSec_CAF1 1156 117 + 1
AGCAGCAAACGAAGCUGAACUGCCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCCGCUGCUGUAGCUGCCCCCUCCCAAGAAACAAAAAAAAAAUCCCCCUUGAAAACCCCCUCUCA---C
.((((((..((.(((((((.((((...............)))).)))))))..)).)))))).............((((...................))))..............---. ( -23.17)
>DroSim_CAF1 1185 116 + 1
AGCAGCAAACGAAGCUGAACUGCCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCCGCUGCUGUAGCUGCCCCCUCCCAA-AAACAAAAAAAAAAUCCCCCUUGAAAACCCCCUCUCG---C
.((((((..((.(((((((.((((...............)))).)))))))..)).))))))................-.....................................---. ( -22.36)
>DroAna_CAF1 2795 106 + 1
AGCAGCAAACGAAGCUGAACUGCCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCUGCUGCUGCUGCUGUU---------GGAGCAAUGGUACUCUGCCCC-----AACCACUUCCCCCUCC
(((((((.....(((((((.((((...............)))).)))))))((....)))))))))(((---------((.(((.........))).))-----)))............. ( -33.06)
>DroPer_CAF1 3154 88 + 1
AGCAGCAAACGAAGCUGAACUACCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCCGCUGCUGCUGCCGCGCC---------------------------GCUGCAUGCCCCCACUC-----
.(((((....(((((..(((.......))))))))....(((((..((((.((....)).))))..)))))---------------------------)))))............----- ( -29.00)
>consensus
AGCAGCAAACGAAGCUGAACUGCCAUCGUUGCUUUUAUCGGCGUUUUAGCUGCCGCUGCUGUAGCUGCCCCCUCCCAA__A_CAAAAAAAAAAUCCCCCUUGAAAACCCCCUCUCA___C
.((((((..((.(((((((.((((...............)))).)))))))..)).)))))).......................................................... (-21.98 = -21.78 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:41 2006