Locus 8004

Sequence ID	3R_DroMel_CAF1
Location	21,469,475 – 21,469,584
Length	109
Max. P	0.996328

overview

Window 3

Location	21,469,475 – 21,469,584
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.61
Mean single sequence MFE	-38.20
Consensus MFE	-28.41
Energy contribution	-29.72
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-4.08
Structure conservation index	0.74
SVM decision value	1.53
SVM RNA-class probability	0.961856
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21469475 109 + 27905053
UCGAUUACGCUGCUCUUGCUG---UUGCUGCAGCGGCGGCUGCUGCAAAAACAAACCAACCAAAAA--------AUGGCUUGGCAAAUCUAGAAGAAUUGGAAGCAAGAGCAAAUCAAAU
..((((....(((((((((((---((..((((((((...))))))))..)))...(((((((....--------.))).))))(((.((.....)).)))..)))))))))))))).... ( -39.00)
>DroSec_CAF1 76245 119 + 1
UCGAUUACGCUGCUCUUGCUGUC-UUGCUGCAGCGGCGGCUGCUGCAAAAACAAACCAACCAAAAAAUAGCAAAAUGGCUUGGCAAAUGUAGAAGAAUUGGAAGCAAGAGCAAAUCAAAU
..((((....((((((((((.((-((.((((((((((....))))).........(((((((.............))).))))....)))))))))......)))))))))))))).... ( -38.42)
>DroSim_CAF1 61401 119 + 1
UCGAUUACGCUGCUCUUGCUGUC-UUGCUGCAGCGGCGGCUGCUGCAAAAACAAACCAACCAAAAAAUGGCAAAAUGGCUUGGCAAAUCUAGAAGAAUUGGAAGCAAGAGCAAAUCAAAU
..((((....((((((((((...-((((((((((((...))))))))....(((.(((.(((.....))).....))).))))))).(((((.....))))))))))))))))))).... ( -38.40)
>DroEre_CAF1 77414 112 + 1
UCGAUUACGUUGCUGUUACUGCGGCGGCUGCUGUGGCGGCUGCUGCAAAAACAAACCAACCAA--A------AAAUAGCUUGGCAAAUGCAGAAGAAUUGGAAGCAAGAGCAAAUCAAAU
..((((..((((.((((..((((((((((((....))))))))))))..))))...))))...--.------.....((((.((....)).......(((....))))))).)))).... ( -37.00)
>consensus
UCGAUUACGCUGCUCUUGCUGUC_UUGCUGCAGCGGCGGCUGCUGCAAAAACAAACCAACCAAAAA______AAAUGGCUUGGCAAAUCUAGAAGAAUUGGAAGCAAGAGCAAAUCAAAU
..((((....((((((((((....((((.(((((....))))).)))).......(((((((.............))).))))...................)))))))))))))).... (-28.41 = -29.72 +   1.31)

alignment

secondary structure

dotplot

Window 4

Location	21,469,475 – 21,469,584
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.61
Mean single sequence MFE	-37.98
Consensus MFE	-32.96
Energy contribution	-34.02
Covariance contribution	1.06
Combinations/Pair	1.11
Mean z-score	-3.62
Structure conservation index	0.87
SVM decision value	2.68
SVM RNA-class probability	0.996328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21469475 109 - 27905053
AUUUGAUUUGCUCUUGCUUCCAAUUCUUCUAGAUUUGCCAAGCCAU--------UUUUUGGUUGGUUUGUUUUUGCAGCAGCCGCCGCUGCAGCAA---CAGCAAGAGCAGCGUAAUCGA
..((((((((((((((((............((((..(((((.(((.--------....))))))))..))))((((.(((((....))))).))))---.))))))))))....)))))) ( -40.00)
>DroSec_CAF1 76245 119 - 1
AUUUGAUUUGCUCUUGCUUCCAAUUCUUCUACAUUUGCCAAGCCAUUUUGCUAUUUUUUGGUUGGUUUGUUUUUGCAGCAGCCGCCGCUGCAGCAA-GACAGCAAGAGCAGCGUAAUCGA
..((((((((((((((((....................(((((((....((((.....))))))))))).((((((.(((((....))))).))))-)).))))))))))....)))))) ( -40.70)
>DroSim_CAF1 61401 119 - 1
AUUUGAUUUGCUCUUGCUUCCAAUUCUUCUAGAUUUGCCAAGCCAUUUUGCCAUUUUUUGGUUGGUUUGUUUUUGCAGCAGCCGCCGCUGCAGCAA-GACAGCAAGAGCAGCGUAAUCGA
..((((((((((((((((..(((.((.....)).))).(((((((....((((.....))))))))))).((((((.(((((....))))).))))-)).))))))))))....)))))) ( -43.60)
>DroEre_CAF1 77414 112 - 1
AUUUGAUUUGCUCUUGCUUCCAAUUCUUCUGCAUUUGCCAAGCUAUUU------U--UUGGUUGGUUUGUUUUUGCAGCAGCCGCCACAGCAGCCGCCGCAGUAACAGCAACGUAAUCGA
..((((((((((.((((.............(((...(((((.(.....------.--..).))))).)))...(((.((.((.((....)).)).)).))))))).))))....)))))) ( -27.60)
>consensus
AUUUGAUUUGCUCUUGCUUCCAAUUCUUCUACAUUUGCCAAGCCAUUU______UUUUUGGUUGGUUUGUUUUUGCAGCAGCCGCCGCUGCAGCAA_GACAGCAAGAGCAGCGUAAUCGA
..(((((((((((((((...................(((((.(((.............)))))))).((((.((((.(((((....))))).)))).)))))))))))))....)))))) (-32.96 = -34.02 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:05 2006